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Genetic diversity and phylogeny of antagonistic bacteria against Phytophthora nicotianae isolated from tobacco rhizosphere.

Jin F, Ding Y, Ding W, Reddy MS, Fernando WG, Du B - Int J Mol Sci (2011)

Bottom Line: A total of 25 16S-RFLP patterns were identified representing over 33 species from 17 different genera.Our results also found a significant amount of bacterial diversity among the antagonistic bacteria compared to other published reports.For the first time; Delftia tsuruhatensis, Stenotrophomonas maltophilia, Advenella incenata, Bacillus altitudinis, Kocuria palustris, Bacillus licheniformis, Agrobacterium tumefaciens and Myroides odoratimimus are reported to display antagonistic activity towards Phytophthora nicotianae.

View Article: PubMed Central - PubMed

Affiliation: Shandong Key Laboratory of Agricultural Microbiology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China; E-Mails: jfl315@163.com (F.J.); dingyq6885@163.com (Y.D.).

ABSTRACT
The genetic diversity of antagonistic bacteria from the tobacco rhizosphere was examined by BOXAIR-PCR, 16S-RFLP, 16S rRNA sequence homology and phylogenetic analysis methods. These studies revealed that 4.01% of the 6652 tested had some inhibitory activity against Phytophthora nicotianae. BOXAIR-PCR analysis revealed 35 distinct amplimers aligning at a 91% similarity level, reflecting a high degree of genotypic diversity among the antagonistic bacteria. A total of 25 16S-RFLP patterns were identified representing over 33 species from 17 different genera. Our results also found a significant amount of bacterial diversity among the antagonistic bacteria compared to other published reports. For the first time; Delftia tsuruhatensis, Stenotrophomonas maltophilia, Advenella incenata, Bacillus altitudinis, Kocuria palustris, Bacillus licheniformis, Agrobacterium tumefaciens and Myroides odoratimimus are reported to display antagonistic activity towards Phytophthora nicotianae. Furthermore, the majority (75%) of the isolates assayed for antagonistic activity were Gram-positives compared to only 25% that were Gram-negative bacteria.

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16S-RFLP patterns obtained from restriction digestion gel photos with Alu I, Hae III, Hinf I, and Msp I. Lanes (1–12) represent the 16S-RFLP groups 1, 3, 5, 6, 9, 11, 13, 15, 18, 21, 23 and 24. Lanes M are the marker 100 bp DNA ladder; A, B, C, and D represent restriction digestion gel photos with Msp I, Alu I, Hinf I, and Hae III.
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f4-ijms-12-03055: 16S-RFLP patterns obtained from restriction digestion gel photos with Alu I, Hae III, Hinf I, and Msp I. Lanes (1–12) represent the 16S-RFLP groups 1, 3, 5, 6, 9, 11, 13, 15, 18, 21, 23 and 24. Lanes M are the marker 100 bp DNA ladder; A, B, C, and D represent restriction digestion gel photos with Msp I, Alu I, Hinf I, and Hae III.

Mentions: The 267 antagonistic bacteria isolates were subjected to 16S-RFLP analysis by digestion of the amplified 16S rRNA gene with four restriction enzymes (Alu I, Hae III, Hinf I and Msp I). Similar banding patterns were obtained after combination analysis of the four independent digestions (Figure 4). These banding patterns were used to generate a dendrogram that separated the 267 isolates into 25 clusters or genotypic groups (Table 1) at the level of 88.5% similarity. As shown in Figure 4, each cluster displayed a specific banding pattern, and groups consisting of different species were clearly differentiated. Groups 1, 16, 20, 22, 24 and 25 each consisted of a single bacteria isolate; Bacillus flexus, Serratia marcescens, Burkholderia arboris, Advenella incenata, Stenotrophomonas maltophilia and Myroides odoratimimus respectively. On the other hand, groups 5 and 6 contained greater bacterial diversity with 57 and 46 antagonistic bacteria isolates, from the genera Bacillus and Brevibacillus, respectively. Therefore, these clustering results indicate that antagonistic bacteria are highly diverse at a phylogenetic level.


Genetic diversity and phylogeny of antagonistic bacteria against Phytophthora nicotianae isolated from tobacco rhizosphere.

Jin F, Ding Y, Ding W, Reddy MS, Fernando WG, Du B - Int J Mol Sci (2011)

16S-RFLP patterns obtained from restriction digestion gel photos with Alu I, Hae III, Hinf I, and Msp I. Lanes (1–12) represent the 16S-RFLP groups 1, 3, 5, 6, 9, 11, 13, 15, 18, 21, 23 and 24. Lanes M are the marker 100 bp DNA ladder; A, B, C, and D represent restriction digestion gel photos with Msp I, Alu I, Hinf I, and Hae III.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3116175&req=5

f4-ijms-12-03055: 16S-RFLP patterns obtained from restriction digestion gel photos with Alu I, Hae III, Hinf I, and Msp I. Lanes (1–12) represent the 16S-RFLP groups 1, 3, 5, 6, 9, 11, 13, 15, 18, 21, 23 and 24. Lanes M are the marker 100 bp DNA ladder; A, B, C, and D represent restriction digestion gel photos with Msp I, Alu I, Hinf I, and Hae III.
Mentions: The 267 antagonistic bacteria isolates were subjected to 16S-RFLP analysis by digestion of the amplified 16S rRNA gene with four restriction enzymes (Alu I, Hae III, Hinf I and Msp I). Similar banding patterns were obtained after combination analysis of the four independent digestions (Figure 4). These banding patterns were used to generate a dendrogram that separated the 267 isolates into 25 clusters or genotypic groups (Table 1) at the level of 88.5% similarity. As shown in Figure 4, each cluster displayed a specific banding pattern, and groups consisting of different species were clearly differentiated. Groups 1, 16, 20, 22, 24 and 25 each consisted of a single bacteria isolate; Bacillus flexus, Serratia marcescens, Burkholderia arboris, Advenella incenata, Stenotrophomonas maltophilia and Myroides odoratimimus respectively. On the other hand, groups 5 and 6 contained greater bacterial diversity with 57 and 46 antagonistic bacteria isolates, from the genera Bacillus and Brevibacillus, respectively. Therefore, these clustering results indicate that antagonistic bacteria are highly diverse at a phylogenetic level.

Bottom Line: A total of 25 16S-RFLP patterns were identified representing over 33 species from 17 different genera.Our results also found a significant amount of bacterial diversity among the antagonistic bacteria compared to other published reports.For the first time; Delftia tsuruhatensis, Stenotrophomonas maltophilia, Advenella incenata, Bacillus altitudinis, Kocuria palustris, Bacillus licheniformis, Agrobacterium tumefaciens and Myroides odoratimimus are reported to display antagonistic activity towards Phytophthora nicotianae.

View Article: PubMed Central - PubMed

Affiliation: Shandong Key Laboratory of Agricultural Microbiology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China; E-Mails: jfl315@163.com (F.J.); dingyq6885@163.com (Y.D.).

ABSTRACT
The genetic diversity of antagonistic bacteria from the tobacco rhizosphere was examined by BOXAIR-PCR, 16S-RFLP, 16S rRNA sequence homology and phylogenetic analysis methods. These studies revealed that 4.01% of the 6652 tested had some inhibitory activity against Phytophthora nicotianae. BOXAIR-PCR analysis revealed 35 distinct amplimers aligning at a 91% similarity level, reflecting a high degree of genotypic diversity among the antagonistic bacteria. A total of 25 16S-RFLP patterns were identified representing over 33 species from 17 different genera. Our results also found a significant amount of bacterial diversity among the antagonistic bacteria compared to other published reports. For the first time; Delftia tsuruhatensis, Stenotrophomonas maltophilia, Advenella incenata, Bacillus altitudinis, Kocuria palustris, Bacillus licheniformis, Agrobacterium tumefaciens and Myroides odoratimimus are reported to display antagonistic activity towards Phytophthora nicotianae. Furthermore, the majority (75%) of the isolates assayed for antagonistic activity were Gram-positives compared to only 25% that were Gram-negative bacteria.

Show MeSH
Related in: MedlinePlus