Diversity of Phytophthora, Pythium, and Phytopythium Species in Recycled Irrigation Water in a Container Nursery

Redekar, Neelam; Eberhart, Joyce; Parke, Jennifer L.

doi:10.1094/pbiomes-10-18-0043-r

Cited by 54 publications

(35 citation statements)

References 67 publications

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“…More than 330 species of Pythium have been identified to date ( ), of which many are pathogenic to plants. These pseudo-fungi cause many plant diseases, including damping-off, root rot, collar rot, soft rot, and stem rot in different production systems such as nurseries, greenhouses, and agricultural fields [ 45 , 46 , 47 ]. In C. annuum plants, many Pythium spp.…”

Section: Pythium Species: Causal Agent Of Damping-off and Root Rotmentioning

confidence: 99%

Pythium Damping-Off and Root Rot of Capsicum annuum L.: Impacts, Diagnosis, and Management

Arora

Sharma

et al. 2021

Microorganisms

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Capsicum annuum L. is a significant horticulture crop known for its pungent varieties and used as a spice. The pungent character in the plant, known as capsaicinoid, has been discovered to have various health benefits. However, its production has been affected due to various exogenous stresses, including diseases caused by a soil-borne pathogen, Pythium spp. predominantly affecting the Capsicum plant in younger stages and causing damping-off, this pathogen can incite root rot in later plant growth stages. Due to the involvement of multiple Pythium spp. and their capability to disperse through various routes, their detection and diagnosis have become crucial. However, the quest for a point-of-care technology is still far from over. The use of an integrated approach with cultural and biological techniques for the management of Pythium spp. can be the best and most sustainable alternative to the traditionally used and hazardous chemical approach. The lack of race-specific resistance genes against Pythium spp. can be compensated with the candidate quantitative trait loci (QTL) genes in C. annuum L. This review will focus on the epidemiological factors playing a major role in disease spread, the currently available diagnostics in species identification, and the management strategies with a special emphasis on Pythium spp. causing damping-off and root rot in different cultivars of C. annuum L.

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Section: Pythium Species: Causal Agent Of Damping-off and Root Rotmentioning

confidence: 99%

Pythium Damping-Off and Root Rot of Capsicum annuum L.: Impacts, Diagnosis, and Management

Arora

Sharma

et al. 2021

Microorganisms

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“…In recent years, several outbreaks caused by Phytophthora (P. ramorum, P. kernoviae, P. lateralis, P. pseudosyringae, and P. austrocedri) have emerged in Britain and also worldwide to cause significant mortality on a range of woody hosts [1][2][3][4][5][6][7]. As we witness the devastating impact of Phytophthora on the natural ecosystem, an increasing number of studies have looked at species composition in diverse environments such as nurseries [8][9][10][11], agricultural and urban environments [12][13][14], and semi-and natural environments [15][16][17][18][19][20]. As a result, many new species have been recovered with a lot of these not formally described yet.…”

Section: Introductionmentioning

confidence: 99%

Diversity of Phytophthora Species Detected in Disturbed and Undisturbed British Soils Using High-Throughput Sequencing Targeting ITS rRNA and COI mtDNA Regions

Landa

Arias-Giraldo

Henricot

et al. 2021

Forests

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Disease outbreaks caused by introduced Phytophthora species have been increasing in British forests and woodlands in recent years. A better knowledge of the Phytophthora communities already present in the UK is of great importance when developing management and mitigation strategies for these diseases. To do this, soils were sampled in “disturbed” sites, meaning sites frequently visited by the public, with recent and new plantings or soil disturbances versus more “natural” forest and woodland sites with little disturbance or management. Phytophthora diversity was assessed using high-throughput Illumina sequencing targeting the widely accepted barcoding Internal Transcribed Spacer 1 (ITS1) region of rRNA and comparing it with the mitochondrial cytochrome c oxidase I (COI) gene. Isolation of Phytophthora was run in parallel. Nothophytophthora spp. and Phytophthora spp. were detected in 79 and 41 of the 132 locations of the 14 studied sites when using ITS or COI, respectively. A total of 20 Phytophthora amplicon sequence variants (ASVs) were assigned to known Phytophthora species from eight clades (1a, 2, 2b, 3a, 5, 6b, 7a, 8b, 8c, 8d, 10a, and 10b) and 12 ASVs from six clades (1a, 2c, 3a, 3b, 6b, 7a, 8b, 8c, and 8d) when using ITS or COI, respectively. Only at two locations were the results in agreement for ITS, COI, and isolation. Additionally, 21 and 17 unknown Phytophthora phylotypes were detected using the ITS and COI, respectively. Several Phytophthora spp. within clades 7 and 8, including very important forest pathogens such as P. austrocedri and P. ramorum, were identified and found more frequently at “disturbed” sites. Additionally, eight ASVs identified as Nothophytophthora spp. were detected representing the first report of species within this new genus in Britain. Only three species not known to be present in Britain (P. castaneae, P. capsici, and P. fallax) were detected with the ITS primers and not with COI. To confirm the presence of these or any potential new Phytophthora species, sites should be re-sampled for confirmation. Additionally, there is a need to confirm if these species are a threat to British trees and try to establish any eradication measures required to mitigate Phytophthora spread in Britain.

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“…Phylogenetic analysis of the ITS1 among Pythium species and OTU assignments. Some species of Phytophthora and Pythium share identical ITS1 sequences and this is a challenge faced by others in microbiome studies (Redekar et al 2019). For this study a customized database was developed from accessions of the ITS (1 and 2) and the 5.8 gene of the nuclear rRNA of voucher specimens used by Lévesque and De Cock (2004); sequences were retrieved from NCBI nucleotide database.…”

Section: Methodsmentioning

confidence: 99%

The Effect of Incubation Temperature on the Species Composition ofPhytophthora,Phytopythium, andPythiumCommunities Associated with Soybean

Navarro-Acevedo

Wijeratne

Culman

et al. 2021

Phytobiomes Journal

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Multiple species of Phytophthora, Phytopythium, and Pythium cause detrimental effects to soybean and one or more species have been recovered from symptomatic seedlings or roots, suggesting that these occur as species complexes. Our objective was to assess the species diversity and abundance of Phytophthora, Phytopythium, and Pythium associated with soybean seedlings at two different incubation temperatures from soils collected from the same 81 ha farm, but from five fields with a different history of production practices. To determine the effect of incubation temperature on the species detected, soils were baited with soybean seedlings at 15 and 25oC. At each temperature isolates were directly recovered from seedling roots and the associated rhizosphere soil was assayed via amplicon sequencing with oomycete specific primers. Regardless of incubation temperature or field site, Py. sylvaticum, and Py. ultimum were isolated through the baiting procedure and these along with Py. acrogynum, Py. attrantheridium, and Py. heterothallicum were detected with amplicon sequencing. Some Pythium species were more abundant at 15o C while others were favored by 25o C. This study demonstrated that the species diversity of Phytophthora, Phytopythium, and Pythium, detected on seedling roots and rhizosphere of soybean can be influenced by incubation temperature. This may explain, in part the differences in the species composition reported from previous surveys and suggests that production practices influence the species complexes of Phytophthora, Phytopythium, and Pythium.

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Diversity of Phytophthora, Pythium, and Phytopythium Species in Recycled Irrigation Water in a Container Nursery

Cited by 54 publications

References 67 publications

Pythium Damping-Off and Root Rot of Capsicum annuum L.: Impacts, Diagnosis, and Management

Pythium Damping-Off and Root Rot of Capsicum annuum L.: Impacts, Diagnosis, and Management

Diversity of Phytophthora Species Detected in Disturbed and Undisturbed British Soils Using High-Throughput Sequencing Targeting ITS rRNA and COI mtDNA Regions

The Effect of Incubation Temperature on the Species Composition ofPhytophthora,Phytopythium, andPythiumCommunities Associated with Soybean

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