Multiple-strand displacement and identification of single nucleotide polymorphisms as markers of genotypic variation of Pasteuria penetrans biotypes infecting root-knot nematodes

Nong, Guangmin; Chow, Virginia; Schmidt, Liesbeth M.; Dickson, D. W.; Preston, James F.

doi:10.1111/j.1574-6941.2007.00340.x

Cited by 12 publications

(10 citation statements)

References 30 publications

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“…; Nong et al . ). However, in this study, they appeared to be insufficient to resolve populations at the intraspecies level as observed previously by Mauchline et al .…”

Section: Discussionmentioning

confidence: 97%

Genotyping of single spore isolates of aPasteuria penetranspopulation occurring in Florida using SNP-based markers

et al. 2016

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Aims To generate single spore lines of a population of bacterial parasite of root‐knot nematode (RKN), Pasteuria penetrans, isolated from Florida and examine genotypic variation and virulence characteristics exist within the population. Methods and Results Six single spore lines (SSP), 16SSP, 17SSP, 18SSP, 25SSP, 26SSP and 30SSP were generated. Genetic variability was evaluated by comparing single‐nucleotide polymorphisms (SNPs) in six protein‐coding genes and the 16S rRNA gene. An average of one SNP was observed for every 69 bp in the 16S rRNA, whereas no SNPs were observed in the protein‐coding sequences. Hierarchical cluster analysis of 16S rRNA sequences placed the clones into three distinct clades. Bio‐efficacy analysis revealed significant heterogeneity in the level virulence and host specificity between the individual clones. Conclusions The SNP markers developed to the 5′ hypervariable region of the 16S rRNA gene may be useful in biotype differentiation within a population of P. penetrans. Significance and Impact of the Study This study demonstrates an efficient method for generating single spore lines of P. penetrans and gives a deep insight into genetic heterogeneity and varying level of virulence exists within a population parasitizing a specific Meloidogyne sp. host. The results also suggest that the application of generalist spore lines in nematode management may achieve broad RKN control.

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“…; Nong et al . ). However, in this study, they appeared to be insufficient to resolve populations at the intraspecies level as observed previously by Mauchline et al .…”

Section: Discussionmentioning

confidence: 97%

Genotyping of single spore isolates of aPasteuria penetranspopulation occurring in Florida using SNP-based markers

et al. 2016

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“…They are distributed throughout the genomes of closely related Bacillus spp. (27) and so should provide a clear understanding of protein-encoding gene variation on a global scale in P. penetrans. We also examine equivalent genes in two other related species of Pasteuria to improve the classification of this family.…”

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confidence: 99%

Identification of New Single Nucleotide Polymorphism-Based Markers for Inter- and Intraspecies Discrimination of Obligate Bacterial Parasites (Pasteuria spp.) of Invertebrates

Mauchline

Knox

Mohan

et al. 2011

Appl Environ Microbiol

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Protein-encoding and 16S rRNA genes of Pasteuria penetrans populations from a wide range of geographic locations were examined. Most interpopulation single nucleotide polymorphisms (SNPs) were detected in the 16S rRNA gene. However, in order to fully resolve all populations, these were supplemented with SNPs from protein-encoding genes in a multilocus SNP typing approach. Examination of individual 16S rRNA gene sequences revealed the occurrence of "cryptic" SNPs which were not present in the consensus sequences of any P. penetrans population. Additionally, hierarchical cluster analysis separated P. penetrans 16S rRNA gene clones into four groups, and one of which contained sequences from the most highly passaged population, demonstrating that it is possible to manipulate the population structure of this fastidious bacterium. The other groups were made from representatives of the other populations in various proportions. Comparison of sequences among three Pasteuria species, namely, P. penetrans, P. hartismeri, and P. ramosa, showed that the protein-encoding genes provided greater discrimination than the 16S rRNA gene. From these findings, we have developed a toolbox for the discrimination of Pasteuria at both the inter-and intraspecies levels. We also provide a model to monitor genetic variation in other obligate hyperparasites and difficult-to-culture microorganisms.The genus Pasteuria, a group of endospore-producing Grampositive bacteria, belongs to the Bacillus-Clostridium clade (9). Of those characterized, all are parasites of free-living and plant parasitic nematodes, with the exception of Pasteuria ramosa (24), a parasite of the water flea (Cladocera, Daphnia spp.).Pasteuria penetrans is an obligate parasite of plant parasitic nematodes belonging to Meloidogyne spp., which are responsible worldwide for more than $100 billion worth of annual crop damage (30). Populations, defined here as collections of endospores obtained from field isolates of particular host female nematodes in distinct geographic locations, have been isolated from Meloidogyne spp. from around the globe, but there is very little understanding of the genetic variation between and within populations. Previous studies have focused on the position of P. penetrans in the bacterial kingdom (9, 31, 34) and the use of consensus 16S rRNA gene sequences (6,7,18) to differentiate between species and populations of Pasteuria (5, 16, 33). However, this information has not been extensively supported with sequence data from protein-encoding genes, which potentially provide an additional source of discrimination, with the exception of one study examining partial coding sequences of some genes in P. ramosa populations (32), as well as a recent study of genes encoding collagen-like proteins in this species (22a).Geographically distinct populations of P. penetrans display various degrees of host specificity (11) through mechanisms that are not fully understood. It has been shown that cuticle heterogeneity, as exhibited by endospore attachment, is not linked...

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“…It is thus ideal for unculturable bacteria. Nong et al (2007) applied this approach to females of M. incognita infected with vegetative cells of P. penetrans. They found that 2,000 vegetative Pasteuria cells were sufficient to give complete genome coverage of the MDA-amplified template following PCR with specific primers.…”

Section: S Rrna Gene Fragmentsmentioning

confidence: 99%

Pasteuria penetrans and Its Parasitic Interaction with Plant Parasitic Nematodes

Bishop

2011

Soil Biology

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Until quite recently, bacteriology has been the study of culturable organisms. The proportion of unculturable bacteria in the soil is commonly put at over 99% (Sharma et al. 2005). The ecology of many of these will be very difficult to discover (Nannipieri et al. 2003;Riesenfeld et al. 2004) but this is not the case for one extraordinary group of non-culturable, aerobic, spore-forming bacteria: members of the genus Pasteuria. The composite species are exclusively obligate parasites of either water fleas or plant parasitic nematodes. These represent the two lineages of the different species of Pasteuria. This chapter predominantly focuses on the nematode parasites because of their residence in soil.The first time that the characteristic spores of this genus were represented in publication were as drawings by Metchnikoff (1888) of what is now called Pasteuria ramosa (Ebert et al. 1996), the parasite of the water fleas Daphnia magna and D. pulex. This is now the type species of the genus Pasteuria and was recognized by Metchnikoff (1888) as an endospore-forming bacterium. A Pasteuria sp. was first reported in a nematode (Dorylaimus bulbiferous), by Cobb (1906), and the suggestion was made that it should be classified as a protozoan. In keeping with this suggestion the nematode parasite was later named Duboscqia penetrans by Thorne (1940) and placed in the family Microsporidiae.Until quite recently, developments in taxonomy were based solely upon observations and measurements made from electron micrographs. Mankau (1975) noted that the parasite of the root knot nematode (RKN) Meloidogyne javanica divided with the formation of cross walls reminiscent of bacteria, and that it formed spores similar to those of known endospore-formers. He suggested the adoption of a position within the eubacteria with the name Bacillus penetrans n. comb. In spite of the outlandish appearance of the highly differentiated vegetative phase (Fig. 9.1)

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Multiple-strand displacement and identification of single nucleotide polymorphisms as markers of genotypic variation of Pasteuria penetrans biotypes infecting root-knot nematodes

Cited by 12 publications

References 30 publications

Genotyping of single spore isolates of aPasteuria penetranspopulation occurring in Florida using SNP-based markers

Genotyping of single spore isolates of aPasteuria penetranspopulation occurring in Florida using SNP-based markers

Identification of New Single Nucleotide Polymorphism-Based Markers for Inter- and Intraspecies Discrimination of Obligate Bacterial Parasites (Pasteuria spp.) of Invertebrates

Pasteuria penetrans and Its Parasitic Interaction with Plant Parasitic Nematodes

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