The previous chapters of this thesis describe results obtained in several separate experiments.


In this last chapter, the main results of these experiments are discussed in view of the hypotheses given in the General Introduction. Finally, some perspectives for further research are presented.

7.1 Importance of a polyphasic approach in identifying bacterial isolates

The exact taxonomic affiliation of some microorganisms can only be ascertained by using a polyphasic taxonomic approach. The present study genetically characterised two bacterial isolates isolated from plant endorhizosphere and compared these results against those derived from bacteriological and metabolic identification techniques to assess the need for a polyphasic approach to identify bacteria.

At the first stage of our investigation, we identified the strains at genus level only (chapter 2). Majority were identified as Bacillus sp. The remaining isolates were identified as Pseudomanas, Burkholderia, Klebsiella and others. 


For both strains of interest, BL43 and Xs148 which have been selected for further studies for their universal PGP effect on wheat, cauliflower, cucumber, paprika and tomato plants, BIOLOG test based identifications did not agree with the sequence-based identification (chapter 3). Although the BIOLOG system has been evaluated as having the large database (Holmes et al. 1994), this system’s identification did not always agree with biochemical criteria belonging to some genera including  Bacillus (Tang et al. 1998). Therefore, failure of the BIOLOG system to identify isolate BL43 could be explained by the fact that this isolate belongs to the genera  Bacillus as established using rRNA sequence tests (chapter 3). Also for Xs148, the BIOLOG test resulted in Burkholderia glumae being identified, whereas 16S rRNA sequence-based analysis showed the highest matches to Xanthomonas. The EMBL-Bank sequences of Burkholderia were not even shown on the BLAST match list due to too low similarity. Since, we found that there are more than 600 entries for cultured Burkholderia species in the EMBL-Bank (January 2006), such a number should be enough to determine the sequence in question, at least to the genus level, if the target bacteria belonged to this genus.

Because the 16S rDNA gene is highly conserved, determination of species and strain distinctions relies upon the resolution of only small differences between sequences. Moreover, as two distinct species may possess identical 16S rRNA sequences including Bacillus, gene sequence identification is not foolproof (Ash et al. 1991, Fox et al. 1992, Clarridge 2004). Therefore, taken together, we suggest that 16S rRNA-based identification of strains of some genera at the species level is not reliable enough and requires additional tests. Moreover, reliance on a single molecular method for species definition, such as 16S rRNA gene sequencing, cannot take into account small evolutionary changes, such as point mutations (Stackebrandt et al. 2002). Thus, in practice, a polyphasic approach including alternate gene targets performed in parallel with the examination of a number of phenotypic properties is necessary for definitive species identification.

The 16S-23S rRNA ISR proved to be the best alternate target to 16S rRNA because we found a high consensus between results from 16S rRNA and 16S-23S rRNA ISR sequence-based identification for isolate Xs148. Direct sequence determination of 16S-23S ISR fragments represented a highly accurate method for bacterial identification to the species level, even when the species in question was notoriously difficult to identify by 16S rRNA sequence-based identification. This is because 16S-23S rRNA ISR similarities reflect phylogenetic relationships and has more discriminative nucleotide stretches, which allow identifying in species, even to the strain level (Blackwood et al. 2004). Since, the 16S-23S rRNA ISR-based approach failed to identify isolate BL43 producing differing data to both the basic bacteriological and 16S rRNA sequence-based identification results, we suggest that the potential of ISR analysis for bacteria identification is likely to depend on specific nucleotide stretches of the ISR or on the bacteria species studied (Yoon et al. 1997, Yoon et al. 1998, Kuwahara et al. 2001).


In this study, genotypic methods based on rRNA sequence analysis improved the identification of plant-inhabiting diazotrophic bacteria, thereby completing the identification results obtained using conventional biochemical methods and the BIOLOG® test. From our analyses, we conclude that rRNA sequence-based identification should be performed in conjunction with traditional biochemical bacteriological tests that provide basic information about the microorganism in query.

7.2 Potential of different databases and search programs in molecular identification of bacteria

To demonstrate the quality and accuracy of results provided from different programs and databases, searches for sequence similarity analysis were performed using programs such as BLASTN, FASTA comparing the sequence to the databases EMBL-Bank and RDP-II.

The identification of bacteria based on 16S rRNA sequences was complicated due to numerous ambiguous results.


1. Different results were obtained even when the sequence was compared against the same database (EMBL-Bank) by using different programs (FASTA and BLASTN), resulting in the assignment of different identities. For example, for isolate Xs148, using BLAST searches resulted in the highest matches to the Pseudomonas genus, while using the FASTA program, isolate Xs148 was closest in identity to the Xanthomonas species (chapter 3). 2. 16S rRNA sequence based searching results were not specific enough to differentiate the isolate to the species level. For example, BL43 was 99% identical to many different species of Bacillus subtilis group: B. licheniformis,


 B. subtilis, B. mojavensis and


B. vallismortis and also

B. amyloliquefaciens.


3. 16S rRNA sequence based search result disagreed with the phenotypic characterization of the strain. For BL43, BLAST searches showed 99% identity of the sequence in query to a micro-organism belonging to gram-negative bacteria, Pseudomonas sp. As sequences can be deposited in the GenBank-EMBL and RDP-II databases without undergoing any checks, it is not surprising that errors do occur as regards species assignment (Harmsen et al. 2003).

4. RDP-II database based searches showed highly ambiguous results, most probably, due to the limited number of sequences included in the sequence match search (Chapter 3, Tab. 12b).

5. We found, that the RIDOM database is not useful for identification of the bacterial strains investigated in this study, although Blackwood et al. (2004) reported that 16S rRNA gene sequences for 65 (of all 83) type strains of the Bacillus genus have been submitted to the RIDOM database at http://rdna.ridom.de/.


From our analyses, we conclude that (i) for similarity scores of different species belonging to the same genus of less than 1 % dissimilarity, the FASTA program displays more accurate values, i.e. to 3 decimal places, than BLAST, and (ii)16S rRNA in conjunction with 16S-23S rRNA ISR sequence-based identification can be used to identify and differentiate between the species only if the quality of the database is high enough, i.e. it contains a high number of reliable sequence entries taken from a comprehensive range of species.

7.3 Effect of supplied nitrogen level on the abundance and activity of natural and introduced diazotrophic bacteria on plant root


Various studies indicated that the abundance of total diazotrophs or of specific populations in both pure culture and environmental samples can be influenced by the amounts of inorganic N applied (Cejudo and Paneque 1986, Herridge and Brockwell 1988, Limmer and Drake 1998, Fuentes-Ramirez et al. 1999, Tan et al. 2003).

We have studied (i) the abundance of natural diazotrophic bacteria in plant tissue by quantifying nifH gene copies using a new method developed in this study (chapter 5), and (ii) the colonization ability of certain bacteria in plant root and shoot by quantifying strain-specific ISR using real-time PCR approaches (chapters 4, 6). The quantified nifH gene values reflect the abundance of diazotrophic populations associated with the plant.

Effective colonization of plant roots by PGPB plays an important role in growth promotion, irrespective of the mechanism of action (Bolwerk et al. 2003, Raaijmakers et al. 1995).


It is well recognized that N availability is mostly negatively correlated with inoculated diazotrophic bacteria abundance (Cejudo and Paneque 1986, Limmer and Drake 1998; Tan et al. 2003). We document that N availability affected different diazotrophic bacterial species in different level (chapter 6). Quantification results showed that N availability was negatively correlated to Xanthomonas sp. Xs148 abundance showing relatively less bacteria abundance in high N supplied plants (Fig. 3), while B. licheniformis BL43 abundance in high N supplied plants were significantly higher than low N supplied plants. The strong effect of N fertilization on diazotrophic bacteria abundance demonstrates the importance to determine optimal N fertilizer levels for efficient inoculation experiments.

Measurements of introduced bacteria like bacteria population in +B and -B plants showed that, although, the abundance of both introduced bacteria in +B plants and introduced bacteria like natural bacteria populations in -B plants was significantly decreased in response to high N fertilization (chapters 2, 6), inoculation of plant with diazotrophic bacteria allowed to provide highly abundance of diazotrophic community in inoculated plant root even in high N fertilization providing high potential of diazotrophic community to fix atmospheric N2.

Results showed that the effect of N availability on diazotrophs may be plant-species dependent, as in tomato roots (chapter 6), the diazotrophic communities were suppressed by higher mineral N fertilization, while higher N supply stimulated the growth of diazotrophic bacteria population in cucumber roots. We suggest that a significantly higher diazotrophic bacteria abundance in high N supplied cucumber plants can be partly explained by a significantly larger root system developed (chapter 5, Tab. 15) compared to the low N supplied plants, providing favorable conditions for microorganism growth, including those for diazotrophic bacteria.


Our comparative quantified-gene analyses indicated that methods which centre on only introduced diazotrophs, would ignore the possible effect of introduced bacteria on the native diazotrophic population inhabiting the plant and can led to the wrong conclusion that plant N nutrition was improved by another plant growth promoting effects of introduced bacteria. We observed significantly higher nifH gene abundance in inoculated plant roots compared to control plant roots, while introduced bacteria was not colonized significantly, indicating that increasing of nifH gene pool in plant root was not due to the contribution of introduced bacteria, but it was shown to be the effect of introduced diazotrophic bacteria on the abundance of natural diazotrophic population (chapter 6).

7.4 Relationship between nifH-gene abundance and plant N nutrition 

Although the DNA-based PCR method is not directly related to nifH gene expression, it does allow comparison of the effects of different treatments on the N2–fixing potential of the microbial community in plant samples by quantification of nifH gene abundance in plant. Therefore, it can be suggested that significantly close relationships of nifH gene abundance and tomato plant N content (correlation coefficient of 1.00 and 0.71 for low and high N supplied, respectively; data not shown) can indicate evidence for direct contribution of natural diazotrophic population to plant N nutrition.

Regression analysis to determine the relationships of those introduced diazotrophic bacteria and nifH gene abundance, and the significant correlation of their abundance to plant N content (Chapter 6, Tab. 21) could be employed to identify the possible contribution of biological N2-fixation by introduced bacteria to plant N nutrition. Introducing the active members of diazotrophs to plant root increased the amount of this contribution, however, relatively less close relationships of nifH gene abundance and plant N nutrition of +B plants in comparison to -B plants was observed (Tab. 21). It may be due to the secondary mechanisms, like root growth promotion by phytohormonal effects (Tab. 19), of introduced bacteria contributed to general N nutrition of plant (Bashan et al. 1989, Hurek et al. 1994).


Regression analysis allowed to evaluate the effect of supplied N to the supposed activity of nifH gene existed in plant root. The correlation between nifH gene and plant N nutrition for low N supplied plants was stronger in comparison to high N supplied plants (Tab. 21) indicating that an increased N input does not only induce changes in the abundance of nifH gene, but also influences the potential activity of this gene suggesting that the proportion of biological N2-fixation was higher at low N levels (Chapter 6).

7.5 PGP effect of inoculated bacteria

The importance of bacterial strain Bacillus licheniformis BL43 and Xanthomonas sp. Xs148 was particularly significant regarding its beneficial effects on the plant growth and suppression the growth of plant pathogens. They stimulate the growth of wheat, and that PGPBs of wheat tested were not strictly plant-specific stimulating the different vegetable species.

Since, plants were grown in sand and supplied with half-strength Hoagland solution, the significant positive influence of inoculated bacteria on plant growth emphasizes that the bacteria tested can influence plant growth even in the presence of a nutrient solution. These findings suggest that plants may be grown with lower amounts of applied fertilizers and implies (1) a reduction in the cost associated with growing plants and (2) a reduction in the pollution associated with agricultural practices.

7.6 Perspectives for further research


This thesis covered several aspects of the influence of PGPB on plant growth.

New questions arose during the study that should be investigated in more detail in further experiments. Some of these points are summarized in the following.

New technologies and methods to investigate microbial communities are being developed at a rapid pace and provide new opportunities to link community structure to ecosystem processes. In this study, the combination of nifH-gene quantification and plant N-uptake measurements was shown to be a possible tool to evaluate the contribution of the N2–fixing plant-inhabiting diazotrophic community to plant N nutrition. The positive correlation between nifH gene abundance and plant N nutrition highlights the potential value of studying functional genes in the context of ecosystem processes. However, these results are only suggestive of this relationship, and future studies should focus on measuring the relationships of gene abundance to the target gene expression and activity simultaneously. The herein described DNA-based real-time PCR quantification of nifH gene abundance in plant tissues can be extended to RNA-based approaches as DNA is more likely to reflect the standing biomass of a particular community and mRNA should be more closely related to activity rates (Bürgmann et al. 2003).


Additionally, the relationship between the diversity of special diazotrophic bacterial populations and their sensitivity to environmental changes should be examined.

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