Partial characterization of nif genes from the bacterium Azospirillum amazonense

Gold nanoparticle-assisted polymerase chain reaction: effects of surface ligands, nanoparticle shape and material

The concentration, shape, material, and surface functionalization effects of gold nanoparticles on PCR outcome have been studied with two PCR gene diagnostic models.

Tools for genetic manipulation of the plant growth-promoting bacterium Azospirillum amazonense

Background

Azospirillum amazonense has potential to be used as agricultural inoculant since it promotes plant growth without causing pollution, unlike industrial fertilizers. Owing to this fact, the study of this species has gained interest. However, a detailed understanding of its genetics and physiology is limited by the absence of appropriate genetic tools for the study of this species.

Results

Conjugation and electrotransformation methods were established utilizing vectors with broad host-replication origins (pVS1 and pBBR1). Two genes of interest - glnK and glnB, encoding PII regulatory proteins - were isolated. Furthermore, glnK-specific A. amazonense mutants were generated utilizing the pK19MOBSACB vector system. Finally, a promoter analysis protocol based on fluorescent protein expression was optimized to aid genetic regulation studies on this bacterium.

Conclusion

In this work, genetic tools that can support the study of A. amazonense were described. These methods could provide a better understanding of the genetic mechanisms of this species that underlie its plant growth promotion.

Endophytic bacteria and their potential to enhance heavy metal phytoextraction

Pollution of soils with heavy metals is becoming one of the most severe environmental and human health hazards. Due to its widespread contamination finding innovative ways to clean metal pollutant has become a priority in the remediation field. Phytoremediation, the use of plants for the restoration of environments contaminated with pollutants is a relatively new technology that is more benign than current engineering solutions to treat contaminated sites. Recently, the benefits of combining endophytic bacteria with plants for increased remediation of pollutants have been successfully tried for toxic metal removal from contaminated soils. Endophytic bacteria reside within plant hosts without causing disease symptoms. Further, the metal resistant endophytes are reported to be present in various hyperaccumulator plants growing on heavy metal contaminated soils and play an important role in successful survival and growth of plants. Moreover, the metal resistant endophytes are reported to promote plant growth by various mechanisms such as nitrogen fixation, solubilization of minerals, production of phytohormones, siderophores, utilization of 1-aminocyclopropane-1-carboxylic acid as a sole N source and transformation of nutrient elements. In this review we highlight the diversity and plant growth promoting features of metal resistant endophytic bacteria and discuss their potential in phytoextraction of heavy metals from contaminated soils.

Endophytic colonization ofTypha australisby a plant growth-promoting bacteriumKlebsiella oxytocastrain GR-3

AIMS

To isolate and characterize endophytic diazotrophic bacteria from a semi-aquatic grass (Typha australis) which grows luxuriantly with no addition of any nitrogen source.

METHODS AND RESULTS

Ten endophytic diazotrophic bacteria from surface-sterilized roots and culm of T. australis were isolated and screened for plant growth-promoting activities employing standard methods. Based on the rate of nitrogenase activity, indole acetic acid (IAA) production and phosphate (P) solubilization, one root isolate namely GR-3 was found to be the most efficient one. This isolate was identified as Klebsiella oxytoca on the basis of 16S rDNA sequence analysis. Amplification of nifH by polymerase chain reaction (PCR) and detection of dinitrogenase reductase by western blot confirmed the diazotrophic nature of GR-3. It was tagged with gusA fused to a constitutive promoter and the resulting transconjugant was inoculated onto endophyte-free rice variety Malviya dhan-36 seedlings to express cross-infection ability which resulted in a significant increase in root/shoot length and chlorophyll a content.

CONCLUSIONS

Roots and culm of T. australis harbour several endophytic diazotrophic bacteria. One root isolate, identified as K. oxytoca GR-3, seems to be an efficient plant growth-promoting bacterium.

SIGNIFICANCE AND IMPACT OF THE STUDY

Plant growth-promoting properties of GR-3 suggest that this promising isolate merits further investigations for potential application in agriculture.

Identification ofnif genes in N2-fixing bacterial strains isolated from rice fields along the Yangtze River Plain

The aim of this research was to identify nifH and nifHDKYE ' genes in twenty strains of N2-fixing heterotrophic bacteria isolated from rice fields in the Yangtze River Plain. Southern hybridization of the total DNA from each strain was performed with the Klebsiella pneumoniae nifHDKYE ' gene probe (6.2 kb Eco RI fragment from pSA30) and the Azospirillum brasilense nifH gene probe (0.6 kb Eco RI-Hin dIII fragment from pHU8). We found that Eco RI fragments of total DNA from Aeromonas hydrophila HY2, Bacillus azotoformans FD, Bacillus licheniformis NCH1, NCH5, WH4, Bacillus brevis NC2, Bacillus pumilus NC12, Bacillus cereus NCH2, Citrobacter freundii HY5, HY9, Derxia gummosa HZ5, Pseudomonas mendocina HZ1 and Pseudomonas pseudoalcaligenes WH3 were positively hybridized with both of the probes. Agrobacterium radiobacter HY17, Corynebacterium sp. HY12, YZ and Pseudomonas sp. HY11 had Eco RI fragments hybridized with the K. pneumoniae nifHDKYE ' gene probe. An Eco RI fragment of total DNA from Bacillus megaterium YY4 was positively hybridized to the A. brasilense nifH gene probe. No hybridization sign was found in the total DNA fragments from Alcaligenes cupidus YY6 and Corynebacterium sp. NC11 hybridized with either of the gene probes. The data provide the number and size of EcoRI fragments of the total DNA hybridized with the nif gene probes for these strains of rarely studied species, suggesting additional evidence for N2 fixing and nif gene diversity of N2-fixing bacteria in rice fields along the Yangtze River Plain.

History on the biological nitrogen fixation research in graminaceous plants: special emphasis on the Brazilian experience

This review covers the history on Biological Nitrogen Fixation (BNF) in Graminaceous plants grown in Brazil, and describes research progress made over the last 40 years, most of whichwas coordinated by Johanna Döbereiner. One notable accomplishment during this period was the discovery of several nitrogen-fixing bacteria such as the rhizospheric (Beijerinckia fluminensis and Azotobacter paspali), associative (Azospirillum lipoferum, A. brasilense, A. amazonense) and the endophytic (Herbaspirillum seropedicae, H. rubrisubalbicans, Gluconacetobacter diazotrophicus, Burkholderia brasilensis and B. tropica). The role of these diazotrophs in association with grasses, mainly with cereal plants, has been studied and a lot of progress has been achieved in the ecological, physiological, biochemical, and genetic aspects. The mechanisms of colonization and infection of the plant tissues are better understood, and the BNF contribution to the soil/plant system has been determined. Inoculation studies with diazotrophs showed that endophytic bacteria have a much higher BNF contribution potential than associative diazotrophs. In addition, it was found that the plant genotype influences the plant/bacteria association. Recent data suggest that more studies should be conducted on the endophytic association to strengthen the BNF potential. The ongoing genome sequencing programs: RIOGENE (Gluconacetobacter diazotrophicus) and GENOPAR (Herbaspirillum seropedicae) reflect the commitment to the BNF study in Brazil and should allow the country to continue in the forefront of research related to the BNF process in Graminaceous plants.

Characterization of amplified polymerase chain reaction glnB and nifH gene fragments of nitrogen-fixing Burkholderia species

AIMS

To clone and sequence polymerase chain reaction (PCR)-amplified glnB and nifH genes of the nitrogen-fixing bacteria Burkholderia brasilensis strain M130, B. tropicalis strain PPe8 and B. kururiensis strain KP23.

METHODS AND RESULTS

The glnB and nifH gene fragments were amplified by PCR using universal degenerated primers. A very high percentage of similarity for the nifH (100%) and glnB (96%) genes was observed between strains M130 and KP23. A similarity of 100% for the nifH gene was also observed between strains M130 and PPe8. However, the identity for the glnB gene was 98% and the similarity 88%. The phylogenetic tree of the nifH gene showed a very high degree of similarity to the 16S rDNA gene.

CONCLUSIONS

The nitrogen-fixing bacteria of the Burkholderia genus formed a cluster separated from the other species of the genus mainly when the nifH rather than the glnB gene was used to construct the phylogenetic tree.

SIGNIFICANCE AND IMPACT OF THE STUDY

Knowledge of the nifH and glnB gene sequences of B. brasilensis, B. tropicalis and B. kururiensis will support new studies on the diversity of these diazotrophs in natural environments.