Phylogenetic Analysis of Pasteuria penetrans by Use of Multiple Genetic Loci

Abstract

Pasteuria penetrans is a gram-positive, endospore-forming eubacterium that apparently is a member of the Bacillus-Clostridium clade. It is an obligate parasite of root knot nematodes (Meloidogyne spp.) and preferentially grows on the developing ovaries, inhibiting reproduction. Root knot nematodes are devastating root pests of economically important crop plants and are difficult to control. Consequently, P. penetrans has long been recognized as a potential biocontrol agent for root knot nematodes, but the fastidious life cycle and the obligate nature of parasitism have inhibited progress on mass culture and deployment. We are currently sequencing the genome of the Pasteuria bacterium and have performed amino acid level analyses of 33 bacterial species (including P. penetrans) using concatenation of 40 housekeeping genes, with and without insertions/deletions (indels) removed, and using each gene individually. By application of maximum-likelihood, maximum-parsimony, and Bayesian methods to the resulting data sets, P. penetrans was found to cluster tightly, with a high level of confidence, in the Bacillus class of the gram-positive, low-G؉C-content eubacteria. Strikingly, our analyses identified P. penetrans as ancestral to Bacillus spp. Additionally, all analyses revealed that P. penetrans is surprisingly more closely related to the saprophytic extremophile Bacillus haladurans and Bacillus subtilis than to the pathogenic species Bacillus anthracis and Bacillus cereus. Collectively, these findings strongly imply that P. penetrans is an ancient member of the Bacillus group. We suggest that P. penetrans may have evolved from an ancient symbiotic bacterial associate of nematodes, possibly as the root knot nematode evolved to be a highly specialized parasite of plants.Pasteuria penetrans is an endospore-forming, gram-positive, obligate parasitic bacterium of the root knot nematodes (RKN), Meloidogyne spp. RKN have a very broad host range, which includes more than 2,000 plant species, and most cultivated crops are attacked by at least one species of Meloidogyne (33); this causes economic losses of more than $50 billion per year. The problem in the subtropics and tropics is particularly severe, and many developing nations are seriously affected in terms of both food security and economics by RKN. Mature female RKN release hundreds of eggs into a proteinaceous matrix on the surface of the root. Following a first molt in the egg, a motile second-stage (J2) juvenile hatches in the soil and typically reinfects the same plant. The RKN J2 destructively penetrates the root, preferentially in the zone of elongation or at the site of lateral root emergence, and migrates intercellularly into the vascular cylinder, causing little or no injury. Once in the vascular cylinder, the nematode makes a commitment to establish a highly specialized feeding site, referred to as a giant cell. The relationship between an RKN and its host is both intimate and complex and involves dramatic changes both in the plant and in the nematode, leading t...

Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium)

“…Thus atpD, gap and pnp resulted in trees in which other taxa were grouped between or within the Ensifer clusters. This different placement of species in individual gene tree analyses may be due to different evolutionary histories of the genes, intragenomic rearrangements or horizontal gene transfer and subsequent recombination events (Charles et al, 2005;Christensen et al, 2004;Rokas et al, 2003). Christensen & Olsen (1998) previously reported conflicting results when comparing atpD with other housekeeping genes and the 23S rRNA gene in Salmonella.…”

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

“…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).…”

“…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.…”

Statement on the update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 3: Suitability of taxonomic units notified to EFSA until September 2015

“…Sequencing of sporulation genes and multilocus sequence typing also place these organisms as members of the order Bacillales (Preston el al., 2003;Trotter and Bishop, 2003;Charles et al, 2005). All Pasteuria species described so far are obligate parasites of invertebrates, including plant parasitic nematodes and planktonic freshwater crustaceans of the genus Daphnia, and none have been grown in vitro.…”