TY  - CHAP
AU  - Obradović, Aleksa
AU  - Jones, Jeffrey B
AU  - Botond, Balogh
AU  - Gašić, Katarina
PY  - 2020-06
UR  - https://plantarum.izbis.bg.ac.rs/handle/123456789/764
AB  - Lytic bacteriophages (phages) have the potential for controlling susceptible bacteria in the rhizosphere or phyllosphere. The success of phage application in plant disease control requires that high populations of both phage and bacterium exist in order to initiate a chain reaction of bacterial lysis. Physical factors in natural environments such as the presence of biofilms that trap phages, low soil pH which inactivates phages, low rates of diffusion of phages in soil that prevent contact with target bacteria, and inactivation of phages upon exposure to ultraviolet (UV) light and desiccation, all impact successful use of phages in control of plant pathogenic bacteria. Other considerations relate to the bacterial strains which exist in nature. The bacterial species may have a low or high degree of variation in sensitivity to phages. Therefore, phage selection for field use requires careful monitoring of the targeted bacterial strains in the field due to the potential for strain variation and the likelihood for development of resistance to the deployed phages. Application timing has also been shown to be an important factor in improving the efficacy of phages. For instance, UV light is deleterious to phages and upon exposure phage populations plummet; therefore, evening applications of phages result in persistence on leaf surfaces for longer periods of time and may result in improved disease control. Extending the period of time that phages persist in the phyllosphere has been a major hurdle. Formulations have been identified which improve the persistence of phages on leaf surfaces; however, there is a need to identify superior formulations that extend the life on leaf surfaces from hours to days. Another strategy for maintaining high populations of phages has been to use non-pathogenic bacterial strains that are sensitive to the phage(s) or a closely related organism that does not cause disease on the plant host. Finally, phages may have value as part of an integrated management strategy.
PB  - Caister Academic Press
T2  - In: Bacterial Viruses: Exploitation for Biocontrol and Therapeutics (eds. Coffey, A. and Buttimer, C.), Caister Academic Press, Poole, UK, pp: 257-282.
T1  - Considerations for Using Bacteriophages in Plant Pathosystems
EP  - 282
SP  - 257
DO  - 10.21775/9781913652517.07
ER  - 

@inbook{
author = "Obradović, Aleksa and Jones, Jeffrey B and Botond, Balogh and Gašić, Katarina",
year = "2020-06",
abstract = "Lytic bacteriophages (phages) have the potential for controlling susceptible bacteria in the rhizosphere or phyllosphere. The success of phage application in plant disease control requires that high populations of both phage and bacterium exist in order to initiate a chain reaction of bacterial lysis. Physical factors in natural environments such as the presence of biofilms that trap phages, low soil pH which inactivates phages, low rates of diffusion of phages in soil that prevent contact with target bacteria, and inactivation of phages upon exposure to ultraviolet (UV) light and desiccation, all impact successful use of phages in control of plant pathogenic bacteria. Other considerations relate to the bacterial strains which exist in nature. The bacterial species may have a low or high degree of variation in sensitivity to phages. Therefore, phage selection for field use requires careful monitoring of the targeted bacterial strains in the field due to the potential for strain variation and the likelihood for development of resistance to the deployed phages. Application timing has also been shown to be an important factor in improving the efficacy of phages. For instance, UV light is deleterious to phages and upon exposure phage populations plummet; therefore, evening applications of phages result in persistence on leaf surfaces for longer periods of time and may result in improved disease control. Extending the period of time that phages persist in the phyllosphere has been a major hurdle. Formulations have been identified which improve the persistence of phages on leaf surfaces; however, there is a need to identify superior formulations that extend the life on leaf surfaces from hours to days. Another strategy for maintaining high populations of phages has been to use non-pathogenic bacterial strains that are sensitive to the phage(s) or a closely related organism that does not cause disease on the plant host. Finally, phages may have value as part of an integrated management strategy.",
publisher = "Caister Academic Press",
journal = "In: Bacterial Viruses: Exploitation for Biocontrol and Therapeutics (eds. Coffey, A. and Buttimer, C.), Caister Academic Press, Poole, UK, pp: 257-282.",
booktitle = "Considerations for Using Bacteriophages in Plant Pathosystems",
pages = "282-257",
doi = "10.21775/9781913652517.07"
}

Obradović, A., Jones, J. B., Botond, B.,& Gašić, K.. (2020-06). Considerations for Using Bacteriophages in Plant Pathosystems. in In: Bacterial Viruses: Exploitation for Biocontrol and Therapeutics (eds. Coffey, A. and Buttimer, C.), Caister Academic Press, Poole, UK, pp: 257-282.
Caister Academic Press., 257-282.
https://doi.org/10.21775/9781913652517.07

Obradović A, Jones JB, Botond B, Gašić K. Considerations for Using Bacteriophages in Plant Pathosystems. in In: Bacterial Viruses: Exploitation for Biocontrol and Therapeutics (eds. Coffey, A. and Buttimer, C.), Caister Academic Press, Poole, UK, pp: 257-282.. 2020;:257-282.
doi:10.21775/9781913652517.07 .

Obradović, Aleksa, Jones, Jeffrey B, Botond, Balogh, Gašić, Katarina, "Considerations for Using Bacteriophages in Plant Pathosystems" in In: Bacterial Viruses: Exploitation for Biocontrol and Therapeutics (eds. Coffey, A. and Buttimer, C.), Caister Academic Press, Poole, UK, pp: 257-282. (2020-06):257-282,
https://doi.org/10.21775/9781913652517.07 . .

TY  - JOUR
AU  - Newberry, Eric
AU  - Ebrahim, Mohamed
AU  - Timilsina, Sujan
AU  - Zlatković, Nevena
AU  - Obradović, Aleksa
AU  - Bull, Carolee
AU  - Goss, Erica
AU  - Huguet Tapia, Jose
AU  - Paret, Mathews
AU  - Jones, Jeffrey
AU  - Potnis, Neha
PY  - 2019
UR  - https://plantarum.izbis.bg.ac.rs/handle/123456789/960
AB  - Pseudomonas syringae sensu strict , (phylogroup 2; referred to as P. syringae) consists of an environmentally ubiquitous bacterial population associated with diseases of numerous plant species. Recent studies using multilocus sequence analysis have indicated the clonal expansion of several P. syringae lineages, located in phylogroups 2a and 2b, in association with outbreaks of bacterial spot disease of watermelon, cantaloupe, and squash in the United States. To investigate the evolutionary processes that led to the emergence of these epidemic lineages, we sequenced the genomes of six P. syringae strains that were isolated from cucurbits grown in the United States, Europe, and China over a period of more than a decade, as well as eight strains that were isolated from watermelon and squash grown in six different Florida counties during the 2013 and 2014 seasons. These data were subjected to comparative analyses along with 42 previously sequenced genomes of P. syringae stains collected from diverse plant species and environments available from GenBank. Maximum likelihood reconstruction of the P. syringae core genome revealed the presence of a hybrid phylogenetic group, comprised of cucurbit strains collected in Florida, Italy, Serbia, and France, which emerged through genome-wide homologous recombination between phylogroups 2a and 2b. Functional analysis of the recombinant core genome showed that pathways involved in the ATP-dependent transport and metabolism of amino acids, bacterial motility, and secretion systems were enriched for recombination. A survey of described virulence factors indicated the convergent acquisition of several accessory type 3 secreted effectors (T3SEs) among phylogenetically distinct lineages through integrative and conjugative element and plasmid loci. Finally, pathogenicity assays on watermelon and squash showed qualitative differences in virulence between strains of the same clonal lineage, which correlated with T3SEs acquired through various mechanisms of horizontal gene transfer (HGT). This study provides novel insights into the interplay of homologous recombination and HGT toward pathogen emergence and highlights the dynamic nature of P. syringae sensu lato genomes.
PB  - Frontiers Media Sa, Lausanne
T2  - Frontiers in Microbiology
T1  - Inference of Convergent Gene Acquisition Among Pseudomonas syringae Strains Isolated From Watermelon, Cantaloupe, and Squash
EP  - 18
SP  - 1
VL  - 10
DO  - 10.3389/fmicb.2019.00270
ER  - 

@article{
author = "Newberry, Eric and Ebrahim, Mohamed and Timilsina, Sujan and Zlatković, Nevena and Obradović, Aleksa and Bull, Carolee and Goss, Erica and Huguet Tapia, Jose and Paret, Mathews and Jones, Jeffrey and Potnis, Neha",
year = "2019",
abstract = "Pseudomonas syringae sensu strict , (phylogroup 2; referred to as P. syringae) consists of an environmentally ubiquitous bacterial population associated with diseases of numerous plant species. Recent studies using multilocus sequence analysis have indicated the clonal expansion of several P. syringae lineages, located in phylogroups 2a and 2b, in association with outbreaks of bacterial spot disease of watermelon, cantaloupe, and squash in the United States. To investigate the evolutionary processes that led to the emergence of these epidemic lineages, we sequenced the genomes of six P. syringae strains that were isolated from cucurbits grown in the United States, Europe, and China over a period of more than a decade, as well as eight strains that were isolated from watermelon and squash grown in six different Florida counties during the 2013 and 2014 seasons. These data were subjected to comparative analyses along with 42 previously sequenced genomes of P. syringae stains collected from diverse plant species and environments available from GenBank. Maximum likelihood reconstruction of the P. syringae core genome revealed the presence of a hybrid phylogenetic group, comprised of cucurbit strains collected in Florida, Italy, Serbia, and France, which emerged through genome-wide homologous recombination between phylogroups 2a and 2b. Functional analysis of the recombinant core genome showed that pathways involved in the ATP-dependent transport and metabolism of amino acids, bacterial motility, and secretion systems were enriched for recombination. A survey of described virulence factors indicated the convergent acquisition of several accessory type 3 secreted effectors (T3SEs) among phylogenetically distinct lineages through integrative and conjugative element and plasmid loci. Finally, pathogenicity assays on watermelon and squash showed qualitative differences in virulence between strains of the same clonal lineage, which correlated with T3SEs acquired through various mechanisms of horizontal gene transfer (HGT). This study provides novel insights into the interplay of homologous recombination and HGT toward pathogen emergence and highlights the dynamic nature of P. syringae sensu lato genomes.",
publisher = "Frontiers Media Sa, Lausanne",
journal = "Frontiers in Microbiology",
title = "Inference of Convergent Gene Acquisition Among Pseudomonas syringae Strains Isolated From Watermelon, Cantaloupe, and Squash",
pages = "18-1",
volume = "10",
doi = "10.3389/fmicb.2019.00270"
}

Newberry, E., Ebrahim, M., Timilsina, S., Zlatković, N., Obradović, A., Bull, C., Goss, E., Huguet Tapia, J., Paret, M., Jones, J.,& Potnis, N.. (2019). Inference of Convergent Gene Acquisition Among Pseudomonas syringae Strains Isolated From Watermelon, Cantaloupe, and Squash. in Frontiers in Microbiology
Frontiers Media Sa, Lausanne., 10, 1-18.
https://doi.org/10.3389/fmicb.2019.00270

Newberry E, Ebrahim M, Timilsina S, Zlatković N, Obradović A, Bull C, Goss E, Huguet Tapia J, Paret M, Jones J, Potnis N. Inference of Convergent Gene Acquisition Among Pseudomonas syringae Strains Isolated From Watermelon, Cantaloupe, and Squash. in Frontiers in Microbiology. 2019;10:1-18.
doi:10.3389/fmicb.2019.00270 .

Newberry, Eric, Ebrahim, Mohamed, Timilsina, Sujan, Zlatković, Nevena, Obradović, Aleksa, Bull, Carolee, Goss, Erica, Huguet Tapia, Jose, Paret, Mathews, Jones, Jeffrey, Potnis, Neha, "Inference of Convergent Gene Acquisition Among Pseudomonas syringae Strains Isolated From Watermelon, Cantaloupe, and Squash" in Frontiers in Microbiology, 10 (2019):1-18,
https://doi.org/10.3389/fmicb.2019.00270 . .

TY  - JOUR
AU  - Ivanović, Milan M
AU  - Obradović, Aleksa
AU  - Gašić, Katarina
AU  - Minsavage, Gerald V
AU  - Dickstein, Ellen R
AU  - Jones, Jeffrey B
PY  - 2012
UR  - https://plantarum.izbis.bg.ac.rs/handle/123456789/219
PB  - Springer, Dordrecht
T2  - European Journal of Plant Pathology
T1  - Erratum to: Exploring diversity of Erwinia amylovora population in Serbia by conventional and automated techniques and detection of new PFGE patterns (vol 133, pg 545, 2012)
EP  - 443
IS  - 2
SP  - 443
VL  - 134
DO  - 10.1007/s10658-012-0037-y
ER  - 

@article{
author = "Ivanović, Milan M and Obradović, Aleksa and Gašić, Katarina and Minsavage, Gerald V and Dickstein, Ellen R and Jones, Jeffrey B",
year = "2012",
publisher = "Springer, Dordrecht",
journal = "European Journal of Plant Pathology",
title = "Erratum to: Exploring diversity of Erwinia amylovora population in Serbia by conventional and automated techniques and detection of new PFGE patterns (vol 133, pg 545, 2012)",
pages = "443-443",
number = "2",
volume = "134",
doi = "10.1007/s10658-012-0037-y"
}

Ivanović, M. M., Obradović, A., Gašić, K., Minsavage, G. V., Dickstein, E. R.,& Jones, J. B.. (2012). Erratum to: Exploring diversity of Erwinia amylovora population in Serbia by conventional and automated techniques and detection of new PFGE patterns (vol 133, pg 545, 2012). in European Journal of Plant Pathology
Springer, Dordrecht., 134(2), 443-443.
https://doi.org/10.1007/s10658-012-0037-y

Ivanović MM, Obradović A, Gašić K, Minsavage GV, Dickstein ER, Jones JB. Erratum to: Exploring diversity of Erwinia amylovora population in Serbia by conventional and automated techniques and detection of new PFGE patterns (vol 133, pg 545, 2012). in European Journal of Plant Pathology. 2012;134(2):443-443.
doi:10.1007/s10658-012-0037-y .

Ivanović, Milan M, Obradović, Aleksa, Gašić, Katarina, Minsavage, Gerald V, Dickstein, Ellen R, Jones, Jeffrey B, "Erratum to: Exploring diversity of Erwinia amylovora population in Serbia by conventional and automated techniques and detection of new PFGE patterns (vol 133, pg 545, 2012)" in European Journal of Plant Pathology, 134, no. 2 (2012):443-443,
https://doi.org/10.1007/s10658-012-0037-y . .

TY  - JOUR
AU  - Ivanović, Milan M
AU  - Obradović, Aleksa
AU  - Gašić, Katarina
AU  - Minsavage, Gerald V
AU  - Dickstein, Ellen R
AU  - Jones, Jeffrey B
PY  - 2012
UR  - https://plantarum.izbis.bg.ac.rs/handle/123456789/213
AB  - Forty Erwinia amylovora strains originating from different host plants and locations in Serbia and one strain from Montenegro were characterized by conventional, automated and molecular techniques. All strains were Gram-negative, nonfluorescent, facultative anaerobes, oxidase negative, levan positive, produced necrotic lesions followed by bacterial exudate on artificially inoculated immature pear fruits and caused HR on tobacco. Based on carbon source utilization, all strains tested with the Biolog system were identified as E. amylovora. Based on fatty acid profiles all tested strains clustered into three groups in which strains from north Serbia differed from strains isolated in central and south parts of the country. Restriction analysis of genomic DNA using XbaI and PFGE resulted in six different patterns differentiating the strains into six groups. Most of the investigated strains clustered in one group having the pattern type similar to Pt2 group described earlier as dominant in East Europe and the Mediterranean region. Two strains showed PFGE pattern similar to the previously described Pt3 pattern and one strain had pattern similar to Pt6. Based on size and number of the bands, new restriction patterns, assigned as Pt7, Pt8 and Pt9 were observed. PFGE results showed that E. amylovora population in Serbia is not homogenous and was possibly introduced from different directions. This is the first characterization of E. amylovora collection of strains from Serbia using fatty acid analysis and PFGE.
PB  - Springer, Dordrecht
T2  - European Journal of Plant Pathology
T1  - Exploring diversity of Erwinia amylovora population in Serbia by conventional and automated techniques and detection of new PFGE patterns
EP  - 727
IS  - 3
SP  - 715
VL  - 133
DO  - 10.1007/s10658-012-9950-3
ER  - 

@article{
author = "Ivanović, Milan M and Obradović, Aleksa and Gašić, Katarina and Minsavage, Gerald V and Dickstein, Ellen R and Jones, Jeffrey B",
year = "2012",
abstract = "Forty Erwinia amylovora strains originating from different host plants and locations in Serbia and one strain from Montenegro were characterized by conventional, automated and molecular techniques. All strains were Gram-negative, nonfluorescent, facultative anaerobes, oxidase negative, levan positive, produced necrotic lesions followed by bacterial exudate on artificially inoculated immature pear fruits and caused HR on tobacco. Based on carbon source utilization, all strains tested with the Biolog system were identified as E. amylovora. Based on fatty acid profiles all tested strains clustered into three groups in which strains from north Serbia differed from strains isolated in central and south parts of the country. Restriction analysis of genomic DNA using XbaI and PFGE resulted in six different patterns differentiating the strains into six groups. Most of the investigated strains clustered in one group having the pattern type similar to Pt2 group described earlier as dominant in East Europe and the Mediterranean region. Two strains showed PFGE pattern similar to the previously described Pt3 pattern and one strain had pattern similar to Pt6. Based on size and number of the bands, new restriction patterns, assigned as Pt7, Pt8 and Pt9 were observed. PFGE results showed that E. amylovora population in Serbia is not homogenous and was possibly introduced from different directions. This is the first characterization of E. amylovora collection of strains from Serbia using fatty acid analysis and PFGE.",
publisher = "Springer, Dordrecht",
journal = "European Journal of Plant Pathology",
title = "Exploring diversity of Erwinia amylovora population in Serbia by conventional and automated techniques and detection of new PFGE patterns",
pages = "727-715",
number = "3",
volume = "133",
doi = "10.1007/s10658-012-9950-3"
}

Ivanović, M. M., Obradović, A., Gašić, K., Minsavage, G. V., Dickstein, E. R.,& Jones, J. B.. (2012). Exploring diversity of Erwinia amylovora population in Serbia by conventional and automated techniques and detection of new PFGE patterns. in European Journal of Plant Pathology
Springer, Dordrecht., 133(3), 715-727.
https://doi.org/10.1007/s10658-012-9950-3

Ivanović MM, Obradović A, Gašić K, Minsavage GV, Dickstein ER, Jones JB. Exploring diversity of Erwinia amylovora population in Serbia by conventional and automated techniques and detection of new PFGE patterns. in European Journal of Plant Pathology. 2012;133(3):715-727.
doi:10.1007/s10658-012-9950-3 .

Ivanović, Milan M, Obradović, Aleksa, Gašić, Katarina, Minsavage, Gerald V, Dickstein, Ellen R, Jones, Jeffrey B, "Exploring diversity of Erwinia amylovora population in Serbia by conventional and automated techniques and detection of new PFGE patterns" in European Journal of Plant Pathology, 133, no. 3 (2012):715-727,
https://doi.org/10.1007/s10658-012-9950-3 . .