Two new species of Pythium, P. senticosum and P. takayamanum,isolated from cool-temperate forest soil in Japan

Diversity of Pythium Species Recovered from Float-Bed Tobacco Transplant Production Greenhouses

Pythium diseases are common in hydroponic crop production and often threaten the greenhouse production of cucumber, tomato, lettuce, and other crops. In tobacco transplant production, where float-bed hydroponic greenhouses are commonly used, Pythium diseases can cause up to 70% seedling loss. However, there have been few comprehensive studies on the composition and diversity of Pythium communities in tobacco greenhouses. In a 2017 survey, 360 Pythium isolates were collected from 41 tobacco greenhouses across four states (VA, MD, GA, and PA). Samples were collected from one to seven sites within each greenhouse. Twelve described Pythium species were identified (P. adhaerens, P. aristosporum, P. attrantheridium, P. catenulatum, P. coloratum, P. dissotocum, P. inflatum, P. irregulare, P. myriotylum, P. pectinolyticum, P. porphyrae, and P. torulosum) among the isolates obtained. Approximately 80% of the surveyed greenhouses harbored Pythium in at least one of four sites (bay water, tobacco seedlings, weeds, and center walkways) within the greenhouse. The structure of Pythium communities was diverse among the surveyed greenhouses: multiple Pythium species coexisted in the same sample, and multiple species were present within the same greenhouse at different sites. This diversity appeared to be influenced by the sampling sites within the surveyed tobacco greenhouses, sample type, and sampling time. Intraspecific variation may also exist among the P. dissotocum populations found in this study. These results uncovered the complexity and diversity of the Pythium communities within float tobacco transplant greenhouses, which could play a role in the variation in Pythium diseases observed in these production systems.

Whole genome sequencing and phylogenomic analysis show support for the splitting of genus Pythium

The genus Pythium (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of Pythium, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into Pythium sensu stricto (s.s.), Elongisporangium, Globisporangium, Ovatisporangium (= Phytopythium), and Pilasporangium using morphological characters and phylogenies of the mt cytochrome c oxidase subunit 2 (cox2) and D1-D2 domains of nuc 28S rDNA. Although the split was fairly justified by the delineating morphological characters, there were weaknesses in the molecular analyses, which created reluctance in the scientific community to adopt these new genera for the description of new species. In this study, this issue was addressed using phylogenomics. Whole genomes of 109 strains of Pythium and close relatives were sequenced, assembled, and annotated. These data were combined with 10 genomes sequenced in previous studies. Phylogenomic analyses were performed with 148 single-copy genes represented in at least 90% of the taxa in the data set. The results showed support for the division of Pythium s.l. The status of alternative generic names that have been used for species of Pythium in the past (e.g., Artotrogus, Cystosiphon, Eupythium, Nematosporangium, Rheosporangium, Sphaerosporangium) was investigated. Based on our molecular analyses and review of the Pythium generic concepts, we urge the scientific community to adopt the generic names Pythium, Elongisporangium, Globisporangium, and their concepts as proposed by Uzuhashi and colleagues in 2010 in their work going forward. In order to consolidate the taxonomy of these genera, some of the recently described Pythium spp. are transferred to Elongisporangium and Globisporangium.

Pythium intermedium, a species complex consisting of three phylogenetic species found in cool-temperate forest ecosystems

Pythium intermedium plays a vital role in the carbon cycle of cool-temperate forests and is widely distributed in Japan's forest soils. In this study, we performed a phylogenetic analysis of the P. intermedium species complex using DNA sequences from multiple loci. The study included 35 isolates from cool-temperate forest soils, seven known P. intermedium isolates, and six known Pythium attrantheridium isolates. We also performed morphological observations and mating tests. Our results showed that all the isolates formed one large clade but were divided into three subclades. Furthermore, we observed many mating reactions between isolates from different subclades, including between P. attrantheridium and P. intermedium. Therefore, we suggest that P. intermedium, P. attrantheridium, and another phylogenetic species belong to one species complex. This is the first report of a species complex within P. intermedium and will be helpful in understanding the evolution of Pythium species in natural ecosystems.

Myco-Suppression Analysis of Soybean (Glycine max) Damping-Off Caused by Pythium aphanidermatum

The role of Pythium oligandrum as a biocontrol agent against Pythium aphanidermatum was investigated to avoid the harmful impacts of fungicides. Three isolates of P. oligandrum (MS15, MS19, and MS31) were assessed facing the plant pathogenic P. aphanidermatum the causal agent of Glycine max damping-off. The tested Pythium species were recognized according to their cultural and microscopic characterizations. The identification was confirmed through sequencing of rDNA-ITS regions including the 5.8 S rDNA. The biocontrol agent, P. oligandrum, isolates decreased the mycelial growth of the pathogenic P. aphanidermatum with 71.3%, 67.1%, and 68.7% through mycoparasitism on CMA plates. While the half-strength millipore sterilized filtrates of P. oligandrum isolates degrade the pathogenic mycelial linear growth by 34.1%, 32.5%, and 31.7%, and reduce the mycelial dry weight of the pathogenic P. aphanidermatum by 40.1%, 37.4%, and 36.8%, respectively. Scanning electron microscopy (SEM) of the most effective antagonistic P. oligandrum isolate (MS15) interaction showed coiling, haustorial parts of P. oligandrum to P. aphanidermatum hyphae. Furthermore, P. oligandrum isolates were proven to enhance the germination of Glycine max seedling to 93.3% in damping-off infection using agar pots and promote germination of up to 80% during soil pot assay. On the other hand, P. oligandrum isolates increase the shoot, root lengths, and the number of lateral roots.

Phylogeny and morphology of new species of Globisporangium

An isolate originally obtained from pond water in Osaka in 1992 and identified as Pythium marsipium, was subsequently classified as Globisporangium marsipium. According to molecular phylogenetic analyses based on the internal transcribed spacer regions of the nuclear ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1 genes, this isolate was shown to represent a new species, described here as G. lacustre sp. nov. In addition, two further new combinations are introduced in Globisporangium as G. camurandrum and G. takayamanum based on their DNA phylogeny.

Towards a universal barcode of oomycetes--a comparison of the cox1 and cox2 loci

Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide and include several devastating plant pathogens, for example Phytophthora infestans (potato late blight). The cytochrome c oxidase subunit 2 gene (cox2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. The cox1 locus has been used in some studies of Pythium and Phytophthora, but has rarely been used for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine which out of cox1 or cox2 is best suited as a universal oomycete barcode, we compared these two genes in terms of (i) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (ii) sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding-type material. Sequence data for several historic type specimens exist for cox2, but there are none for cox1. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. The cox2-1 spacer could be a useful marker below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.

Pythium rishiriense sp. nov. from water and P. alternatum sp. nov. from soil, two new species from Japan

In an investigation of Pythium species in natural ecosystems of Rishiri Island in Northern Japan, two new species, Pythium rishiriense and P. alternatum, were identified based on morphological and molecular analyses. Pythium rishiriense differed morphologically from other Pythium species by its characteristic oogonial formation which occasionally arranged in chains. Pythium alternatum differed morphologically from other Pythium species by its distinguishing sexual organs where oogonia occasionally arranged alternately with antheridia in chains. Pythium rishiriense is a fast growing, high-temperature loving species, while P. alternatum is a slow growing species. Phylogenetic analyses based on the internal transcribed spacer region and cytochrome c oxidase 1 gene sequences showed that these two species are clearly separate from morphologically similar species.

Two pathogenic species of Pythium: P. aphanidermatum and P. diclinum from a wheat field

During a survey of pathogenic and non-pathogenic Pythium spp. in different localities in Egypt, several isolates of Pythia were obtained and maintained on corn meal agar. Among these isolates, Pythium aphanidermatum and Pythium diclinum were obtained from rhizosphere of wheat plants grown in Dear Attia village, Minia, Egypt. Identification was made using morphological and molecular analyses. P. aphanidermatum and P. diclinum were able to cause reductions in emergence and adulating in wheat in laboratory scale. P. aphanidermatum appeared to be the most aggressive parasite under agar and pot experimental conditions.