Table of Contents:

• Taxonomy Information
• Lifecycle Information
• Genome Information
• Biosafety Information
• Culturing Information
• Epidemiology Information
• Diagnostic Tests Information
• Infected Hosts Information
• Phinet: Pathogen-Host Interaction Network
• Lab Animal Pathobiology & Management
• References
• Data Provenance and Curators

1. Species:
   1. Phakopsora pachyrhizi (Website 1):
      1. GenBank Taxonomy No.: 170000
      2. Description: Soybean Rust (SRB) is caused by two related species of fungi, the most aggressive is Phakopsora pachyrhizi Sydow (anamorph Malupa sojae), and the less virulent species, Phakopsora meibomiae (Arthur) Arthur (anamorph Malupa vignae) which has only been found in limited areas in the Western Hemisphere and is not known to cause severe yield losses in soybean(Hartman et al., 1996). P. meibomiae, is referred to as the tropical, Latin American or New World rust strain(Website 49). The Asian strain of soybean rust caused by P. pachyrhizi is extremely aggressive and is listed as a select biological agent (Title 7, Code of Federal Regulations, Part 331.2), determined to have the potential to pose a threat to plant health or plant products(Website 49). Phakopsora pachyrhizi, is ranked #22 of the top 100 most dangerous and exotic pests and diseases(Website 46). Phakopsora pachyrhizi is an air-borne fungal pathogen that is not present in the continental United States. Under conducive environmental conditions, this pathogen could cause serious economic and crop losses in major soybean production regions of the United States. The probability of long-distance spread of P. pachyrhizi across U.S. borders may be reduced through strong international cooperation to reduce inoculum levels beyond our borders. However, it is anticipated that the disease will eventually reach the U.S. and establish in major soybean growing regions via wind currents. The confirmation of the presence of Asian SBR in soybean production regions of Argentina, Bolivia, Brazil and Paraguay has lead to heightened concerns regarding the potential for spread to the continental United States. In particular, there is concern about potential introduction of Asian SBR in the importation of soybean seed, meal, and grain of host plant members of the pea and bean family (Leguminosae)(Website 49). Extreme weather events (such as a hurricane) carried P. pachyrhizi from infested areas to the United States(Website 49). Long-distance dispersal of fungal spores by the wind can spread plant diseases across and even between continents and reestablish diseases in areas where host plants are seasonally absent. For such epidemics to occur, hosts that are susceptible to the same pathogen genotypes must be grown over wide areas, as is the case with many modern crops(Brown and Hovmoller, 2002). Besides via wind current from Africa or South America, experts predict there are several ways spores could potentially be carried into this country. Those include: by tourists who have traveled internationally, via the movement of plant materials from infected countries, through the land bridge of Central America or even intentionally, through bioterrorism(Website 44). To compound the fears, soybean cultivars show little promise for genetic resistance or tolerance. There are only four known resistance genes for soybean, but all can be overcome by at least one of the many P. pachyrhizi isolates. In a search for genetic resistance, 940 soybean cultivars currently grown in the US and 12,000 soybean accessions from the USDA germplasm collection were evaluated in seedling assays against soybean rust at the BSL-3 containment greenhouse at Ft. Detrick, MD. None were found to be resistant and fewer than 100 showed any promise for disease tolerance(Website 46). WASHINGTON, Nov 10, 2004 -- The U.S. Department of Agriculture's Animal and Plant Health Inspection Service today confirmed the presence of soybean rust on soybean leaf samples taken from two plots associated with a Louisiana State University research farm Saturday(Website 61). On December 1, researchers at the National Plant Germplasm and Biotechnology Laboratory in Beltsville, Md., said today that one of two soybean leaf samples collected near Memphis, Tenn., has tested positive for Phakopsora pachyrhizi, or soybean rust.Soybean rust, has been confirmed in nine states since it was first discovered in the United States on Nov. 10 in Louisiana. Other states include Alabama, Arkansas, Florida, Georgia, Mississippi, Missouri and South Carolina.USDA encourages growers to contact USDA's Extension Service, their State Department of Agriculture, and their crop consultants to obtain information on what fungicides are registered for use in their states, as well as when these fungicides should be used.">(Website 62). May 2, 2005 INDIANAPOLIS --The states of Georgia, Wisconsin and West Virginia have received Section 18 emergency exemptions for EC, Laredo EW and fungicides to be used for the control of soybean rust.Laredo EC and Laredo EW contain the active ingredient myclobutanil, while PropiMax contains the active ingredient propiconazole. Both fungicides provide preventive and curative control of soybean rust. Laredo EC and Laredo EW contain the active ingredient myclobutanil, while PropiMax contains the active ingredient propiconazole. Both fungicides provide preventive and curative control of soybean rust(Website 70).

1. Soybean rust life cycle
   1. Stage Information:
      1. Urediniospores (urediospores, uredospore, uredinospore) from infected host(Website 49):
         • Size: Uredinospores are 18-34 to 15-24 microns.
         • Shape: Urediniospores are sessile, obovoid to broadly ellipsoid, and minutely and densely echinulate, and the walls are about 1 micron thick. The color of the urediniospores range from pale yellowish-brown to colorless.
         • Picture(s):
           • Soybean rust spores. (Photo courtesy of Dr. Glen Hartman.) (Website 66)
             
             
             
             Description: Diagnostic Characters for Soybean Rust Identification(Website 56).
         • Description: Primary inocula for new infections are urediniospores(Website 49).
      2. Uredinia bearing uredinospores:
         • Size: Subepidermal in origin, the uredinia are surrounded by paraphyses arising from peridioid pseudoparenchyma; in addition the uredinia have hymenal paraphyses.. Paraphyses are 25-50 by 5-14 microns slightly to conspicuously thickened (-18 microns) apically.
         • Shape: Uredinia are amphigenous (growing all round), mostly hypophyllous (on the under surfaces of leaves), minute, scattered or in groups on discolored lesions.. The paraphyses are cylindric to clavate. Openings are through central apertures. In appearance, the uredinia are pulverulent (appearing as if powdered); in color, uredinia are pale cinnamon-brown.
      3. Telia bearing teliospores(Ono et al., 1992):
         • Size: Teliospores are 15-26 by 6-12 microns.
         • Shape: Telia are 2-7-spored layered. Often mixed with uredinia, the subepidermal telia are hypophyllus and crustose. The teliospores are single-celled, oblong to ellipsoid. The telia are chesnut-brown to chocolate brown; the teliospores are pale yellowish-brown to colorless.
         • Description: Telia and teliospores have been reported on only six of 87 hosts in nature(Sinclair, 1982). Teliospores are generally over-seasoning structures, and have been germinated under laboratory conditions to produce basidiospores(Saksirirat and Hoppe, 1991). The importance of the telial stage in the development of soybean rust in the field is unknown(Website 49). Teliospores are not generally considered the primary source of inoculum and are not often observed in the field(Ono et al., 1992).
      4. Urediospores disseminated by wind:
         • Description: Wind dissemination of urediniospores facilitates short- and long-distance spread of the pathogen(Marchetti et al., 1976).
      5. Susceptible host:
         • Description: New disease foci can develop as long as living host plants are available. Urediniospores infect native hosts (legumes, volunteer host plants and weeds) allowing the disease cycle to continue(Website 49).
      6. Healthy host:
         • Description: New disease foci can develop as long as living host plants are available. Urediniospores infect native hosts (legumes, volunteer host plants and weeds) allowing the disease cycle to continue(Website 49).
   2. Progression Information:
      1. Life cycle of P. pachyrhizi:
         • From Stage: Urediniospores (urediospores, uredospore, uredinospore) from infected host
         • To Stage: Susceptible host
         • Description: Urediospores germinate and the new uredinia matures in 10 days and they are capable of producing new urediospores for 3 weeks thereafter. The new urediospores may infect healthy plants, or an alternate or over-wintering host (such as kudzu)(Website 53). Urediniospores are the most common spore type found during the growing season. These urediniospores are the primary inoculum source and with prevailing winds and conducive environmental conditions can initiate soybean rust epidemic(Yeh et al., 1976).
   3. Picture(s):
      • Life cycle of soybean rust (Website 53)
        
        
        
        Description: Soybean rust has a rapid repeating life cycle period (modified to gif from: http://www.cai.iastate.edu/SoybeanRust/Lifecycle.swf)(Website 53).

1. Genome of Phakopsora pachyrhizi
   1. Description: The P. pachyrizhi genome is currently being sequenced(Website 58).
   2. 1. Size: .
      2. Gene Count: .
      3. Description: .

1. General biosafety information
   1. Level: 3. There are over 16,000 soybean accessions in the USDA Germplasm Collection located at the University of Illinois. These soybean accessions are being evaluated for resistance to P. pachyrhizi in the USDA-ARS FDWSRU Biosafety Level 3 Containment Greenhouses at Fort Detrick, MD, along with commercial and public cultivars grown in the U.S(Website 58).
   2. Precautions: If soybean rust is suspected to be present on soybean or other hosts in the continental U.S., samples are to be submitted to the plant disease diagnostic laboratory at state universities for identification(Website 60). The soybean rust pathogen is on the U. S. Select Agent list produced by the U. S. Dept. of Homeland Security. This rust pathogen cannot be transported across state lines without the appropriate permit. Testing of suspect soybean rust material should be done within the state(Website 50). If university or state departments of agriculture laboratories determine that a sample is Phakopsora spp. on soybean or another leguminous hosts, further identification to the species level will be necessary. There are no Phakopsora species on legume hosts recorded in the continental Unites States. A new Phakopsora record, because of its potential economic importance, will require verification by the PPQ national mycologist in Beltsville, Maryland. Verification will utilize the validated PCR-based molecular test. Diagnostic laboratories should contact Dr. Mary Palm at (301) 504-5327 or Dr. John McKemy at (301) 504-5280 if Phakopsora spp. on a legume host is found(Website 59). The preparation and distribution of information regarding survey and identification procedures is the foundation for the early detection of ASBR. The early detection and diagnosis of the pathogen relies on producers, crop consultant, or handler referral of symptomatic material. It is absolutely essential that appropriate program training and detection aides showing symptoms and instructions for referring specimens be provided to the public frequenting soybean production and other host's areas(Website 59).

1. Outbreak Locations:
   1. Soybean rust caused by Phakopsora pachyrhizi was first observed in Japan in 1902, and by 1934 the pathogen was found throughout most Asian countries and in Australia. The current distribution of P. pachyrhizi includes countries in Africa, Asia, Australia and most recently South America. Asian soybean rust (ASBR) causes serious crop losses in most infested soybean production regions. The disease has not yet been detected in Europe. SBR has been reported in the main soybean growing regions of Brazil including the states of Parana, Rio Grande do Sul, Mato Grosso do Sul and Goais. About 2.6 percent of the 15 million hectares planted to soybean in Brazil tested positive for the P. pachyrhizi, and the disease caused 10 percent loss in the 2000-2001 soybean crop in affected fields. In the Brazilian regions of Mato Grosso do Sul and Goais, ABR reduced yield by up to 75% in some fields. During the 2001-2002 growing season, Brazilian growers lost approximately 112 thousand tons of their annual soybean production. P. pachyrhizi is suspected to have been introduced to Brazil via air currents from Africa and/or Asia(Website 49). Phakopsora pachyrhizi is present throughout the soybean production areas of Australia, Burma, Cambodia, China, Congo, Ghana, India, Indonesia, Japan, Kenya, Korea, Malaysia, Mozambique, Nepal, Nigeria, New Guinea, Philippines, Rwanda, Sierra Leone, South Africa, Taiwan, Thailand, Uganda, Vietnam, Zambia, and Zimbabwe. Soybean rust was observed in Hawaii in 1994 on the islands of Oahu, Kakaha, Kauai, and Hilo, where it is thought to have arrived in fresh soybean plants smuggled in for use in ethnic Laotian cuisine. P. pachyrhizi was first detected on the South American continent in Paraguay in 2001, where it was widely spread, then was wind spread across the border into Argentina. SBR was recently found in Bolivia in July, 2003(Website 49). In Uganda, the disease was first observed on experimental plots in 1996, and thereafter the disease was observed on farmer's field throughout the country with all the commercial cultivars succumbing to the disease(Kawuki et al. 2004). WASHINGTON, Nov 10, 2004 -- The U.S. Department of Agriculture's Animal and Plant Health Inspection Service today confirmed the presence of soybean rust on soybean leaf samples taken from two plots associated with a Louisiana State University research farm Saturday(Website 61). On December 1, researchers at the National Plant Germplasm and Biotechnology Laboratory in Beltsville, Md., said today that one of two soybean leaf samples collected near Memphis, Tenn., has tested positive for Phakopsora pachyrhizi, or soybean rust.Soybean rust, has been confirmed in nine states since it was first discovered in the United States on Nov. 10 in Louisiana. Other states include Alabama, Arkansas, Florida, Georgia, Mississippi, Missouri and South Carolina.USDA encourages growers to contact USDA's Extension Service, their State Department of Agriculture, and their crop consultants to obtain information on what fungicides are registered for use in their states, as well as when these fungicides should be used.">(Website 62). Soybean rust was introduced into the continental United States in the fall of 2004, presumably as a consequence of tropical storm activity. Model predictions indicated that soybean rust had been widely dispersed throughout the southeastern United States, and subsequent field and laboratory observations confirmed this distribution. Figures 1 and 2 provide information on spore deposition in late 2004 and overwintering areas for soybean rust in the continental United States(Website 67). The Asian soybean rust found Monday and confirmed today (4/27/2005) on volunteer soybeans in Seminole County, Georgia, was visible and sporulating on several plants across the field, according to the county agent who found it. And those plants are right next to a large acreage of very young commercial snap beans(Website 68). Kemerait said the kudzu samples, found right next to the infected volunteer soybeans and in a patch that was positive for rust last year, had so many other diseases on them those particular ones might not test positive at the USDA lab."I believe it's in the kudzu," he said. "They had the same spores, and were right next to each other," he said of the kudzu and the rust-positive volunteer soybeans, both found near Donalsvonville in the extreme southwest corner of the state."We're at the very beginning of an epidemic," he said, "and you have to really believe it's there and try hard to see it to be able to find it at this early stage."(Website 68).
2. Transmission Information:
   1. From: Urediniospores on infected plants. (at lifecycle stage: Urediniospores (urediospores, uredospore, uredinospore) from infected host) , To: Healthy host. (at lifecycle stage: Healthy host)
      Mechanism: Soybean rust spreads primarily by wind-borne spores across regions dependent upon prevailing winds and environmental conditions conducive to disease development(Website 59). The disease is likely to be restricted to parts of Florida and the southern Texas during the winter in the frost-free areas or areas where the fungus could overcome short periods of below-freezing temperatures. Occurrence of rust epidemics within the U. S. soybean belt would depend on south-to-north dispersal of urediospores(Pivonia and Yang, 2004). Kudzu is a common weed in the southern U.S. and is great concern that it could serve as a continual source of P. pachyrhizi inocula. Kudzu begins growth in the spring before soybeans are planted and thus, the weed could act as a "disease bridge" by allowing build-up of the fungus followed by movement into soybean(Website 43).
3. Environmental Reservoir:
   1. Infected living host:
      1. Description: P. pachyrhizi is still known as an obligate parasite. Uredospores survive (in resting or dormant state) less than 2 days under natural outdoor conditions. They do not survive in dried or decayed tissues or in the soil(Ilag, 1977).
      2. Survival: When soybean plants are not present in the field the fungus is viable only when transferred to another living host(Ilag, 1977). One widespread host in the United States is kudzu, Pueraria montana var. lobata, that could serve as a reservoir for soybean rust. There are a variety of other important hosts that are leguminous crops or weeds that have shown varying degrees of susceptibility to both species of Soybean rust. Some other common hosts are yellow sweet clover (Melilotus officinalis), vetch (Vicia dasycarpa), medic (Medicago arborea), lupine (Lupinus hirsutus), green and kidney bean (Phaseolus vulgaris), lima and butter bean (Phaseolus lunatus), and cowpea or backeyed pea (Vigna unguiculata)(Website 55). Unfortunately, P. pachyrhizi infects and develops on kudzu but the weed is not adversely affected by the disease(Website 53).
4. Intentional Releases:
   1. Currently no intentional releases information is available.

1. Organism Detection Test:
   1. Light microscopy (Website 59):
      1. Description: Soybean symptoms can be distinguished by two microscopic characteristics. Uredial pustules open through a round ostiole and white clumps of urediniospores can generally be observed on top of the uredial cone sometimes emerging in columns. Uredinospores can be identify by mounting them on a microscope slide and examined under a compound microscope(Website 59).
      2. False Positive: Early symptoms of soybean rust are easily confused with bacterial pustule (Xanthomonas campestris pv. phaseoli), or bacterial blight (Pseudomonas glycinea), and brown spot (Septoria glycines).The diseases also occcur often on the underside of soybean leaves causing a raised light brown blister within a lesion. A hand lens is usually used to distinguished these disease symptoms from ASBR, but early the stages of disease are difficult to distinguished if no spores, conidia or bacteria are evident(Website 59). Also bacterial lesions can be differentiated by the cracks that usually appear in host tissue with a bacterial pustule lesion(Hartman et al., 1996).
   2. Isoenzymes :
      1. Time to Perform: unknown
      2. Description: Isozyme analysis supported the identification of P. pachyrhizi and P. meibomiae as separate species. When multilocus banding patterns were compared among Asian and New World rust isolates, no differences were found among the Asian isolates, nor among the New World isolates. However, the two groups differed greatly from one another, with the maximum coefficient of similarity estimated at 0.07 (7% of alleles in common) for the 14 loci examined(Bonde et al., 1988). They reported that the lack of isoenzymes variation within P. pachyrhizi might be due to the lack of an effective sexual cycle.(Bonde et al., 1988). Although teliospores of the pathogen have been observed, germination may be rare or absent.(Bonde et al., 1988). While isozymes represent an important research tool, they are generally not considered appropriate for use as a diagnostic test(Website 49).
2. Nucleic Acid Detection Test: