Reference
Akira, S., & Hemmi, H. (2003). Recognition of pathogen-associated
molecular patterns by TLR family. Immunology letters, 85 (2),
85-95.
Alvarez-Perez, S., de Vega, C., & Herrera, C. M. (2013). Multilocus
sequence analysis of nectar pseudomonads reveals high genetic diversity
and contrasting recombination patterns. PloS one, 8 (10), e75797.
doi:10.1371/journal.pone.0075797
Anderson, M. J. (2001). A new method for non-parametric multivariate
analysis of variance. Austral Ecology, 26 (26), 36-42.
Andreani, N. A., Martino, M. E., Fasolato, L., Carraro, L., Montemurro,
F., Mioni, R., . . . Cardazzo, B. (2014). Tracking the blue: a MLST
approach to characterise the Pseudomonas fluorescens group. Food
Microbiol, 39 , 116-126. doi:10.1016/j.fm.2013.11.012
Arnold, D. L., & Preston, G. M. (2019). Pseudomonas syringae:
enterprising epiphyte and stealthy parasite. Microbiology,
165 (3), 251-253. doi:10.1099/mic.0.000715
Bailey, M. J., Lilley, A. K., Thompson, I. P., Rainey, P. B., & Ellis,
R. J. (1995). Site directed chromosomal marking of a fluorescent
pseudomonad isolated from the phytosphere of sugar beet; stability and
potential for marker gene transfer. Molecular ecology, 4 (6),
755-763. doi:10.1111/j.1365-294x.1995.tb00276.x
Bennasar, A., Mulet, M., Lalucat, J., & Garcia-Valdes, E. (2010).
PseudoMLSA: a database for multigenic sequence analysis of Pseudomonas
species. BMC microbiology, 10 , 118. doi:10.1186/1471-2180-10-118
Castaneda-Montes, F. J., Avitia, M., Sepulveda-Robles, O., Cruz-Sanchez,
V., Kameyama, L., Guarneros, G., & Escalante, A. E. (2018a). Population
structure of Pseudomonas aeruginosa through a MLST approach and
antibiotic resistance profiling of a Mexican clinical collection.Infection Genetics and Evolution, 65 , 43-54.
Castaneda-Montes, F. J., Avitia, M., Sepulveda-Robles, O., Cruz-Sanchez,
V., Kameyama, L., Guarneros, G., & Escalante, A. E. (2018b). Population
structure of Pseudomonas aeruginosa through a MLST approach and
antibiotic resistance profiling of a Mexican clinical collection.Infect Genet Evol, 65 , 43-54. doi:10.1016/j.meegid.2018.06.009
Compant, S., Samad, A., Faist, H., & Sessitsch, A. (2019). A review on
the plant microbiome: Ecology, functions, and emerging trends in
microbial application. J Adv Res, 19 , 29-37.
doi:10.1016/j.jare.2019.03.004
Dean, A. M. (1995). A molecular investigation of genotype by environment
interactions. Genetics, 139 (1), 19-33.
Ellis, R. J., Timms-Wilson, T. M., & Bailey, M. J. (2000).
Identification of conserved traits in fluorescent pseudomonads with
antifungal activity. Environmental microbiology, 2 (3), 274-284.
doi:10.1046/j.1462-2920.2000.00102.x
Flury, P., Vesga, P., Pechy-Tarr, M., Aellen, N., Dennert, F., Hofer,
N., . . . Maurhofer, M. (2017). Antimicrobial and Insecticidal: Cyclic
Lipopeptides and Hydrogen Cyanide Produced by Plant-Beneficial
Pseudomonas Strains CHA0, CMR12a, and PCL1391 Contribute to Insect
Killing. Front Microbiol, 8 , 100. doi:10.3389/fmicb.2017.00100
Frapolli, M., Defago, G., & Moenne-Loccoz, Y. (2007). Multilocus
sequence analysis of biocontrol fluorescent Pseudomonas spp. producing
the antifungal compound 2,4-diacetylphloroglucinol. Environmental
microbiology, 9 (8), 1939-1955. doi:10.1111/j.1462-2920.2007.01310.x
Frapolli, M., Pothier, J. F., Defago, G., & Moenne-Loccoz, Y. (2012).
Evolutionary history of synthesis pathway genes for phloroglucinol and
cyanide antimicrobials in plant-associated fluorescent pseudomonads.Mol Phylogenet Evol, 63 (3), 877-890.
doi:10.1016/j.ympev.2012.02.030
Gal, M., Preston, G. M., Massey, R. C., Spiers, A. J., & Rainey, P. B.
(2003). Genes encoding a cellulosic polymer contribute toward the
ecological success of Pseudomonas fluorescens SBW25 on plant surfaces.Molecular ecology, 12 (11), 3109-3121.
doi:10.1046/j.1365-294x.2003.01953.x
Garrido-Sanz, D., Meier-Kolthoff, J. P., Goker, M., Martin, M., Rivilla,
R., & Redondo-Nieto, M. (2016). Genomic and Genetic Diversity within
the Pseudomonas fluorescens Complex. PloS one, 11 (2).
Gonzalez-Torres, P., Rodriguez-Mateos, F., Anton, J., & Gabaldon, T.
(2019). Impact of Homologous Recombination on the Evolution of
Prokaryotic Core Genomes. mBio, 10 (1). doi:10.1128/mBio.02494-18
Haubold, B., & Rainey, P. B. (1996). Genetic and ecotypic structure of
a fluorescent Pseudomonas population. Molecular ecology, 5 (6),
747-761. doi:10.1111/j.1365-294X.1996.tb00371.x
Hol, W. H., Bezemer, T. M., & Biere, A. (2013). Getting the ecology
into interactions between plants and the plant growth-promoting
bacterium Pseudomonas fluorescens. Front Plant Sci, 4 , 81.
doi:10.3389/fpls.2013.00081
Hsu, C. K., & Micallef, S. A. (2017). Plant-mediated restriction of
Salmonella enterica on tomato and spinach leaves colonized with
Pseudomonas plant growth-promoting rhizobacteria. Int J Food
Microbiol, 259 , 1-6. doi:10.1016/j.ijfoodmicro.2017.07.012
Humphris, S. N., Bengough, A. G., Griffiths, B. S., Kilham, K., Rodger,
S., Stubbs, V., . . . Young, I. M. (2005). Root cap influences root
colonisation by Pseudomonas fluorescens SBW25 on maize. FEMS
microbiology ecology, 54 (1), 123-130. doi:10.1016/j.femsec.2005.03.005
Hwang, M. S., Morgan, R. L., Sarkar, S. F., Wang, P. W., & Guttman, D.
S. (2005). Phylogenetic characterization of virulence and resistance
phenotypes of Pseudomonas syringae . Applied and
environmental microbiology, 71 (9), 5182-5191.
doi:10.1128/AEM.71.9.5182-5191.2005
Jaderlund, L., Hellman, M., Sundh, I., Bailey, M. J., & Jansson, J. K.
(2008). Use of a novel nonantibiotic triple marker gene cassette to
monitor high survival of Pseudomonas fluorescens SBW25 on winter wheat
in the field. FEMS microbiology ecology, 63 (2), 156-168.
doi:10.1111/j.1574-6941.2007.00420.x
Kidd, T. J., Ritchie, S. R., Ramsay, K. A., Grimwood, K., Bell, S. C.,
& Rainey, P. B. (2012). Pseudomonas aeruginosa exhibits frequent
recombination, but only a limited association between genotype and
ecological setting. PloS one, 7 (9), e44199.
doi:10.1371/journal.pone.0044199
Kishino, H., & Hasegawa, M. (1989). Evaluation of the maximum
likelihood estimate of the evolutionary tree topologies from DNA
sequence data, and the branching order in hominoidea. J Mol Evol,
29 (2), 170-179. doi:10.1007/bf02100115
Kosakovsky Pond, S. L., Posada, D., Gravenor, M. B., Woelk, C. H., &
Frost, S. D. (2006). GARD: a genetic algorithm for recombination
detection. Bioinformatics, 22 (24), 3096-3098.
doi:10.1093/bioinformatics/btl474
Liu, Y., Rainey, P. B., & Zhang, X. X. (2015). Molecular mechanisms of
xylose utilization by Pseudomonas fluorescens: overlapping genetic
responses to xylose, xylulose, ribose and mannitol. Molecular
microbiology, 98 (3), 553-570. doi:10.1111/mmi.13142
Liu, Z., Beskrovnaya, P., Melnyk, R. A., Hossain, S. S., Khorasani, S.,
O’Sullivan, L. R., . . . Haney, C. H. (2018). A Genome-Wide Screen
Identifies Genes in Rhizosphere-Associated Pseudomonas Required to Evade
Plant Defenses. mBio, 9 (6). doi:10.1128/mBio.00433-18
McCann, H. C., Li, L., Liu, Y., Li, D., Pan, H., Zhong, C., . . . Huang,
H. (2017). Origin and Evolution of the Kiwifruit Canker Pandemic.Genome Biol Evol, 9 (4), 932-944. doi:10.1093/gbe/evx055
McVean, G. (2002). A genealogical interpretation of linkage
disequilibrium. Genetics, 162 (2), 987-991.
McVean, G., Awadalla, P., & Fearnhead, P. (2002). A coalescent-based
method for detecting and estimating recombination from gene sequences.Genetics, 160 (3), 1231-1241.
Nemergut, D. R., Schmidt, S. K., Fukami, T., O’Neill, S. P., Bilinski,
T. M., Stanish, L. F., . . . Ferrenberg, S. (2013). Patterns and
processes of microbial community assembly. Microbiology and
molecular biology reviews : MMBR, 77 (3), 342-356.
doi:10.1128/MMBR.00051-12
Nowell, R. W., Laue, B. E., Sharp, P. M., & Green, S. (2016).
Comparative genomics reveals genes significantly associated with woody
hosts in the plant pathogen Pseudomonas syringae. Molecular Plant
Pathology, 17 (9), 1409-1424.
Ogura, K., Shimada, K., & Miyoshi-Akiyama, T. (2019). A multilocus
sequence typing scheme of Pseudomonas putida for clinical and
environmental isolates. Sci Rep, 9 (1), 13980.
doi:10.1038/s41598-019-50299-6
Oteino, N., Lally, R. D., Kiwanuka, S., Lloyd, A., Ryan, D., Germaine,
K. J., & Dowling, D. N. (2015). Plant growth promotion induced by
phosphate solubilizing endophytic Pseudomonas isolates. Front
Microbiol, 6 , 745. doi:10.3389/fmicb.2015.00745
Peix, A., Ramirez-Bahena, M. H., & Velazquez, E. (2018). The current
status on the taxonomy of Pseudomonas revisited: An update. Infect
Genet Evol, 57 , 106-116. doi:10.1016/j.meegid.2017.10.026
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of
population structure using multilocus genotype data. Genetics,
155 (2), 945-959.
Rainey, P. B. (1999). Adaptation of Pseudomonas fluorescens to
the plant rhizosphere. Environmental microbiology, 1 (3), 243-257.
doi:emi40 [pii]
Rainey, P. B., Bailey, M. J., & Thompson, I. P. (1994). Phenotypic and
genotypic diversity of fluorescent pseudomonads isolated from
field-grown sugar beet. Microbiology, 140 ( Pt 9) , 2315-2331.
doi:10.1099/13500872-140-9-2315
Reasoner, D. J., & Geldreich, E. E. (1985). A new medium for the
enumeration and subculture of bacteria from potable water. Applied
and environmental microbiology, 49 (1), 1-7.
Renaud, S., Dufour, A. B., Hardouin, E. A., Ledevin, R., & Auffray, J.
C. (2015). Once upon Multivariate Analyses: When They Tell Several
Stories about Biological Evolution. PloS one, 10 (7), e0132801.
doi:10.1371/journal.pone.0132801
Sarkar, S. F., & Guttman, D. S. (2004). Evolution of the core genome of
Pseudomonas syringae, a highly clonal, endemic plant pathogen.Applied and environmental microbiology, 70 (4), 1999-2012.
doi:10.1128/aem.70.4.1999-2012.2004
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M.,
Hollister, E. B., . . . Weber, C. F. (2009). Introducing mothur:
open-source, platform-independent, community-supported software for
describing and comparing microbial communities. Applied and
environmental microbiology, 75 (23), 7537-7541. doi:10.1128/AEM.01541-09
Silby, M. W., Cerdeno-Tarraga, A. M., Vernikos, G. S., Giddens, S. R.,
Jackson, R. W., Preston, G. M., . . . Thomson, N. R. (2009). Genomic and
genetic analyses of diversity and plant interactions of Pseudomonas
fluorescens. Genome biology, 10 (5), R51.
doi:10.1186/gb-2009-10-5-r51
Silby, M. W., Winstanley, C., Godfrey, S. A., Levy, S. B., & Jackson,
R. W. (2011). Pseudomonas genomes: diverse and adaptable. FEMS
microbiology reviews, 35 (4), 652-680.
doi:10.1111/j.1574-6976.2011.00269.x
Simpson, E. (1949). Measurement of diversity. Nature, 163 , 688.
Straub, C., Colombi, E., Li, L., Huang, H., Templeton, M. D., McCann, H.
C., & Rainey, P. B. (2018). The ecological genetics of Pseudomonas
syringae from kiwifruit leaves. Environmental microbiology,
20 (6), 2066-2084. doi:10.1111/1462-2920.14092
Stritzler, M., Diez Tissera, A., Soto, G., & Ayub, N. (2018). Plant
growth-promoting bacterium Pseudomonas fluorescens FR1 secrets a novel
type of extracellular polyhydroxybutyrate polymerase involved in abiotic
stress response in plants. Biotechnol Lett, 40 (9-10), 1419-1423.
doi:10.1007/s10529-018-2576-6
Sun, B., Wang, F., Jiang, Y., Li, Y., Dong, Z., Li, Z., & Zhang, X. X.
(2014). A long-term field experiment of soil transplantation
demonstrating the role of contemporary geographic separation in shaping
soil microbial community structure. Ecol Evol, 4 (7), 1073-1087.
doi:10.1002/ece3.1006
Tett, A., Spiers, A. J., Crossman, L. C., Ager, D., Ciric, L., Dow, J.
M., . . . Bailey, M. J. (2007). Sequence-based analysis of pQBR103; a
representative of a unique, transfer-proficient mega plasmid resident in
the microbial community of sugar beet. The ISME journal, 1 (4),
331-340. doi:10.1038/ismej.2007.47
Trippe, K., McPhail, K., Armstrong, D., Azevedo, M., & Banowetz, G.
(2013). Pseudomonas fluorescens SBW25 produces furanomycin, a
non-proteinogenic amino acid with selective antimicrobial properties.BMC microbiology, 13 , 111. doi:10.1186/1471-2180-13-111
Vos, M., & Didelot, X. (2009). A comparison of homologous recombination
rates in bacteria and archaea. The ISME journal, 3 (2), 199-208.
doi:10.1038/ismej.2008.93
Wang, C., Ramette, A., Punjasamarnwong, P., Zala, M., Natsch, A.,
Moenne-Loccoz, Y., & Defago, G. (2001). Cosmopolitan distribution of
phlD-containing dicotyledonous crop-associated biocontrol pseudomonads
of worldwide origin. FEMS microbiology ecology, 37 , 105-116.
doi:10.1111/j.1574-6941.2001.tb00858.x
Zhang, X. X., Chang, H., Tran, S. L., Gauntlett, J. C., Cook, G. M., &
Rainey, P. B. (2012). Variation in transport explains polymorphism of
histidine and urocanate utilization in a natural Pseudomonaspopulation. Environmental microbiology, 14 (8), 1941-1951.
doi:10.1111/j.1462-2920.2011.02692.x
Zhang, X. X., Kosier, B., & Priefer, U. B. (2001). Genetic diversity of
indigenous Rhizobium leguminosarum bv. viciae isolates nodulating two
different host plants during soil restoration with alfalfa.Molecular ecology, 10 (9), 2297-2305.
doi:10.1046/j.0962-1083.2001.01364.x
Zhang, X. X., & Rainey, P. B. (2007). Genetic analysis of the histidine
utilization (hut ) genes in Pseudomonas fluorescens SBW25.Genetics, 176 (4), 2165-2176.
Zhang, X. X., Ritchie, S. R., & Rainey, P. B. (2013). Urocanate as a
potential signaling molecule for bacterial recognition of eukaryotic
hosts. Cell Mol Life Sci, 71 (4), 541-547.
doi:10.1007/s00018-013-1527-6