CHAPTER 15: Molecular Methods for Detection of Plant Pathogens in Irrigation Water

2017 ◽  
pp. 161-174
Author(s):  
Susanne von Bargen
Keyword(s):  
Irrigation Water ◽  
Plant Pathogens ◽  
Molecular Methods

Dynamics of fungal pathogens in host plant tissues

1995 ◽  
Vol 73 (S1) ◽  
pp. 1275-1283 ◽  
Author(s):  
Shigehito Takenaka
Keyword(s):  
Host Plant ◽  
Species Interactions ◽  
Fungal Biomass ◽  
Quantitative Methods ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Molecular Methods ◽  
Plant Colonization ◽  
Fungal Colonization ◽  
Plant Tissues

To develop efficient control measures against fungal plant pathogens, the dynamics of host plant colonization during disease development and the interactions among fungi within host plant tissues need to be clarified. These studies require accurate quantitative estimation of specific fungal biomass in plant tissues. This has been approached by direct-microscopic methods, cultural methods, chemical determinations of fungal components, serological methods, and molecular methods. Among these methods, serological and molecular methods provide rapid, specific, and sensitive quantitative measures of fungal biomass in host plant tissues. Therefore, studies on fungal dynamics of host plant colonization using these two methods are presented. Some examples of species interactions among pathogenic fungi within host plants, such as synergism and competition, are reviewed and the usefulness of serological and molecular methods for studies on these interactions is presented. These quantitative methods will provide helpful information for understanding the ecology of plant pathogenic fungi, such as the dynamics of host plant colonization and species interactions. Key words: quantitative methods, fungal biomass, ELISA, PCR, fungal colonization, species interaction.

scholarly journals Fungi and Oomycetes in the Irrigation Water of Forest Nurseries

Forests ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 459 ◽  
Author(s):  
Adas Marčiulynas ◽  
Diana Marčiulynienė ◽  
Jūratė Lynikienė ◽  
Artūras Gedminas ◽  
Miglė Vaičiukynė ◽  
...  
Keyword(s):  
Irrigation Water ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Irrigation System ◽  
Tree Seedlings ◽  
High Quality ◽  
Forest Nurseries ◽  
Study Sites ◽  
Microbial Samples

The aim of the present study was to assess fungal and oomycete communities in the irrigation water of forest nurseries, focusing on plant pathogens in the hope of getting a better understanding of potential pathogenic microorganisms and spreading routes in forest nurseries. The study sites were at Anykščiai, Dubrava, Kretinga and Trakai state forest nurseries in Lithuania. For the collection of microbial samples, at each nursery five 100-L water samples were collected from the irrigation ponds and filtered. Following DNA isolation from the irrigation water filtrate samples, these were individually amplified using ITS rDNA as a marker and subjected to PacBio high-throughput sequencing. Clustering in the SCATA pipeline and the taxonomic classification of 24,006 high-quality reads showed the presence of 1286 non-singleton taxa. Among those, 895 were representing fungi and oomycetes. The detected fungi were 57.3% Ascomycota, 38.1% Basidiomycota, 3.1% Chytridiomycota, 0.8% Mucoromycota and 0.7% Oomycota. The most common fungi were Malassezia restricta E. Guého, J. Guillot & Midgley (20.1% of all high-quality fungal sequences), Pezizella discreta (P. Karst.) Dennis (10.8%) and Epicoccum nigrum Link (4.9%). The most common oomycetes were Phytopythium cf. citrinum (B. Paul) Abad, de Cock, Bala, Robideau, Lodhi & Lévesque (0.4%), Phytophthora gallica T. Jung & J. Nechwatal (0.05%) and Peronospora sp. 4248_322 (0.05%). The results demonstrated that the irrigation water used by forest nurseries was inhabited by a species-rich but largely site-specific communities of fungi. Plant pathogens were relatively rare, but, under suitable conditions, these can develop rapidly, spread efficiently through the irrigation system and be a threat to the production of high-quality tree seedlings.

scholarly journals A Comparison of Irrigation-Water Containment Methods and Management Strategies Between Two Ornamental Production Systems to Minimize Water Security Threats

Water ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 2558 ◽  
Author(s):  
Andrew Ristvey ◽  
Bruk Belayneh ◽  
John Lea-Cox
Keyword(s):  
Water Quality ◽  
Irrigation Water ◽  
Capital Investment ◽  
Plant Pathogens ◽  
Production Systems ◽  
Water Security ◽  
Plant Production ◽  
Water Quantity ◽  
Return Water ◽  
Plant Nursery

Water security in ornamental plant production systems is vital for maintaining profitability. Expensive, complicated, or potentially dangerous treatment systems, together with skilled labor, is often necessary to ensure water quality and plant health. Two contrasting commercial ornamental crop production systems in a mesic region are compared, providing insight into the various strategies employed using irrigation-water containment and treatment systems. The first is a greenhouse/outdoor container operation which grows annual ornamental plants throughout the year using irrigation booms, drip emitters, and/or ebb and flow systems depending on the crop, container size, and/or stage of growth. The operation contains and recycles 50–75% of applied water through a system of underground cisterns, using a recycling reservoir and a newly constructed 0.25 ha slow-sand filtration (SSF) unit. Groundwater provides additional water when needed. Water quantity is not a problem in this operation, but disease and water quality issues, including agrochemicals, are of potential concern. The second is a perennial-plant nursery which propagates cuttings and produces field-grown trees and containerized plants. It has a series of containment/recycling reservoirs that capture rainwater and irrigation return water, together with wells of limited output. Water quantity is a more important issue for this nursery, but poor water quality has had some negative economic effects. Irrigation return water is filtered and sanitized with chlorine gas before being applied to plants via overhead and micro-irrigation systems. The agrochemical paclobutrazol was monitored for one year in the first operation and plant pathogens were qualified and quantified over two seasons for both production systems. The two operations employ very different water treatment systems based on their access to water, growing methods, land topography, and capital investment. Each operation has experienced different water quantity and quality vulnerabilities, and has addressed these threats using a variety of technologies and management techniques to reduce their impacts.

scholarly journals Diversity ofPhytophthora,Pythium,and PhytopythiumSpecies in Recycled Irrigation Water in a Container Nursery

2019 ◽  
Vol 3 (1) ◽  
pp. 31-45 ◽  
Author(s):  
Neelam R. Redekar ◽  
Joyce L. Eberhart ◽  
Jennifer L. Parke
Keyword(s):  
Irrigation Water ◽  
Plant Pathogens ◽  
Temporal Dynamics ◽  
Water Reservoir ◽  
Water Source ◽  
Biologically Active ◽  
Reference Database ◽  
Phytophthora Megasperma ◽  
Filtration Method ◽  
Container Nursery

Recycling of irrigation water increases disease risks due to spread of waterborne oomycete plant pathogens such as Phytophthora, Pythium, and Phytopythium. A comprehensive metabarcoding study was conducted to determine spatial and temporal dynamics of oomycete communities present in irrigation water collected from a creek (main water source), a pond, retention reservoirs, a chlorinated water reservoir, and runoff channels within a commercial container nursery in Oregon over the course of 1 year. Two methods, filtration and leaf baiting, were compared for the detection of oomycete communities. Oomycete communities in recycled irrigation water were less diverse but highly enriched with biologically active plant pathogens as compared with the creek water. The filtration method captured a larger portion of oomycete diversity, while leaf baiting was more selective for plant-associated oomycete species of Phytophthora and a few Pythium and Phytopythium species. Seasonality strongly influenced oomycete diversity in irrigation water and detection with leaf baiting. Phytophthora was the major colonizer of leaf baits in winter, while all three genera were equally abundant on leaf baits in summer. The metabarcoding approach was highly effective in studying oomycete ecology, however, it failed to distinguish some closely related species. We developed a custom oomycete internal transcribed spacer (ITS)1 reference database containing shorter sequences flanked by ITS6 and ITS7 primers used in metabarcoding and used it to assemble a list of indistinguishable species complexes and clusters to improve identification. The predominant bait-colonizing species detected in recycled irrigation water were the Phytophthora citricola-complex, Phytophthora syringae, Phytophthora parsiana-cluster, Phytophthora chlamydospora, Phytophthora gonapodyides, Phytophthora irrigata, Phytophthora taxon Oaksoil-cluster, Phytophthora citrophthora-cluster, Phytophthora megasperma-cluster, Pythium chondricola-complex, Pythium dissotocum-cluster, and Phytopythium litorale.

scholarly journals Response of Container-grown Nursery Plants to Chlorine Used to Disinfest Irrigation Water

HortScience ◽  
2009 ◽  
Vol 44 (1) ◽  
pp. 164-167 ◽  
Author(s):  
Diane Feliciano Cayanan ◽  
Mike Dixon ◽  
Youbin Zheng ◽  
Jennifer Llewellyn
Keyword(s):  
Irrigation Water ◽  
Picea Glauca ◽  
Plant Pathogens ◽  
Free Chlorine ◽  
Growth Reduction ◽  
Leaf Chlorophyll ◽  
Physocarpus Opulifolius ◽  
Deciduous Shrubs ◽  
Chamaecyparis Pisifera ◽  
Weigela Florida

The recycling of irrigation water may cause the dispersal of plant pathogens. Irrigation water disinfected with 2.4 mg·L−1 of free chlorine for 5 min was overhead-applied to 17 container-grown nursery plants for 11 weeks in a commercial nursery to evaluate the response of container-grown nursery plants to chlorine. No visual symptoms of injury or growth reduction were observed on the evergreen shrubs (Juniperus horizontalis, Thuja occidentalis, Buxus microphylla, Picea glauca, Rhododendron catawbiense, Taxus media, and Chamaecyparis pisifera), but there were visual injuries and/or growth reduction on some of the deciduous shrubs (Salix integra, Hydrangea paniculata, Prunus ×cistena, Weigela florida, Physocarpus opulifolius). Symptoms of anthracnose were reduced on Cornus alba plants treated with chlorinated water. The chlorine treatment did not affect leaf chlorophyll content. The chlorine treatment killed all fungi and oomycetes in the irrigation water (DNA multiscan). Although there were visible leaf injuries and growth reduction on some of the deciduous plants, chlorine injury did not render them unsalable. Results suggest that irrigation water treated with 2.4 mg·L−1 free chlorine for 5 min will effectively control the dispersal of common plant pathogens without reducing the market value of container-grown plants.

scholarly journals Inactivation of plant pathogens in irrigation water runoff using a novel UV disinfection system

2018 ◽  
Vol 153 (3) ◽  
pp. 907-914 ◽  
Author(s):  
Bassam A. Younis ◽  
Laura Mahoney ◽  
Wolfgang Schweigkofler ◽  
Karen Suslow
Keyword(s):  
Irrigation Water ◽  
Plant Pathogens ◽  
Uv Disinfection ◽  
Water Runoff

scholarly journals Illustration of Key Morphological Characteristics of Phytophthora Species Identified in Virginia Nursery Irrigation Water

2006 ◽  
Vol 7 (1) ◽  
pp. 41 ◽  
Author(s):  
Elizabeth A. Bush ◽  
Erik L. Stromberg ◽  
Chuanxue Hong ◽  
Patricia A. Richardson ◽  
Ping Kong
Keyword(s):  
Irrigation Water ◽  
Ornamental Plants ◽  
Morphological Characteristics ◽  
Phytophthora Species ◽  
Molecular Methods ◽  
Morphological Identification ◽  
Taxonomic Identification ◽  
Effluent Water ◽  
Phytophthora Spp ◽  
Diagnostic Characteristics

Phytophthora diseases are commonly diagnosed on ornamental plants, but taxonomic identification to species can be intimidating. This illustrative guide is designed to aid diagnosticians in morphological identification of certain Phytophthora spp. that have been reported in irrigation and effluent water in nurseries. Using both morphological and molecular methods, the authors identify diagnostic characteristics that are consistent and easy to use. Accepted for publication 6 April 2006. Published 21 June 2006.

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