Isolation, Charcaterization and Phylogenetic Analysis of Endophytic Bacteria in Rice Plant Cultivated on Soil of Phu Yen Province, Vietnam

Van Thi Phuong Nhu; Cao Ngoc Diep

doi:doi:10.11648/j.ajls.20140203.11

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Isolation, Charcaterization and Phylogenetic Analysis of Endophytic Bacteria in Rice Plant Cultivated on Soil of Phu Yen Province, Vietnam

Van Thi Phuong Nhu, Cao Ngoc Diep

Published in American Journal of Life Sciences (Volume 2, Issue 3)

Received: 7 May 2014 Accepted: 15 May 2014 Published: 30 May 2014

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Abstract

Endophytic bacterial diversity in Rice plant cultivated on soil of Phu Yen province, Vietnam was studied. Rice plant samples were taken in eight sites (districts) of Phu Yen provinces of this region. Endophytic bacteria were isolated in three kinds of medium (LGI, NFb, RMR) together with 16S rRNA gene fragments amplified from DNA using eubacterial universal primers (p515FPL and p13B). A total of 561 isolates were isolated on three media and all of them have ability of nitrogen fixation and phosphate solubilization together with IAA biosynthesis but there were 73 isolates having the best characteristics and they were identified as rice endophytes and nifH gene. The sequences from selected endophytic bacteria (73 isolates) showed high degrees of similarity to those of the GenBank references strains (between 97% and 100%). From 73 isolates, 23 isolates belonged to Bacillus (31.54%), 44 isolates were Proteobacteria (60.24%), while 6 isolates were Bacteroides (8.22%). Based on Pi value (nucleotide diversity), Bacteroides group had the highest theta values in comparison of three groups and Theta values (per sequence) from S of SNP for DNA polymorphism were calculated for each group and Bacteroides group had the highest values in comparison of three group. From these results showed that thirteen strains (Bacillus megaterium TANa5, Bacillus methylotrophicus TAN17, Bacillus megaterium TALa14, Pseudomonas putida TAL1, Bacillus subtilis TAL4, Burkholderia kururiensis TAL22, Azospirillum amazonense SHL70, Bacillus subtilis DXL 136, Burkholderia kururiensis PHL87, Burkholderia vietnamiensis PHL103, Bacillus megaterium PHL105, Bacillus megaterium DHL154 and Bacillus subtilis SHIM60) revealed promising candidates with multiple beneficial characteristics and they have the potential for application as inoculants or bio-fertilizer adapted to poor soils and high-yielding rice because they are not only famous strains but also are safety strains for agricultural sustainable.

Published in	American Journal of Life Sciences (Volume 2, Issue 3)
DOI	10.11648/j.ajls.20140203.11
Page(s)	117-127
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2014. Published by Science Publishing Group

Keywords

16S rRNA Gene Sequence, Endophytic Bacteria, High-Yielding Rice, Phu Yen Province, Rice Growth Promoting

References

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Van Thi Phuong Nhu, Cao Ngoc Diep. (2014). Isolation, Charcaterization and Phylogenetic Analysis of Endophytic Bacteria in Rice Plant Cultivated on Soil of Phu Yen Province, Vietnam. American Journal of Life Sciences, 2(3), 117-127. https://doi.org/10.11648/j.ajls.20140203.11

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Van Thi Phuong Nhu; Cao Ngoc Diep. Isolation, Charcaterization and Phylogenetic Analysis of Endophytic Bacteria in Rice Plant Cultivated on Soil of Phu Yen Province, Vietnam. Am. J. Life Sci. 2014, 2(3), 117-127. doi: 10.11648/j.ajls.20140203.11

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Van Thi Phuong Nhu, Cao Ngoc Diep. Isolation, Charcaterization and Phylogenetic Analysis of Endophytic Bacteria in Rice Plant Cultivated on Soil of Phu Yen Province, Vietnam. Am J Life Sci. 2014;2(3):117-127. doi: 10.11648/j.ajls.20140203.11

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@article{10.11648/j.ajls.20140203.11,
  author = {Van Thi Phuong Nhu and Cao Ngoc Diep},
  title = {Isolation, Charcaterization and Phylogenetic Analysis of Endophytic Bacteria in Rice Plant Cultivated on Soil of Phu Yen Province, Vietnam},
  journal = {American Journal of Life Sciences},
  volume = {2},
  number = {3},
  pages = {117-127},
  doi = {10.11648/j.ajls.20140203.11},
  url = {https://doi.org/10.11648/j.ajls.20140203.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajls.20140203.11},
  abstract = {Endophytic bacterial diversity in Rice plant cultivated on soil of Phu Yen province, Vietnam was studied. Rice plant samples were taken in eight sites (districts) of Phu Yen provinces of this region. Endophytic bacteria were isolated in three kinds of medium (LGI, NFb, RMR) together with 16S rRNA gene fragments amplified from DNA using eubacterial universal primers (p515FPL and p13B). A total of 561 isolates were isolated on three media and all of them have ability of nitrogen fixation and phosphate solubilization together with IAA biosynthesis but there were 73 isolates having the best characteristics and they were identified as rice endophytes and nifH gene. The sequences from selected endophytic bacteria (73 isolates) showed high degrees of similarity to those of the GenBank references strains (between 97% and 100%). From 73 isolates, 23 isolates belonged to Bacillus (31.54%), 44 isolates were Proteobacteria (60.24%), while 6 isolates were Bacteroides (8.22%). Based on Pi value (nucleotide diversity), Bacteroides group had the highest theta values in comparison of three groups and Theta values (per sequence) from S of SNP for DNA polymorphism were calculated for each group and Bacteroides group had the highest values in comparison of three group. From these results showed that thirteen strains (Bacillus megaterium TANa5, Bacillus methylotrophicus TAN17, Bacillus megaterium TALa14, Pseudomonas putida TAL1, Bacillus subtilis TAL4, Burkholderia kururiensis TAL22, Azospirillum amazonense SHL70, Bacillus subtilis DXL 136, Burkholderia kururiensis PHL87, Burkholderia vietnamiensis PHL103, Bacillus megaterium PHL105, Bacillus megaterium DHL154 and Bacillus subtilis SHIM60) revealed promising candidates with multiple beneficial characteristics and they have the potential for application as inoculants or bio-fertilizer adapted to poor soils and high-yielding rice because they are not only famous strains but also are safety strains for agricultural sustainable.},
 year = {2014}
}

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TY  - JOUR
T1  - Isolation, Charcaterization and Phylogenetic Analysis of Endophytic Bacteria in Rice Plant Cultivated on Soil of Phu Yen Province, Vietnam
AU  - Van Thi Phuong Nhu
AU  - Cao Ngoc Diep
Y1  - 2014/05/30
PY  - 2014
N1  - https://doi.org/10.11648/j.ajls.20140203.11
DO  - 10.11648/j.ajls.20140203.11
T2  - American Journal of Life Sciences
JF  - American Journal of Life Sciences
JO  - American Journal of Life Sciences
SP  - 117
EP  - 127
PB  - Science Publishing Group
SN  - 2328-5737
UR  - https://doi.org/10.11648/j.ajls.20140203.11
AB  - Endophytic bacterial diversity in Rice plant cultivated on soil of Phu Yen province, Vietnam was studied. Rice plant samples were taken in eight sites (districts) of Phu Yen provinces of this region. Endophytic bacteria were isolated in three kinds of medium (LGI, NFb, RMR) together with 16S rRNA gene fragments amplified from DNA using eubacterial universal primers (p515FPL and p13B). A total of 561 isolates were isolated on three media and all of them have ability of nitrogen fixation and phosphate solubilization together with IAA biosynthesis but there were 73 isolates having the best characteristics and they were identified as rice endophytes and nifH gene. The sequences from selected endophytic bacteria (73 isolates) showed high degrees of similarity to those of the GenBank references strains (between 97% and 100%). From 73 isolates, 23 isolates belonged to Bacillus (31.54%), 44 isolates were Proteobacteria (60.24%), while 6 isolates were Bacteroides (8.22%). Based on Pi value (nucleotide diversity), Bacteroides group had the highest theta values in comparison of three groups and Theta values (per sequence) from S of SNP for DNA polymorphism were calculated for each group and Bacteroides group had the highest values in comparison of three group. From these results showed that thirteen strains (Bacillus megaterium TANa5, Bacillus methylotrophicus TAN17, Bacillus megaterium TALa14, Pseudomonas putida TAL1, Bacillus subtilis TAL4, Burkholderia kururiensis TAL22, Azospirillum amazonense SHL70, Bacillus subtilis DXL 136, Burkholderia kururiensis PHL87, Burkholderia vietnamiensis PHL103, Bacillus megaterium PHL105, Bacillus megaterium DHL154 and Bacillus subtilis SHIM60) revealed promising candidates with multiple beneficial characteristics and they have the potential for application as inoculants or bio-fertilizer adapted to poor soils and high-yielding rice because they are not only famous strains but also are safety strains for agricultural sustainable.
VL  - 2
IS  - 3
ER  -

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Author Information

Van Thi Phuong Nhu

Dept. Biology, Phu Yen University, Phu Yen Province, Vietnam
Cao Ngoc Diep

Dept. Microbiology Biotechnology, Biotechnology R&D Institute, Can Tho University, Can Tho City, Vietnam

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Van Thi Phuong Nhu, Cao Ngoc Diep. (2014). Isolation, Charcaterization and Phylogenetic Analysis of Endophytic Bacteria in Rice Plant Cultivated on Soil of Phu Yen Province, Vietnam. American Journal of Life Sciences, 2(3), 117-127. https://doi.org/10.11648/j.ajls.20140203.11

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ACS Style

Van Thi Phuong Nhu; Cao Ngoc Diep. Isolation, Charcaterization and Phylogenetic Analysis of Endophytic Bacteria in Rice Plant Cultivated on Soil of Phu Yen Province, Vietnam. Am. J. Life Sci. 2014, 2(3), 117-127. doi: 10.11648/j.ajls.20140203.11

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AMA Style

Van Thi Phuong Nhu, Cao Ngoc Diep. Isolation, Charcaterization and Phylogenetic Analysis of Endophytic Bacteria in Rice Plant Cultivated on Soil of Phu Yen Province, Vietnam. Am J Life Sci. 2014;2(3):117-127. doi: 10.11648/j.ajls.20140203.11

Copy | Download

@article{10.11648/j.ajls.20140203.11,
  author = {Van Thi Phuong Nhu and Cao Ngoc Diep},
  title = {Isolation, Charcaterization and Phylogenetic Analysis of Endophytic Bacteria in Rice Plant Cultivated on Soil of Phu Yen Province, Vietnam},
  journal = {American Journal of Life Sciences},
  volume = {2},
  number = {3},
  pages = {117-127},
  doi = {10.11648/j.ajls.20140203.11},
  url = {https://doi.org/10.11648/j.ajls.20140203.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajls.20140203.11},
  abstract = {Endophytic bacterial diversity in Rice plant cultivated on soil of Phu Yen province, Vietnam was studied. Rice plant samples were taken in eight sites (districts) of Phu Yen provinces of this region. Endophytic bacteria were isolated in three kinds of medium (LGI, NFb, RMR) together with 16S rRNA gene fragments amplified from DNA using eubacterial universal primers (p515FPL and p13B). A total of 561 isolates were isolated on three media and all of them have ability of nitrogen fixation and phosphate solubilization together with IAA biosynthesis but there were 73 isolates having the best characteristics and they were identified as rice endophytes and nifH gene. The sequences from selected endophytic bacteria (73 isolates) showed high degrees of similarity to those of the GenBank references strains (between 97% and 100%). From 73 isolates, 23 isolates belonged to Bacillus (31.54%), 44 isolates were Proteobacteria (60.24%), while 6 isolates were Bacteroides (8.22%). Based on Pi value (nucleotide diversity), Bacteroides group had the highest theta values in comparison of three groups and Theta values (per sequence) from S of SNP for DNA polymorphism were calculated for each group and Bacteroides group had the highest values in comparison of three group. From these results showed that thirteen strains (Bacillus megaterium TANa5, Bacillus methylotrophicus TAN17, Bacillus megaterium TALa14, Pseudomonas putida TAL1, Bacillus subtilis TAL4, Burkholderia kururiensis TAL22, Azospirillum amazonense SHL70, Bacillus subtilis DXL 136, Burkholderia kururiensis PHL87, Burkholderia vietnamiensis PHL103, Bacillus megaterium PHL105, Bacillus megaterium DHL154 and Bacillus subtilis SHIM60) revealed promising candidates with multiple beneficial characteristics and they have the potential for application as inoculants or bio-fertilizer adapted to poor soils and high-yielding rice because they are not only famous strains but also are safety strains for agricultural sustainable.},
 year = {2014}
}

Copy | Download

TY  - JOUR
T1  - Isolation, Charcaterization and Phylogenetic Analysis of Endophytic Bacteria in Rice Plant Cultivated on Soil of Phu Yen Province, Vietnam
AU  - Van Thi Phuong Nhu
AU  - Cao Ngoc Diep
Y1  - 2014/05/30
PY  - 2014
N1  - https://doi.org/10.11648/j.ajls.20140203.11
DO  - 10.11648/j.ajls.20140203.11
T2  - American Journal of Life Sciences
JF  - American Journal of Life Sciences
JO  - American Journal of Life Sciences
SP  - 117
EP  - 127
PB  - Science Publishing Group
SN  - 2328-5737
UR  - https://doi.org/10.11648/j.ajls.20140203.11
AB  - Endophytic bacterial diversity in Rice plant cultivated on soil of Phu Yen province, Vietnam was studied. Rice plant samples were taken in eight sites (districts) of Phu Yen provinces of this region. Endophytic bacteria were isolated in three kinds of medium (LGI, NFb, RMR) together with 16S rRNA gene fragments amplified from DNA using eubacterial universal primers (p515FPL and p13B). A total of 561 isolates were isolated on three media and all of them have ability of nitrogen fixation and phosphate solubilization together with IAA biosynthesis but there were 73 isolates having the best characteristics and they were identified as rice endophytes and nifH gene. The sequences from selected endophytic bacteria (73 isolates) showed high degrees of similarity to those of the GenBank references strains (between 97% and 100%). From 73 isolates, 23 isolates belonged to Bacillus (31.54%), 44 isolates were Proteobacteria (60.24%), while 6 isolates were Bacteroides (8.22%). Based on Pi value (nucleotide diversity), Bacteroides group had the highest theta values in comparison of three groups and Theta values (per sequence) from S of SNP for DNA polymorphism were calculated for each group and Bacteroides group had the highest values in comparison of three group. From these results showed that thirteen strains (Bacillus megaterium TANa5, Bacillus methylotrophicus TAN17, Bacillus megaterium TALa14, Pseudomonas putida TAL1, Bacillus subtilis TAL4, Burkholderia kururiensis TAL22, Azospirillum amazonense SHL70, Bacillus subtilis DXL 136, Burkholderia kururiensis PHL87, Burkholderia vietnamiensis PHL103, Bacillus megaterium PHL105, Bacillus megaterium DHL154 and Bacillus subtilis SHIM60) revealed promising candidates with multiple beneficial characteristics and they have the potential for application as inoculants or bio-fertilizer adapted to poor soils and high-yielding rice because they are not only famous strains but also are safety strains for agricultural sustainable.
VL  - 2
IS  - 3
ER  -

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