Characterisation and detection of Pythium and Phytophthora species associated with grapevines in South Africa

Abstract

Replant and decline diseases of grapevines not only cause quantitative and qualitative yield losses, but also result in extra costs when vineyards have to be replanted. This study investigated the role of Pythium and Phytophthora in the decline syndrome in South Africa by determining (1) the species associated with nursery and established vines, and (2) pathogenicity of Ph. sp. niederhauserii and P. vexans relative to known grapevine pathogens. Quantitative real-time PCR (qPCR) assays were also developed for detection of the most prevalent oomycete groups. In total, 26 Pythium and three Phytophthora species were identified from grapevine nurseries and established vineyards. The most common infections in sampled nursery vines were caused by P. vexans (16.7%), followed by P. ultimum var. ultimum (15.0%) and P. irregulare (11.7%). In established vineyards, P. irregulare (18.0%) and P. vexans (6.2%) were also among the three most prevalent species, along with P. heterothallicum (7.3%). Three Phytophthora species were also identified from the sampled established vines, of which Ph. cinnamomi (5.1%) was predominant, followed by Ph. sp. niederhauserii (1.1%). In established vineyards a higher incidence and more diverse species composition was observed in spring and winter, than in summer. Pathogenicity studies showed that some Ph. sp. niederhauserii and P. vexans isolates were as aggressive as the known grapevine pathogens Ph. cinnamomi and P. irregulare. Sensitive qPCR assays were developed for the detection of P. ultimum var. ultimum, P. irregulare, P. vexans and the genus Phytophthora. These assays will be invaluable in limiting pathogen dispersal through screening of nursery material. This is especially important since pathogenic species were also isolated from healthy looking vines in nurseries.

Phytophthora niederhauserii sp. nov., a polyphagous species associated with ornamentals, fruit trees and native plants in 13 countries

“…The symptoms in spring were failure to leaf out, death of the scion and sprouting from the rootstock. The name Phytophthora niederhauserii is a nomen nudum due to the publication of the species in previous manuscripts using this name before the official description of the species, according to Kroon et al (2012) (Martini et al 2007, Luongo et al 2010, Spies et al 2011. To remedy this situation, we herein validate the name of this species as Phytophthora niederhauserii Z.G.…”

“…In South Africa the new species was isolated from grapevine nurseries and established vineyards and was shown to cause stunting of grapevines in greenhouse pathogenicity trials (Spies et al 2011). The isolation of P. niederhauserii from the crowns of nursery vines in that study indicated the potential of the species to cause crown rot in grapevines (Spies et al 2011) . P. niederhauserii also was found in 2009 on almonds in Turkey.…”

Oogonial biometry and phylogenetic analyses of the Pythium vexans species group from woody agricultural hosts in South Africa reveal distinct groups within this taxon

“…Pythium vexans isolates, which were identified using ITS sequence data, were obtained from (i) roots and soils of grapevines collected in nurseries and established vineyards (Spies 2010), (ii) citrus orchard soils , and (iii) apple orchard soil and roots (Tewoldemedhin et al 2010). No more than two isolates from a single grapevine or orchard (apple and citrus) were included for characterisation, resulting in a P. vexans collection of 35 isolates from grapevine, eight from apple and three from citrus (Table 1).…”

“…In South Africa, P. vexans isolates (identified using ITS sequence data) have recently been recovered from, and shown to be pathogenic to both grapevines (Spies 2010) and apple seedlings (Tewoldemedhin et al 2010). Additionally, this species has also been recovered from citrus orchards .…”

Characterization of species associated with Pythium soft rot of ginger and evaluation of Pythium Oligandrum as a biocontrol

“…By monitoring either directly amplified PCR products bound with a fluorescent dye or complementary probe, or indirectly generated fluorescence applying the exonuclease activity of Taq polymerase, proportions of the PCR products or fluorescence could be determined directly (Okubara et al, 2005 Kernaghan et al (2008) also fully amplified ITS regions of P. ultimum and P. irregulare group I and IV in American ginseng field soil samples by using specifically designed primers. Additionally, qPCR was implemented to identify and quantify P. vexans based on the small subunit (SSU) and ITS region of the genome (Bent et al, 2009;Spies et al, 2011b). There are more than 20 different primer sets working specifically on a broad range of Pythium spp.…”