scholarly journals Isolation of Endophytic Bacteria and Amplification of 16SrDNA on Citrus in Zhaoqing Districts

2015 ◽  
Vol 7 (12) ◽  
pp. 198
Author(s):  
Chongbi Li ◽  
S. N. Liang ◽  
F. Y. Gao ◽  
K. N. Chen ◽  
J. Wang ◽  
...  
Keyword(s):  
16S Rdna ◽  
Theoretical Basis ◽  
Endophytic Bacteria ◽  
Sequencing Analysis ◽  
Uncultured Bacterium ◽  
Citrus Plant ◽  
Citrus Huanglongbing ◽  
Specific Fragment ◽  
Endogenous Bacteria

<p>Zhaoqing is the main source of Citrus in China. However, the reason of citrus Huanglongbing (HLB) is unclear and may be from endophyte. Therefore, the study of citrus endophyte is necessary. The experiment would be carried out by endophyte being isolated from citrus plant and amplifying the specific 16SrDNA fragment from endogenous bacteria to know the relation of citrus HLB to 16S rDNA of endogenous bacteria. The results showed that total 55 strains of endophytic bacteria were identified. And one specific fragment long of 1261 nt was got. Sequencing analysis showed for 91.3% homology to uncultured bacterium clone. And the 16SrDNA fragment was identified by PCR. The experiments would provide a theoretical basis for understanding the differences in pathomechanism among various HLB isolates.</p>

scholarly journals Bacterial diversity of soil under eucalyptus assessed by 16S rDNA sequencing analysis

2006 ◽  
Vol 41 (10) ◽  
pp. 1507-1516 ◽  
Author(s):  
Érico Leandro da Silveira ◽  
Rodrigo Matheus Pereira ◽  
Denilson César Scaquitto ◽  
Eliamar Aparecida Nascimbém Pedrinho ◽  
Silvana Pómpeia Val-Moraes ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
16S Rdna ◽  
Phylogenetic Analyses ◽  
Chemical Properties ◽  
Pcr Primers ◽  
Native Forest ◽  
Sequencing Analysis ◽  
Soil Dna ◽  
Rdna Sequencing ◽  
The Impact

Studies on the impact of Eucalyptus spp. on Brazilian soils have focused on soil chemical properties and isolating interesting microbial organisms. Few studies have focused on microbial diversity and ecology in Brazil due to limited coverage of traditional cultivation and isolation methods. Molecular microbial ecology methods based on PCR amplified 16S rDNA have enriched the knowledge of soils microbial biodiversity. The objective of this work was to compare and estimate the bacterial diversity of sympatric communities within soils from two areas, a native forest (NFA) and an eucalyptus arboretum (EAA). PCR primers, whose target soil metagenomic 16S rDNA were used to amplify soil DNA, were cloned using pGEM-T and sequenced to determine bacterial diversity. From the NFA soil 134 clones were analyzed, while 116 clones were analyzed from the EAA soil samples. The sequences were compared with those online at the GenBank. Phylogenetic analyses revealed differences between the soil types and high diversity in both communities. Soil from the Eucalyptus spp. arboretum was found to have a greater bacterial diversity than the soil investigated from the native forest area.

Identification ofEnterococcus sp. from midgut of silkworm based on biochemical and 16S rDNA sequencing analysis

2006 ◽  
Vol 56 (3) ◽  
pp. 201-205 ◽  
Author(s):  
Chen Fei ◽  
Xing-meng Lu ◽  
Yong-hua Qian ◽  
Haiyan Zhang ◽  
Qaisar Mahmood
Keyword(s):  
16S Rdna ◽  
Sequencing Analysis ◽  
16S Rdna Sequencing ◽  
Rdna Sequencing

scholarly journals Identifikasi Molekuler Bakteri Endofit Penghasil L-asparaginase yang Diisolasi dari Mangrove Buta-Buta (Excoecaria agallocha)

2019 ◽  
Vol 14 (1) ◽  
pp. 29
Author(s):  
Asep Awaludin Prihanto ◽  
Randy Fahrudin Ardiansyah ◽  
Ken Audia Pradarameswari
Keyword(s):  
16S Rdna ◽  
Molecular Identification ◽  
Endophytic Bacteria ◽  
Sequence Data ◽  
Enterobacter Cloacae ◽  
Selective Medium ◽  
Mangrove Plant ◽  
Excoecaria Agallocha ◽  
Molecular Phylogenetic ◽  
Phylogenetic Identification

AbstrakL-asparaginase (EC 3.5.1.1) adalah enzim yang menghidrolisis asam amino L-asparagin menjadi amonia dan asam aspartat. Enzim ini mempunyai manfaat utama dalam bidang farmasi dan industri pangan. Enzim L-asparaginase tersebar secara luas pada mikroorganisme. Mikroorganisme yang mempunyai potensi menghasilkan enzim ini adalah mikroorganisme endofit dari tumbuhan mangrove. Penelitian ini bertujuan untuk mengisolasi dan mengidentifikasi bakteri endofit penghasil L-asparaginase dari tumbuhan mangrove Buta-buta (E. agallocha). Skrining dilakukan dengan menggunakan medium selektif untuk mendapatkan bakteri penghasil enzim L-asparaginase. Identifikasi molekuler dilakukan dengan menggunakan analisis filogenetik berdasarkan data sekuen 16S rDNA. Dari hasil penelitian ini didapatkan lima isolat bakteri endofit penghasil enzim L-asparaginase, di mana isolat penghasil L-asparaginase tertinggi diidentifikasi secara molekuler. Hasil identifikasi filogenetik molekuler menunjukkan bahwa isolat kode D.104 teridentifikasi sebagai Enterobacter cloacae. Molecular Identification of L-asparaginase-Producing Endophytic Bacteria Isolated from Mangrove Buta-Buta (Excoecaria agallocha)AbstractL-asparaginase (EC 3.5.1.1) is an enzyme which hydrolyze amino acid L-asparagine to aspartate and ammonia. Two main applications of this enzyme are in the pharmaceutical and food industries. The enzyme is widely distributed on microorganism. A potential source of L-asparaginase-producing bacteria is an endophytic bacteria from mangrove plant. This study aimed to isolate and identify L-asparaginase-producing endophytic bacteria from a mangrove plant, E. agallocha (Buta-buta). A screening was carried out using a selective medium to obtain the L-asparaginase enzyme producing bacteria. Molecular identification was carried out using phylogenetic analysis based on 16S rDNA sequence data. In this study, five isolates of the L-asparaginase-producing endophytic bacteria were obtained. The molecular phylogenetic identification showed that the highest L-asparaginase-producing bacterial isolate (code D.104) was identified as Enterobacter cloacae.

scholarly journals Strategies for differentiation, identification and typing of medically important species of mycobacteria by molecular methods

2001 ◽  
Vol 46 (No. 11–12) ◽  
pp. 309-328 ◽  
Author(s):  
L. Dvorská ◽  
M. Bartoš ◽  
G. Martin ◽  
W. Erler ◽  
I. Pavlík
Keyword(s):  
Molecular Biology ◽  
16S Rdna ◽  
Dna Fingerprinting ◽  
Dna Sequence ◽  
Internal Transcribed Spacer ◽  
Bacterial Species ◽  
Beta Subunit ◽  
Sequencing Analysis ◽  
Important Species ◽  
Comprehensive Information

Molecular biology methods offer new opportunities to differentiate, identify and type bacterial species and strains. These methods use the variability of nucleic sequences of genes such as 16S rDNA,&nbsp;beta subunit RNA-ase (rpoB), gyrase (gyrB), rDNA internal transcribed spacer and other genes. The aim of this paper is to provide comprehensive information about the methods available to differentiate and identify species of mycobacteria at the DNA sequence level. The methods discussed in the review include PCR, PCR-REA, sequencing analysis, spoligotyping and DNA fingerprinting. These methods have been applied to both the &ldquo;universal&rdquo; part of the genome and to specific mycobacterial genes.

BACTERIAS ENDOFÍTICAS DE ELODEA POTAMOGETON (“LLACHU”) DEL LAGO TITICACA

SCIENTIARVM ◽  
2015 ◽  
Vol 1 (1) ◽  
pp. 35-38
Author(s):  
Pedro Ubaldo Coila Añasco ◽  
◽  
Julio César Bernabé Ortiz ◽  
Domingo Alberto Ruelas ◽  
◽  
...  
Keyword(s):  
16S Rdna ◽  
Endophytic Bacteria ◽  
Phylogenetic Trees ◽  
Isoamyl Alcohol ◽  
The United States ◽  
Luria Bertani ◽  
16S Rdna Gene ◽  
Symbiotic Interaction ◽  
Rdna Gene ◽  
Raoultella Terrigena

ABTRACT: The “llachu” (Elodea potamogeton) is an aquatic plant from Lake Titicaca, food for the cattle of the circumlacustrine ring. Some areas of the lake have been eutrophied by pollution; even so, the plant grows. Being one of the survival mechanisms, the symbiotic interaction with microorganisms, the objective of the study was to isolate and molecularly characterize some endophytic bacteria of the plant. For isolation, the samples were washed and disinfected with 70% alcohol, 0.5% sodium hypochlorite and 80% Tween; then, it was homogenized and an aliquot seeded in Luria-Bertani (LB) medium, three strains were chosen to be reseeded on solid LB agar. From the pure strains, DNA was extracted with the phenol-chloroform-isoamyl alcohol mixture, quantifying by spectrophotometry. The 16S rDNA gene was amplified by PCR; amplicons were submitted to Functional Biosciences Inc. in the United States for sequencing. The sequences were edited with BioEdit 7.0.0 and similar sequences were chosen with BLASTn from GenBank, to perform multiple alignment of sequences with Clustal W. To determine evolutionary relationships, MEGA7 was used, constructing phylogenetic trees by the Neighbor-Joining method. Molecular analysis shows that the Sample10ped strain corresponds to Pantoea sp. with an identity greater than 76%; the Sample11pe strain to Pseudomonas sp. with 100% identity; and, to the strain Sample12ped to Raoultella terrígena sp. or Klebsiella sp. with an identity of 99%. The sequences of the last two were registered in GenBank, whose accessions are SUB4288247 and SUB4252655. Keywords: Endophytic bacteria, Elodea potamogeton, 16S rDNA gene, phylogeny

Physiological and genetic characterization of fluorescentPseudomonasassociated withCantharellus cibarius

2002 ◽  
Vol 48 (8) ◽  
pp. 739-748 ◽  
Author(s):  
J Ignacio Rangel-Castro ◽  
Jolanta J Levenfors ◽  
Eric Danell
Keyword(s):  
16S Rdna ◽  
Fungal Mycelium ◽  
Sequencing Analysis ◽  
Carbon Utilization ◽  
Pseudomonas Spp ◽  
Fluorescent Pseudomonas ◽  
Rdna Sequencing ◽  
Pcr Rflp ◽  
Polymerase Chain

Fluorescent Pseudomonas spp. isolated from fruiting bodies (FB) of Cantharellus cibarius were characterized physiologically and genetically and were compared with fluorescent Pseudomonas from forest soil and with sequences from the GenBank database. Pseudomonas spp. from FB differed physiologically from isolates from soil lacking FB and had some similarities with the strains obtained from soil underneath the FB. Analyses of the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) patterns and partial sequencing analysis of the 16S-rDNA region indicated that the bacteria isolated from these environments were different. However, there was no specific Pseudomonas genotype restricted to the FB environment. Utilization of the reported fungal exudates trehalose and mannitol may explain how millions of bacteria survive in the C. cibarius FB without deteriorating the fungal mycelium. The importance of the metabolic characterization of bacteria and the possible mechanisms involved in the association with C. cibarius are discussed. Our study showed that standard processes for bacterial identification, e.g., Biolog®and 16S-rDNA are insufficient until databases for different ecosystems are created.Key words: Cantharellus cibarius, fluorescent Pseudomonas, carbon utilization, PCR–RFLP, 16S-rDNA sequencing.

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