Abstract
Plant diseases are among the most limiting factors in agricultural production all over the world, particularly when the causal agent is characterized as quarantine pathogen. One of the most devastating diseases is bacterial wilt of potato and tomato caused by Ralstonia solanacearum (Rs) which is regarded as an epidemic soil-borne quarantine pathogen. The persistence and survival of Rs in soil for years and its ability to colonize a huge number of hosts and non-host crops poses a huge agricultural threat. In order to cope with such pathogen, investigations into the microbial diversity and suppressive potential in the soil and hizosphere of potential host plants are fundamental. In this context, we elucidated the effect of the soil types (DS, LL and AL) and the potato plant sphere (rhizosphere, endorhiza, endocaulosphere; tuber ecto- and endosphere) on the proportion and diversity of in vitro antagonists towards Rs. For this purpose, potato plants were grown under field conditions in three soil types that were stored at a unique experimental field site for more than ten years under the same weather conditions and cropping history. Screening equal numbers of dominant randomly picked colonies from each sphere for in vitro antagonistic activity towards Rs showed that in all spheres antagonists were detected among the dominant cultivable bacteria and that the highest proportion of antagonists was observed in the endophytic compartments. While several genotypes were detected only in one soil, other genotypes were isolated from two or three soils and in some cases with a preference to a particular soil. Based on these results, it is possible to conclude that both, plant sphere and soil types, affect the diversity and proportion of bacteria with in vitro antagonistic activity towards Rs. More antagonists with beneficial characteristics were isolated from plants grown in DS soils. However, to get more insights into the effect of the three soil types on the bacterial community associated with different plant spheres, denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments amplified from total community DNA (TC-DNA) was employed to compare the bacterial communities associated with the five spheres of potato plants grown in the three soil types. Our results showed that, based on the soil types, bacterial communities associated with potato plant spheres differed significantly only in the rhizosphere and in the soil attached to tuber while the endophytic bacterial communities were more variable and less influenced by the soil type. Additionally, bacterial community composition significantly differed between different potato spheres of the plants that were grown in the same soil type indicating niche-specific bacterial communities. Furthermore, our results indicated that the effect of the plant sphere was more pronounced than that of the soil type. Most of the antagonists obtained in our first study (Chapter 2) were affiliated with the genus Pseudomonas which is often enriched in the rhizosphere due to their good rhizosphere competence as well as their ability to rapidly respond to root exudates and to produce multiple compounds with plant beneficial activity. We explored the influence of the three soil types on the abundance of Pseudomonas populations and genes related to beneficial traits in different potato plant spheres. Pseudomonas community composition associated with potato plant spheres was analyzed by DGGE of Pseudomonas-specific 16S rRNA gene fragments amplified from TC-DNA and Pseudomonas-specific real-time PCR as influenced by the soil types and/or potato plant spheres. PCR-Southern blot hybridization was used to investigate the prevalence and distribution of Pseudomonas-specific genes encoding biological control and plant growth promoting related functions (phl, phz, prnD, hcnBC, pcbC, pqqE and gacA) in different plant spheres and soil types. The Pseudomonas community composition and abundance was significantly influenced by the soil type. The effect of soil types was only pronounced in the bulk soil and the soil tightly attached to the yield tubers. Both soil type and plant sphere had a very distinct effect on the distribution of Pseudomonas functional genes. Southern blot hybridization indicated the highest abundance of all tested genes was detected in the rhizosphere of potato plants grown in the LL soils, except for the 2,4-diacetyl phloroglucinol (phl). Our study indicated that Pseudomonas populations carrying the tested genes correlated with the type of soil and the enrichment of these genes, depended on the soil type-dependent rhizosphere effect. Finally, three greenhouse experiments with tomato plants were performed to evaluate the rhizocompetence of in vitro antagonists and their ability to control Rs. The population densities of Rs and antagonists were estimated by selective plating and in TC-DNA by means of real-time PCR and fliC gene PCR-Southern blot hybridization. Bacillus vallismortis (B63) and Pseudomonas brassicacearum (AL2YTEN-142)-inoculated plants showed a pronounced delay or no disease symptoms and significantly decreased in Rs population compared to the uninoculated plants. Amplicon sequencing of 16S rRNA gene fragments amplified from TC-DNA revealed pronounced treatment-dependent shifts in bacterial communities of the tomato rhizosphere. Most important, the strong reduction of Rs in the presence of the antagonists was confirmed and dynamic taxa in response to Rs or the inoculants were identified. Confocal laser scanning microscopy uncovered colonization patterns of the AL2YTEN-142. Gfp-positive cells were detected in lateral roots, root hairs and epidermal cells and within xylem vessels. Both inoculants hold great promise to control Rs under field conditions. In conclusion, this thesis provides deeper insights into the influence of different soil types and plant microenvironments on total bacterial and Pseudomonas communities regarding their composition and functional diversity, paying particular attention to the diversity and abundance of antagonists of Ralstonia solanacearum. A selection of antagonists was tested for in planta biological control of Rs, and the complex interactions between antagonists, pathogen and indigenous rhizosphere microbiome were investigated. In future studies, the biological control of Rs and the plant growth promotion will be tested on potatoes under field conditions in Egypt.
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Claims 20
Claim · model-written summary
Antagonists occurred in all potato plant spheres and were most frequent in endophytic compartments.
- Taxon
- potato
Solanum tuberosumt0 - Organ / stage
- endophytic compartmentse0
- Interactor
- antagonistse0biocontrol_agent
- Outcome
- highest proportion of antagonistse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“in all spheres antagonists were detected among the dominant cultivable bacteria and that the highest proportion of antagonists was observed in the endophytic compartments”
t0“bacterial wilt of potato and tomato”
Claim · model-written summary
Antagonist genotypes differed among soils.
- Taxon
- potatoSolanum tuberosumt0
- Outcome
- genotypes were detected only in one soile0
Not reportedInteractor
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“several genotypes were detected only in one soil, other genotypes were isolated from two or three soils and in some cases with a preference to a particular soil”
t0“bacterial wilt of potato and tomato”
Claim · model-written summary
More beneficial antagonists were isolated from potato plants grown in DS soils.
- Taxon
- potatoSolanum tuberosume1
- Interactor
- antagonistse0biocontrol_agent
- Outcome
- antagonists with beneficial characteristicse0
- Direction
- Moree0
- Setting
- DS soilse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“More antagonists with beneficial characteristics were isolated from plants grown in DS soils.”
e1“potato plants were grown under field conditions”
Claim · model-written summary
Soil type significantly differentiated potato bacterial communities in rhizosphere and tuber-attached soil.
- Taxon
- potatoSolanum tuberosume0
- Outcome
- bacterial communitiese0
- Setting
- rhizosphere and in the soil attached to tubere0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“bacterial communities associated with potato plant spheres differed significantly only in the rhizosphere and in the soil attached to tuber”
Claim · model-written summary
Potato endophytic bacterial communities were more variable and less influenced by soil type.
- Taxon
- potatoSolanum tuberosume1
- Outcome
- endophytic bacterial communitiese0
- Direction
- less influencede0
- Setting
- soil typee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the endophytic bacterial communities were more variable and less influenced by the soil type”
e1“different potato plant spheres”
Claim · model-written summary
Bacterial community composition differed significantly among potato spheres within a soil type.
- Taxon
- potatoSolanum tuberosume1
- Organ / stage
- potato spherese0
- Outcome
- bacterial community compositione0
- Direction
- differede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“bacterial community composition significantly differed between different potato spheres of the plants that were grown in the same soil type”
e1“different potato plant spheres”
Claim · model-written summary
Plant sphere had a more pronounced effect than soil type on potato bacterial communities.
- Taxon
- potatoSolanum tuberosume1
- Outcome
- effect of the plant spheree0
- Direction
- more pronouncede0
- Comparator
- soil typee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the effect of the plant sphere was more pronounced than that of the soil type”
e1“different potato plant spheres”
Claim · model-written summary
Most potato antagonists were affiliated with Pseudomonas.
- Taxon
- potatoSolanum tuberosume1
- Interactor
- Pseudomonas
Pseudomonase0biocontrol_agent - Outcome
- affiliated with the genus Pseudomonase0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Most of the antagonists obtained in our first study (Chapter 2) were affiliated with the genus Pseudomonas”
e1“different potato plant spheres”
Claim · model-written summary
Soil type significantly influenced Pseudomonas composition and abundance in potato spheres.
- Taxon
- potatoSolanum tuberosume1
- Interactor
- PseudomonasPseudomonase0biocontrol_agent
- Outcome
- Pseudomonas community composition and abundancee0
- Setting
- soil typee0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The Pseudomonas community composition and abundance was significantly influenced by the soil type.”
e1“different potato plant spheres”
Claim · model-written summary
Soil effects on Pseudomonas were pronounced in bulk and tuber-attached soils.
- Taxon
- potatoSolanum tuberosume1
- Outcome
- effect of soil typese0
- Setting
- bulk soil and the soil tightly attached to the yield tuberse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The effect of soil types was only pronounced in the bulk soil and the soil tightly attached to the yield tubers.”
e1“different potato plant spheres”
Claim · model-written summary
Soil type and plant sphere each affected distribution of Pseudomonas functional genes.
- Taxon
- potatoSolanum tuberosume1
- Interactor
- PseudomonasPseudomonase0biocontrol_agent
- Outcome
- distribution of Pseudomonas functional genese0
- Setting
- soil typee0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Both soil type and plant sphere had a very distinct effect on the distribution of Pseudomonas functional genes.”
e1“different potato plant spheres”
Claim · model-written summary
Tested genes were most abundant in rhizosphere of potato grown in LL soil, apart from phl.
- Taxon
- potatoSolanum tuberosume0
- Organ / stage
- rhizospheree0
- Outcome
- abundance of all tested genese0
- Direction
- higheste0
- Qualifier
- except for the 2,4-diacetyl phloroglucinol (phl)e0
- Setting
- LL soilse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“highest abundance of all tested genes was detected in the rhizosphere of potato plants grown in the LL soils, except for the 2,4-diacetyl phloroglucinol (phl)”
Claim · model-written summary
Pseudomonas gene carriage correlated with soil type.
- Taxon
- potatoSolanum tuberosume1
- Interactor
- PseudomonasPseudomonase0biocontrol_agent
- Outcome
- Pseudomonas populations carrying the tested genese0
- Setting
- type of soile0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Pseudomonas populations carrying the tested genes correlated with the type of soil and the enrichment of these genes, depended on the soil type-dependent rhizosphere effect.”
e1“different potato plant spheres”
Claim · model-written summary
Bacillus vallismortis B63 delayed or prevented tomato disease symptoms.
- Taxon
- tomato
Solanum lycopersicume1 - Treatment
- Bacillus vallismortis (B63)e0
- Interactor
- Rse0pathogen
- Second interactor
- Bacillus vallismortisBacillus vallismortise0biocontrol_agent
- Outcome
- disease symptomse0
- Direction
- delaye0
- Comparator
- uninoculated plantse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Bacillus vallismortis (B63) and Pseudomonas brassicacearum (AL2YTEN-142)-inoculated plants showed a pronounced delay or no disease symptoms and significantly decreased in Rs population compared to the uninoculated plants.”
e1“greenhouse experiments with tomato plants”
Claim · model-written summary
Pseudomonas brassicacearum AL2YTEN-142 delayed or prevented tomato disease symptoms.
- Taxon
- tomatoSolanum lycopersicume1
- Treatment
- Pseudomonas brassicacearum (AL2YTEN-142)-inoculatede0
- Interactor
- Rse0pathogen
- Second interactor
- Pseudomonas brassicacearumPseudomonas brassicacearume0biocontrol_agent
- Outcome
- disease symptomse0
- Direction
- delaye0
- Comparator
- uninoculated plantse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Bacillus vallismortis (B63) and Pseudomonas brassicacearum (AL2YTEN-142)-inoculated plants showed a pronounced delay or no disease symptoms and significantly decreased in Rs population compared to the uninoculated plants.”
e1“greenhouse experiments with tomato plants”
Claim · model-written summary
Bacillus vallismortis B63 significantly reduced Rs population in tomato.
- Taxon
- tomatoSolanum lycopersicume1
- Treatment
- Bacillus vallismortis (B63)e0
- Interactor
- Rse0pathogen
- Second interactor
- Bacillus vallismortisBacillus vallismortise0biocontrol_agent
- Outcome
- Rs populatione0
- Direction
- decreasede0
- Comparator
- uninoculated plantse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Bacillus vallismortis (B63) and Pseudomonas brassicacearum (AL2YTEN-142)-inoculated plants showed a pronounced delay or no disease symptoms and significantly decreased in Rs population compared to the uninoculated plants.”
e1“greenhouse experiments with tomato plants”
Claim · model-written summary
Pseudomonas brassicacearum AL2YTEN-142 significantly reduced Rs population in tomato.
- Taxon
- tomatoSolanum lycopersicume1
- Treatment
- Pseudomonas brassicacearum (AL2YTEN-142)-inoculatede0
- Interactor
- Rse0pathogen
- Second interactor
- Pseudomonas brassicacearumPseudomonas brassicacearume0biocontrol_agent
- Outcome
- Rs populatione0
- Direction
- decreasede0
- Comparator
- uninoculated plantse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Bacillus vallismortis (B63) and Pseudomonas brassicacearum (AL2YTEN-142)-inoculated plants showed a pronounced delay or no disease symptoms and significantly decreased in Rs population compared to the uninoculated plants.”
e1“greenhouse experiments with tomato plants”
Claim · model-written summary
Inoculants produced treatment-dependent shifts in tomato rhizosphere communities.
- Taxon
- tomatoSolanum lycopersicume0
- Organ / stage
- rhizospheree0
- Treatment
- Bacillus vallismortis (B63) and Pseudomonas brassicacearum (AL2YTEN-142)-inoculatede1
- Outcome
- bacterial communitiese0
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“pronounced treatment-dependent shifts in bacterial communities of the tomato rhizosphere.”
e1“Bacillus vallismortis (B63) and Pseudomonas brassicacearum (AL2YTEN-142)-inoculated plants”
Claim · model-written summary
AL2YTEN-142 colonized lateral roots, root hairs, epidermal cells and xylem vessels.
- Taxon
- tomatoSolanum lycopersicume2
- Organ / stage
- lateral roots, root hairs and epidermal cells and within xylem vesselse0
- Interactor
- AL2YTEN-142e1biocontrol_agent
- Outcome
- Gfp-positive cells were detectede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Gfp-positive cells were detected in lateral roots, root hairs and epidermal cells and within xylem vessels.”
e1“colonization patterns of the AL2YTEN-142”
e2“tomato plants”
Claim · model-written summary
Both inoculants were promising for field control of Rs.
- Taxon
- tomatoSolanum lycopersicume1
- Interactor
- Rse0pathogen
- Outcome
- control Rs under field conditionse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Both inoculants hold great promise to control Rs under field conditions.”
e1“greenhouse experiments with tomato plants”
The same questions in other papers
Pseudomonas brassicacearum · disease · Solanum lycopersicum (tomato)Positive and negative results
2 in the opposite direction
- negative
- no effect
Claims are grouped by organism, treatment and what was measured or targeted. A paper counts as positive when any of its claims in the group is positive.