1

Reference Manual B

(RM-B)

NATIONAL SEED HEALTH SYSTEM

SEED HEALTH TESTING AND

PHYTOSANITARY FIELD INSPECTION 

METHODS MANUAL

Version dated

 02/27/01
2

"Standard" or "Temporary Standard" test results are

considered valid for determining phytosanitary 

eligibility or seed health when conducted by a NSHS 

accredited entity or other PPQ officially recognized

regulatory laboratory.
3

Contents

SECTION 1- Laboratory Seed Health Testing Methods

Criteria for Laboratory Seed Health Test Methods 5

Vegetable Crops

Bean

Pseudomonas syringae pv. phaseolicola 9

Carrot

Xanthomonas campestris pv. carotae 12

Celery

Septoria apiicola 15

Lettuce

Lettuce Mosaic Virus 17

Pepper& Tomato

Xanthomonas campestris pv. vesicatoria 21

Field Crops

Maize

Clavibacter michiganensis subsp. nebraskensis 28

Pantoea stewartii 30

Soybean

Cercospora kikuchii 34

Phomopsis/Diaporthe complex 37

Sclerotinia sclerotiorum 41

SECTION 2- Phytosanitary Field Inspection Methods

Criteria for Phytosanitary Field Inspection Methods 44

Phytosanitary Inspection Procedures 45

Diagnostic Aids 52
4

SECTION 1

LABORATORY SEED HEALTH 

TESTING METHODS
5

Criteria for approving Laboratory Seed Health Testing Methods for 

the National Seed Health System (NSHS)

Introduction

The National Seed Health System (USA) has developed a peer review system to establish standardized 

seed health test methods for the NSHS. Technical Panels of 3-4 experts evaluate seed health test

methods for groups of seed-borne pathogens. Technical Panel members are drawn from academia and 

the seed industry throughout the world on the basis of their expertise in pathogens of the assigned crop. 

The following criteria are used by the Technical Panels to evaluate seed health testing methods for each 

host/pathogen combination and recommend their acceptance as standardized methods to be published 

in Reference Manual B. Final approval of methods is given, on behalf of USDA-APHIS, by the Seed 

Technical Working Group, a standing committee of NSHS that defines policies and procedures of the 

system.

Technical Package Development

1. The NSHS Administration Unit (AU) develops technical packages of scientific information for each 

host/pathogen combination. This is accomplished by conducting a computerized literature review of the 

pathogen and by direct contact with experts and organizations with special knowledge and/or 

information of the seed-borne aspect of the pathogen. 

Information is assembled on: 

Laboratory seed health tests that are published

Laboratory seed health tests in use but not published

Proprietary methodologies in use * (if any)

Data on test standardization by ISHI, ISTA, or other organizations

Relevant data on seed transmission or detection of the pathogen

* The evaluation of proprietary methods will be governed by a confidentiality agreement.

2. The AU forwards to each panel member a description of all known laboratory seed health tests for 

the particular pathogen. Included in this description will be all relevant scientific documentation on the 

test development and any records of use as routine tests. 

3. The AU will eliminate those laboratory methods judged to be trivial, out of date etc.
6

Technical Panel Responsibilities

Technical Panel members evaluate seed health test methods included in the technical package based 

upon the following criteria:

Criterion 1. Empirical Test Data

New techniques should have the following parameters included in the development process.

Sensitivity. Determine how sensitive the assay is in terms of either percent-infected seed or target 

pathogen quantification, such as CFU, number of conidia, etc.

Panel members may need to make an arbitrary determination whether the methods in question are 

sensitive enough, or they may make a recommendation that the test requires further work. The panel 

members should also make recommendations on sample size if this is not clearly spelled out in the 

existing procedures for that test.

Specificity. Determine whether the assay is capable of detecting a range of isolates of the pathogen 

from different geographical regions, races, etc. Determine whether other closely related organisms are 

separated with the technique.

Repeatability and Reliability. Replicate experiments of 1 and 2 will help determine these parameters. 

Additional experimentation including varying types of seed (varieties, production areas, etc.) samples 

will further refine these parameters.

Criterion 2. Comparative Test Data

Comparisons with already established techniques will yield useful information regarding new techniques. 

If a new technique performs as well or better than an established technique then it should be accepted. 

This information is generated internally through the developmental process or through group 

comparative testing. (These criteria may be of limited applicability to panel members evaluating existing 

test methodologies.)

Criterion 3. Historical Data

If a technique has been used in industry or academia there may be some indication or record of the 

number of uses of that technique. There may also be a record of the number of complaints associated 

with a particular assay. These records may be a good indicator of the effectiveness of the assay.

Other Criteria

Panel members should consider any other criteria that might have significant impact on the 

recommendation for use of a test. These include the cost of the test, facilities required to perform it, time 

to perform test, etc.
7

Technical Panel Report

1. Each Technical Panel (TP) reviewer prepares a report on the form titled “NSHS TECHNICAL 

PANEL REVIEW - Individual Report Form”, rating each of the methods evaluated by these criteria. 

He or she then should state their reasons for their rating, and recommend any further research that may 

be needed.

The panel members should use the following rating system for each method:

Class A – Acceptable as a Standard Test Method.

Class B –Acceptable as a Temporary Standard Test Method. This should include recommendation 

for further research that would make the method acceptable as a Standard Method Test.

Class C –Test should not be approved as a Standard Test Method.

2. Panel members then return their individual report to the Technical Panel Chair.

3. The Technical Panel Chair evaluates the individual reports from all TP members and prepares a 

Technical Report that includes a recommendation for disposition of tests and the scientific basis for the 

recommendations. The recommendation will be made on the form titled “NSHS TECHNICAL 

PANEL REVIEW - Summary Report Form”. This indicates classification of each test as A (Standard), 

B (Temporary Standard), or C (Not Approved). 

4. The Technical Panel Chair submits the Technical Report and recommendation to the Seed Technical 

Working Group of NSHS for final approval. 

5. The Seed Technical Working Group examines the report of the Technical Panel and makes the final 

decision on test classification and publication in Reference Manual B.

6. Approved methods are then entered into Reference Manual B as NSHS Standard or Temporary 

Standard seed health testing methods.
8

VEGETABLE CROPS
9

PATHOGEN: Pseudomonas syringae pv. 

phaseolicola

HOSTS: Bean (Phaseolus spp.)

METHOD 1 Plate Test (STA Laboratories, Longmont, CO)
10

METHOD 1 Plate Test (STA Laboratories, Longmont, CO)

METHOD CLASS: STANDARD

PATHOGEN: Pseudomonas syringae pv. phaseolicola

SAMPLE: 5000 seeds

PROCEDURE:

1. 5 subsamples of 1,000 seeds are placed in 0.85% NaCl buffer in a ratio of 1:3. 

2. Samples are shaken vigorously for 3 to 4 hours, or refrigerated overnight. 

3. Part of the extract is centrifuged at 10,000 rpm for 10 minutes. Most of the supernatant liquid is 

discarded, and pellet is resuspended.

4. Two more dilutions are made, one directly from the bean extract, and a 1:10 dilution from this 

original solution.

5. 0.1ml of each of the three dilutions is plated in duplicate onto KBBC and MSP media. Liquid is 

spread evenly over each plate, and plates are incubated at 27-30oC for 5 to 7 days.

6. Plates are evaluated for suspected P.s. pv. phaseolicola colonies. Suspect colonies are confirmed 

by fluorescence, oxidase, reaction on BBD media, and pathogenicity testing. 

7. Pathogenicity is shown by mixing a slightly turbid solution of the bacterium in sterile water, and 

inoculating the undersides of susceptible bean leaves with a cotton swab. Plants are incubated at 

high humidity for 7 to 10 days, then checked for lesions surrounded by chlorotic halos.

MEDIA PREPARATION:

KBBC:

King’s B media 900ml

After autoclaving filter sterilize the following adding to media just prior to pouring:

Boric acid 100ml of 1.5% aqueous solution

Cephalexin 80mg

Cycloheximide 20mg

MSP:

Sucrose 20g

Peptone 5g

K2HPO4 0.5g

MgSO4 * 7H2O 0.25g

Agar 20g

H2O 1 liter

After autoclaving filter sterilize the following adding to media just prior to pouring:

Cycloheximide 200mg
11

Cephalexin 80mg

Vancomycin 10mg

Bromthymol blue 15mg

BBD:

Yeast extract 1g

Glycerol 5g

Bacto peptone 5g

Bacto agar 15g

H2O 750ml

Autoclave separately for no more than 15 minutes:

Powdered milk 15g

H2O 250ml

REFERENCES:

Saettler, A.W. 1991. Halo blight. Page 30 in: Compendium of Bean Disease. Robert Hall (edit.) 

American Phytopathological Society, St. Paul, MN.

Van Vuurde, J.W.L. and Van den Bovenkamp, G.W. 1989. Detection of Pseudomonas syringae pv. 

phaseolicola in bean. Pages 30-40 in: Detection of bacteria in seed and other planting material. A.W. 

Saettler, N. W. Schaad, and D.A. Roth (Eds.) American Phytopathological Society. St. Paul, MN. 

122 pp.

Mohan, S.K. and Schaad, N.W. 1987. An improved agar plating assay for detecting Pseudomonas

syringae pv. syringae and Pseudomonas syringae pv. phaseolicola in contaminated bean seed. 

Phytopathology 77: 1390-1395.
12

PATHOGEN: Xanthomonas campestris pv. carotae 

HOSTS: Carrot (Daucus carota)

METHOD 1 Seed wash (Kuan et al., 1985)
13

METHOD 1 Seed wash (Kuan et al., 1985)

METHOD CLASS: STANDARD

PATHOGEN: Xanthomonas campestris pv. carotae 

SAMPLE: 20g of seed

PROCEDURE:

1. Twenty grams of seed is added to 100 ml of 0.85% sterile cold aqueous NaCl (saline) in a 250ml 

flask.

2. The flask is swirled to submerge the seeds and incubated in the dark for 16-18 h at 5°C (a 2 hour 

incubation was found to be as effective as a 16-18 hour incubation).

3. Following incubation, two drops of sterile Tween 20 are added to the flask, and the flask is 

vigorously shaken for 1 minute.

4. The resulting suspension is filtered through two layers of sterile cheesecloth, and the seed is rinsed 

with an additional 25 ml of saline.

5. The pooled washings are centrifuged at ca 8000 g for 15 minutes.

6. Pellets are resuspended in 10ml sterile cold saline and serially diluted to 0.000001.

7. Aliquots of 100 μl of each dilution are then plated in triplicate onto MDS and/or XCS media.

MEDIA PREPARATION:

XCS:

Lactose 10g

D+ Trealose 4g

Thiobarbituric acid 0.2g

K2HPO4 0.8g

KH2PO4 0.8g

NH4Cl 1g

Yeast Extract 0.5g

Agar 15g

H2O 1 liter

After autoclaving filter sterilize the following adding to media just prior to pouring:

Ampicillin 1mg

Vancomycin 0.5mg

Cycloheximide 100mg
14

MDS:

K2HPO4 10g

NaH2PO4 1g

NH4Cl 1g

MgSO4 * 7H2O 0.3g

Agar 15g

H2O 1 liter

After autoclaving filter sterilize the following adding to media just prior to pouring:

Cellobiose 10g

Cycloheximide 100mg

REFERENCES:

Kuan TL, Minsavage GV, Gabrielson RL. 1985. Detection of Xanthomonas campestris pv. carotae

in carrot seed. Plant Disease. 69(9):758-760.
15

PATHOGEN: Septoria apiicola

HOSTS: Celery (Apium graveolens)

METHOD 1 Seed Wash (STA Laboratories, 

Longmont, CO)
16

METHOD 1 Seed Wash (STA Laboratories, Longmont, CO)

METHOD CLASS: STANDARD

PATHOGEN: Celery (Apium graveolens)

SAMPLE: 10,000 seeds 

PROCEDURE:

1. Two reps of 5,000 seeds are added to water and shaken for two hours.

2. 1ml of liquid is pipetted into microcentifuge tubes and centrifuged at 8000rpm for 10 minutes. 

3. Discard supernatant and resuspend pellet in DI water.

4. Examine for spores of Septoria on a hemacytometer at 100 to 400x magnification.

5. If spores are found, run a pathogenicity test using the spore suspension from Step 3.

6. For pathogenicity testing, excise leaves from a healthy celery plant, disinfect with 1% NaOCl 

solution and rinse. Place leaves in a 45oC water bath for 15 seconds, then blot leaves dry and place 

in a humid box. Dip a cotton swab in the spore suspension and wipe onto leaves. Incubate 

samples at 20-25oC under light and examine for pycnidia in 7 to 19 days.

REFERENCES:

Hewitt, P.D. 1968. Viable Septoria ssp. in celery seed samples. Ann. Appl. Biol. 61:89-98.

Updates: Cubeta M.A. North Carolina State Research Station.

Disease and pests of vegetable crops in Canada: an illustrated compendium. 1994.
17

PATHOGEN: Lettuce Mosaic Virus

HOSTS: Lettuce (Lactuca sativa)

METHOD 1 Chenopodium (Kimble et al. 1975)

METHOD 2 ISHI Seed (van Ettekoven, 2000)
18

METHOD 1 Chenopodium (Kimble et al. 1975)

METHOD CLASS: STANDARD

PATHOGEN: Lettuce Mosaic Virus

SAMPLE: 30,000 seeds

PROCEDURE:

1. Grind sub-samples of 500 lettuce seeds (total sample 30,000 seeds) in 4ml 0.05M phosphate 

buffer pH 7.7, containing 0.1% thioglycolic acid.

2. Mechanically inoculate five Chenopodium quinoa seedlings with each extract (within 16 minutes of 

making the extract).

3. Observe indicator plants for symptoms 18-20 days after inoculation (chlorotic local lesions followed 

by systemic yellow vein-netting and leaf distortion).

REFERENCES:

Kimble KA, Grogan RG, Greathead AS, Paulus AO, House JK, 1975. Development, application, and 

comparison of methods for indexing lettuce seed for mosaic virus in California. Plant Disease Reporter: 

59(6):461-464.
19

METHOD 2 ISHI Seed (van Ettekoven, 2000)

METHOD CLASS: STANDARD

PATHOGEN: Lettuce Mosaic Virus

SAMPLE: 10,000 seeds

PROCEDURE:

Samples and buffers:

1. Count 20 x 500 seeds for each seed lot, at least 8 x 500 seeds of negative seed lot as negative 

control, and 2 x 500 seeds of a positive seed lot (contaminated leaf sample can be used as additional 

positive control).

2. Prepare the buffer solutions as follows:

PBS-Tween: 

Dissolve 8.0g NaC1, 1.0g KH2P04, 14.5 g Na2HPO4.* 12H2O, and 0.5ml Tween 20, in 

950ml dionized water, adjust pH to 7.2, and adjust volume to 1 liter.

Coating buffer: 

1.59g Na2CO3, 2.93g NaHCO3 in 1 liter dionized water, pH 9.6. 

Extraction buffer: 

Dissolve 20g of polyvinyl pyrrolidone PVP-l0, in 950 ml PBS-Tween, adjust to 1 liter.

Conjugate buffer: 

Dissolve 5.0 g of bovine serumalbumine (or ovalbumine) in 950 ml PBS-Tween, adjust to 1 

liter.

Coating of ELISA microplates:

1. Dilute LMV-antisera in coating buffer to appropriate working dilution.

2. Transfer 200μl of diluted antisera to each well.

3. Incubate microplate 3 hours at 370C, or overnight at 40C.

Extraction from seeds:

1. Grind seeds of each subsample in ca. 5ml extraction buffer using a power driven crusher

(Erich Pollahne type). Alternative extraction devices can be used.

2. Collect the complete seed extract in tube. Process extracts within 4 hours after crushing. Store 

extracts at 40C if not processed immediately.

3. Rinse rollers of crusher between each subsample with water to prevent cross-contamination 

between subsamples.

4. Wash thoroughly rollers between seed lots.
20

Seed extract incubation:

1. Remove coating buffer with diluted antisera from the plates.

Rinse microplate three times for 30 seconds with PBS-Tween, to reduce background.

2. Transfer 200μl of seed subsample extract in two wells for each seed lot, each positive and

negative subsamples as well. Several templates are in use.

3. Incubate microplates overnight at 4oC.

Incubation of conjugated LMV antiserum:

1. Remove seed extracts.

2. Rinse microplate three times 30 seconds with PBS-Tween, to reduce background.

3. Dilute conjugated LMV-antiserum in conjugate buffer to appropriate working dilution.

4. Transfer 200μl of diluted conjugated antiserum to each well.

5. Incubate microplate 3 hours at 37oC, or overnight at 4oC.

Incubation of substrate:

1. Dissolve 20mg of para-nitrophenylphosphate per 20ml of substrate buffer shortly before use.

2. Rinse microplate three times 30 seconds with PBS-Tween, to reduce background

3. Transfer 20μl of substrate buffer to each well of the microplate.

4. Incubate at room temperature in the dark. Measure optical density at 405nm after 30 minutes, 1 

hour, and longer if necessary. Verify always first whether positive and negative controls show 

appropriate reaction, otherwise the test should be repeated.

5. Use negative threshold to determine how many subsamples were infected with LMV.

6. Use Table 1 of ISHI-Veg Manual (2000) to determine the estimated LMV infection rate of the 

seed lot.

REFERENCES:

van Ettekoven, K. (editor). 2000. Seed Health Testing Methods Reference Manual. ISHI-Veg.

Falk BW, Purcifull DE. 1983. Development and application of an enzyme-linked immunosorbent assay 

(ELISA) test to index lettuce seeds for lettuce mosaic virus in Florida. Plant Disease: 67(4):413-416.
21

PATHOGEN: Xanthomonas campestris pv. 

vesicatoria

HOSTS: Pepper (Capsicum annuum), Tomato

(Lycopersicon esculentum)

METHOD 1 ISHI Seed wash for pepper and tomato (van 

Ettekoven, 2000) 
22

METHOD 1 ISHI Seed wash for pepper and tomato (van 

Ettekoven, 2000)

METHOD CLASS: TEMPORARY STANDARD

PATHOGEN: Xanthomonas campestris pv. vesicatoria 

SAMPLE: Minimum number of seeds to be tested is 2000 (protected 

cultivation in temperate conditions) or 30,000 (outdoor cropping in humid 

and warm conditions), which will detect with 95 % reliability seed 

contamination of 0.15 % and 0.01 % respectively.

PROCEDURE:

Sample preparation:

1. Put every subsample into a sterilized flask or other liquid-proof container.

2. Add 0.05M PBT to each flask at a ratio of 3:1 (v:w).

3. Incubate overnight (minimum 14 hrs) at 4oC.

Serial dilution:

1. Directly from the settled seed wash, serial dilute the supernatant to 10-1 by aseptically pipeting 1.0 

ml of the seed wash supernatant into 9ml of sterile 0.85% NaC1 in a sterile culture tube. Label the 

dilution with the appropriate sample number.

2. From the 10-1 dilution, dilute the supernatant to 10-2 by aseptically pipeting 1.0ml of 10-1 dilution into 

9ml of sterile 0.85% NaC1 in a sterile culture tube. Label the dilution with the appropriate sample 

number.

3. Vortex each tube to assure thorough mixing.

Liquid plating:

1. Pipette direct from each sample flask and from the 10-1 and 10-2 dilution, 100μl on two plates 

(duplicate plating) of two semi-selective media.

2. With a sterile glass rod spread the 100μl aliquot evenly over the semi-selective media.

3. Label the plates with the appropriate sample number and dilution factor (direct, 10-1, and 

10-2).

4. Inoculate plates from both media with a known culture of Xcv.

Incubation:

1. Incubate the plates in a dark incubator at 26-28oC.

Examination:

1. Evaluate the plates for suspect Xcv colonies at day 3, 5, and 7 days.

2. Compare them to the known descriptions of Xcv on the used selective media given below.
23

3. Record the number of suspect Xcv colonies and background.

4. Purify the suspect colonies by transferring suspect colonies to a general rich medium plates.

Additional confirmation tests as ELISA, PCR, IF, or biochemical tests are optional.

Xcv descriptions on semi-selective media:

Xcv on TMB:

1. Xcv colonies typically appear and can be identified in 4-7 days.

2. Xcv colonies are yellow, slightly mucoid, mounded and round (circular). 

3. Xcv utilizes Tween and in 3-7 days a white crystalline halo usually forms around the yellow 

colony. 

4. Some strains of Xcv form only a weak halo, clear halo, or only clear on the media under the 

colony (not visible). (NOTE: The white crystalline halo is due to calcium deposits in the clear 

halo caused by Tween utilization.)

Xcv on CKTM:

1. Xcv colonies typically appear and can be identified in 4-7 days.

2. Xcv colonies are similar to the colonies on TMB; yellow, mucoid, mounded and round 

(circular). In 3-7 days a white halo of fine calcium crystals usually forms around the yellow 

colony. Some strains of Xcv form only a weak halo, clear halo, or only clear the media under 

the colony (not visible).

Xcv on NA-Starch:

1. No information provided. Check appearance with known Xcv cultures.

Pathogenicity testing:

1. For best results pepper/tomato seedlings should be at 2-3 true leaves (approx. 3-4 week old 

seedlings).

2. Purify Xcv colonies (suspects) on a general medium suitable for rapid colony growth such as YDC. 

Purify a known Xcv colony for a positive control. Incubate the plates for 24 to 48 hours at 26 to 

28oC.

3. Transfer a mass of the colony aseptically to a culture tube with sterile distilled water.

4. Adjust the inoculum to 108 CFU per ml by visual means or with optical density methods (0.1 to 0.2 

o.d. at 600nm).

5. Infiltrate a leaf of a susceptible pepper/tomato cultivar with the suspension by gently forcing the 

liquid into the underside of the leaf using a sterile syringe without a needle and label the leaf with the 

appropriate sample identification number.

6. Infiltrate a leaf with the positive check and a blank water check (negative control)

7. Incubate the inoculated plants at 90-100% relative humidity and at 27 -32oC with approx. 12 hour 

light.

8. Observe the plants daily and record the day that the water-soaked lesion appears. Generally, 

pathogenic Xcv will develop a water-soaked lesion within 48-96 hours. Non-pathogenic bacteria 

will produce a hypersensitive reaction in about 24 hours, or will not develop a lesion.
24

MEDIA PREPARATION:

PBT:

0.05M Phosphate buffer

0.5% Tween 20

pH 7.2

mTMB:

H2O 990 ml

H3BO3 0.1 g

Bacto peptone 10.0 g

KBr 10.0 g

CaC12 0.25 g

Agar 15.0 g

After autoclaving filter sterilize the following adding to media just prior to pouring:

Tween 80 10.0 ml

Cephalexin 65 mg

5-fluorouracil 12 mg

Tobramycin 0.2 mg

Cycloheximide 200 mg

YDC:

H2O 1000 ml

Yeast extract 10.0 g

CaCO3 20.0 g

Bacto agar 15.0 g

Glucose 20.0 g

NA-Starch:

H2O 1000 ml

Difco nutrient agar 23.0 g

Soluble potato starch 12.0 g

After autoclaving filter sterilize the following adding to media just prior to pouring:

Penicilliun G 50 mg
25

CKTM:

H2O 990 ml

Soy peptone 2.0 g

Bacto typtone 2.0 g

Dextrose 1.0 g

L-glutamine 6.0 g

L-histidine 1.0 g

(NH4)2HPO4 0.8 g

MgSO4. * 7H2O 0.4 g

CaCl2 0.25 g

Pourite (optional) 1 drop

Difco bacto agar 15.0 g

After autoclaving sterilize the following adding to media just prior to pouring:

Tween 80 10 ml

Cephalexin 65 mg

5-fluorouracil 12 mg

Tobramycin 0.4 mg

Cycloheximide 100 mg

Bacitracin 100 mg

Neomycin sulfate 10 mg

REFERENCES:

van Ettekoven, K. (editor). 2000. Seed Health Testing Methods Reference Manual. ISHI-Veg.
26

FIELD CROPS
27

PATHOGEN: Clavibacter michiganensis subsp. 

nebraskensis

HOSTS: Maize (Zea mays)

METHOD 1 sCNS Culture Plate Method (Shepherd, 1999)
28

METHOD 1 sCNS Culture Plate Method (Shepherd, 1999)

METHOD CLASS: STANDARD

PATHOGEN: Clavibacter michiganensis subsp. nebraskensis

SAMPLE: 400 seeds

PROCEDURE:

1. Divide a representative sample of 400 corn seeds into 4 sub-lots of 100.

2. Surface sterilize seeds with 0.5% NaOCl for 3 minutes. Rinse thoroughly with sterile water.

3. Grind each sub-sample until finely pulverized and add to 100ml phosphate buffer saline solution 

(seeds may be ground dry or soaked overnight at 6oC before grinding).

4. Shake sub-samples at room temperature for 1 hour.

5. Prepare a dilution series comprising the original suspension and two 10-fold dilutions. 

6. Plate each of the three dilutions onto sCNS in triplicate.

7. Incubate at 28°C for 5 to 7 days.

8. Any orange colonies that appear in 1 to 3 days should be disregarded. 

9. Round and peach colored colonies (Figure 1) that appear after 3 days and by 9 days are 

putative colonies of C. michiganensis subsp. nebraskensis (Cmn). 

10. Cmn can be confirmation by plant injections of culture suspensions into seedlings of Goss’ wilt 

susceptible corn varieties (such as A632). Seedlings are then examined for typical Goss’ wilt 

symptoms on leaves.

11. Alternatively, Cmn can be confirmed by CORYNE strip tests, performed according to 

manufacturer’s (bioMeriux-Vitek Inc., Hazelwood, MO) directions on colonies plated on TSA 

agar. The positive code for Cmn is 6550004 or 6150004.

MEDIA PREPARATION:

sCNS:

Distilled water 1 liter

Nutrient broth 8.0g

Yeast extract 2.0g

K2HPO4 2.0g

KH2PO4 0.5g

Dextrose 5.0g

MgSO4* 7H2O 0.25

Agar 15g

Bravo 720 (Chlorothalonil) 0.2ml diluted 1:50 in water

Mertect 340F (Thiabendazole) 50μl (1 drop)

Potassium dichromate 0.02g
29

After autoclaving filter sterilize the following adding to media just prior to pouring:

Naladixic acid 40mg

Cycloheximide 100mg

REFERENCES:

Shepherd, LM. 1999. Detection and transmission of Clavibacter michiganesis subsp. nebraskensis

of corn. Ms Thesis, Iowa State University, Ames, IA.
30

PATHOGEN: Pantoea stewartii (syn. Erwinia

stewartii)

HOSTS: Maize (Zea mays)

METHOD 1 ELISA (Enzyme-linked immunosorbent assay)

(Lamka et al, 1991)
31

METHOD 1 ELISA (Enzyme-linked immunosorbent assay)

(Lamka et al, 1991)

METHOD CLASS: STANDARD

PATHOGEN: Pantoea stewartii (syn. Erwinia stewartii)

SAMPLE: 400 seeds

PROCEDURE:

Diagnostic kit: 

This method uses an ELISA kit developed by Agdia, Elkhart, Indiana. The monoclonal antiserum used 

in the kit was made at Iowa State University as described (Lamka et al, 1991).

Extraction of the bacterium:

1. Place 4 replicates of 100 corn kernels, per sample, into 100ml of General Extraction Buffer and 

soak overnight at room temperature.

2. Grind seeds to fine particles. 

3. Disinfect the grinder between replicates and samples by rinsing with distilled water, followed by a 

rinse with a laboratory or hospital standard detergent, then a final rinse with distilled water.

Preparation of Buffers:

PBS-Tween Buffer/Wash

1. Empty contents of the PBS-Tween satchel into 1 liter container. Add distilled water to make 

one liter PBS-Tween (buffer/wash).

2. To make from scratch, dissolve the following in 1 liter distilled water: 8.0g sodium chloride, 

1.15g sodium phosphate (dibasic), 0.2g potassium phosphate (monobasic), 0.2g potassium 

chloride, and 0.5g Tween 20.

General Extraction Buffer

1. Add dry Extraction Buffer provided to 1 liter distilled water provided.

2. Mix the buffer powder with a small amount of distilled water to make a slurry, then gradually 

add more distilled water to the final volume. 

3. Add 20ml Tween 20 per liter of Extraction Buffer and mix well.

4. Store at 4°C.

5. To make from scratch, dissolve the following in 900ml PBS-Tween buffer: 1.3g sodium sulfite, 

2.0g powdered chicken albumin, 20g polyvinylpyrrolidone, 20g Tween 20. 

Preparation of Pantoea stewartii controls:

Add 2ml of the General Extraction Buffer to each of the provided control vials, positive (+) ES and 

negative (-) ES, and mix well. 
32

Loading ELISA plates:

1. Add 100μl of the sample filtrate, of each replicate, to one well on a pre-coated ELISA plate for P. 

stewartii. Change micropipette tips between each replicate.

2. Add 100μl of positive (+) ES and negative (-) ES to control wells.

3. Incubate for 2 hours at room temperature or overnight at 4oC in a humid container.

4. Wash the plates approximately 6 times with PBS-Tween. Tap plate gently after final rinse to 

remove remaining wash buffer.

Addition of enzyme conjugate:

1. Dispense 100μl of prepared enzyme conjugate (as prepared below) into each well and into two 

blank control wells.

2. Add enzyme conjugates A and B at the dilution of 1:100.

3. Incubate for 2 hours at room temperature or overnight at 4oC in a humid container.

4. Wash 6 times with PBS-Tween.

Preparation of enzyme conjugate

To make enzyme conjugate diluent, mix 4 parts of PBS-Tween to 1 part MRS component.

Note: The volume of enzyme conjugate prepared is dependent on the number of test wells that are 

being used. On the basis of 100μl needed for each test well, a helpful way of estimating the amount 

of diluent needed is to prepare 1ml for each 8-well column of test wells. 

Addition of substrate:

1. Dispense 100μl of substrate per well.

2. Incubate for 20 minutes at room temperature in the dark, or until the positive control is showing 

significant color.

3. Add 50μl (one drop) 3M sulfuric acid to stop the color reaction.

Substrate preparation

1. Add 1 OPD stick to 10ml of OPD buffer solution. The paper end of the stick is submerged 

into room temperature OPD buffer solution for 2 min.

2. Swirl the stick slightly before removing from the solution. Always prepare OPD buffer solution 

immediately before use.

Evaluating ELISA plates:

Evaluate visually, or measure on an ELISA plate reader at 490nm. The threshold for a positive reaction 

on the plate reader should be >2X that of the negative control.
33

REFERENCES:

Lamka GL, Hill JH, McGee DC and Braun EJ. 1991. Development of an immunosorbent assay for 

seed-borne Erwinia stewartii. Phytopathology 81:839-846.
34

PATHOGEN: Cercospora kikuchii

HOSTS: Soybean (Glycine max)

METHOD 1 Culture Plate (Jordan et al., 1986)

METHOD 2 Culture Plate (McGee and Nyvall, 1984)
35

METHOD 1 Culture Plate (Jordan et al., 1986)

METHOD CLASS: STANDARD

PATHOGEN: Cercospora kikuchii

SAMPLE: 400 seeds

PROCEDURE:

1. Surface sterilize seeds in 0.5% NaOCl for 4 minutes; wash in distilled water.

2. Plate on potato dextrose agar.

3. Incubate at 25°C in the dark for 10 days.

REFERENCES:

Jordan EG, Manandhar JB, Thapliyal PN, Sinclair JB, 1986. Factors affecting soybean seed quality in 

Illinois. Plant Disease. 70(3):246-248.
36

METHOD 2 Culture Plate (McGee and Nyvall, 1984)

METHOD CLASS: STANDARD

PATHOGEN: Cercospora kikuchii

SAMPLE: 400 seeds

PROCEDURE:

1. Seeds are surface sterilized in 1% NaOCl for 30 seconds and then rinsed in sterile water.

2. Incubate on a moistened blotter at 25°C for 10 days under continuous light.

3. Seeds are evaluated for the presence of Cercospora kikuchii as indicated by purple staining on the 

seed coat under fungal growth. 

REFERENCES:

McGee DC, Brandt CL, Burris JS, 1980. Seed mycoflora of soybeans relative to fungal interactions, 

seedling emergence, and carry over of pathogens to subsequent crops. Phytopathology. 70(7):615-617.

McGee DC, Nyvall RF, 1984. Soybean seed health. Coop. Ext. Serv. Iowa State University, Pm-990.
37

PATHOGEN: Phomopsis/Diaporthe complex

HOSTS: Soybean (Glycine max)

METHOD 1 Culture plate (McGee, 1986)

METHOD 2 Blotter (McGee and Nyvall, 1984)
38

METHOD 1 Culture plate (McGee, 1986)

METHOD CLASS: STANDARD

PATHOGEN: Phomopsis/Diaporthe complex

SAMPLE: 400 seeds

PROCEDURE:

1. Seed are surface sterilized in 0.5% NaOCl for 1 minute and then rinsed in sterile water. 

2. Plate seeds on potato dextrose agar (PDA) adjusted to pH 4.5.

3. Seeds incubation at 25°C for 7 days under continuous light.

4. Seeds are evaluated for presence of the three fungi associated with the Phomopsis/Diaporthe

complex in soybeans according to the following descriptions. 

Note: There is considerable controversy regarding the taxonomy of this group. These descriptions 

should, therefore only be used to identify the Diaporthe/Phomopsis complex and not the individual 

pathogens.

Phomopsis longicolla, previously known as Phomopsis sp. are floccose, dense and white, with 

occasional greenish yellow areas on PDA. In reverse, colonies are colorless, with black, spreading 

stromata. Pycnidia are black, stromatic, solitary or aggregated, unilocular or multilocular, with prominent 

necks more than 200μm long. Alpha conidia are hyaline, ellipsoid to fusiform, guttulate, and measure 5-

9 x 1.5-3.5μm. Beta conidia, which are rarely formed, are hyaline, filiform, and hamate. No perithecia 

are formed on PDA.

Diaporthe phaseolorum var. caulivora cultures on PDA are white, closely appressed, with tufted 

aerial mycelium. In reverse, colonies are colorless, with black circular stromata, less than 2mm in 

diameter. Perithecia are black and globose, measuring 165-340 x 282-412μm, and have a long 

protruding beak. Asci measure 30-40 x 4-7μm. Ascospores are hyaline, elongate-ellipsoidal, twocelled, slightly constricted at the septum, biguttulate in each cell, and measure 8-12 x 3-4μm. Pycnidia 

rarely occur on PDA. 

Diaporthe phaseolorum var. meridionales cultures on PDA are white even colonies with brown 

chlamydospores. Stromata are irregular in shape (2-10mm long). Perithecia are similar in to those of 

D. phaseolorum var. caulivora, but they have wider neck width, i.e. 100 compared to 55μm.

Diaporthe phaseolorum var. sojae cultures on PDA are floccose and rope-like, turning tan to brown 

with age. In reverse, the colonies are tan to dark brown with black, pulvinate stromata. Pycnidia are 

black, stromatic, solitary or aggregated, and usually unilocular, with no beak, or a beak less than 200μm 

long. Alpha conidia are hyaline, usually fusiform, guttulate, and measure 5.5-10.5 x 1.3-3.5μm. Beta 

conidia, which are more commonly produced, are hyaline, filiform, and hamate. Perithecia are nearly 

spherical and measure 148-282 x 185-346μm. They have long, tapered beaks, measuring 60-100 x 
39

60-150μm, and usually are solitary, not clustered. Asci are elongate and clavate, measuring 35-51 x 

3.3-10μm. Ascospores are similar in shape to alpha conidia, but are larger, 9-13 x 2-6μm, and 

bicellular. They are biguttulate in both cells.

REFERENCES:

McGee DC, 1986. Prediction of Phomopsis seed decay by measuring soybean pod infection. Plant 

Disease 70:329-333.
40

METHOD 2 Blotter (McGee and Nyvall, 1984)

METHOD CLASS: STANDARD

PATHOGEN: Phomopsis/Diaporthe complex

SAMPLE: 400 seeds

PROCEDURE:

1. Two sterilized blotters are placed in plastic boxes. 

2. Moisten blotters with 80ml of sterile water, containing 40mg of 2,6 dichloro-6-nitroaniline (Botran 

75W).

3. Four sets of 100 seeds are surface sterilized in 1% NaOCl for 30 seconds and then rinsed in sterile 

water.

4. Seeds are incubated at 25°C for 10 days under continuous light.

5. Seeds are evaluated for the presence of fungi in the Phomopsis/Diaporthe complex characteristic 

dense, white fungal growth.

REFERENCES:

McGee DC, Brandt CL, Burris JS, 1980. Seed mycoflora of soybeans relative to fungal interactions, 

seedling emergence, and carry over of pathogens to subsequent crops. Phytopathology. 70(7):615-617.

McGee DC, Nyvall RF, 1984. Soybean seed health. Coop. Ext. Serv. Iowa State Univ, Pm-990.
41

PATHOGEN: Sclerotinia sclerotiorum 

HOSTS: Soybeans (Glycine max)

METHOD 1 Culture plate (Totir, 2000)
42

METHOD 1 Culture plate (Totir, 2000)

METHOD CLASS: STANDARD

PATHOGEN: Sclerotinia sclerotiorum

SAMPLE: 400 seeds

PROCEDURE:

1. Four sub-samples of 100 seeds are surface sterilized in 1.75% NaOCl for 30 seconds. 

2. Seeds are rinsed three times in sterile water.

3. Incubate seeds on potato dextrose agar for 10 days at 25oC (5 seeds/plate)

4. Seeds with characteristic white mycelium of Sclerotinia sclerotiorum are marked after 3, 5, and 7 

days to account for overgrowth of colonies compromising the final count. 

5. A final count is made of seeds with characteristic white mycelium and/or large black sclerotia, at 10 

days. 

REFERENCES:

Totir, C. 2000. Seed transmission and control of Sclerotinia sclerotiorum in soybean seeds. Ms. 

Thesis, Iowa State University, Ames, IA.
43

SECTION 2

PHYTOSANITARY FIELD 

INSPECTION METHODS
44

Criteria for Phytosanitary Field Inspection Methods Approved for the 

National Seed Health System (NSHS)

Phytosanitary field inspection procedures described in this manual were developed by a sub-committee 

of the NSHS-STWG, representing USDA-APHIS, the National Plant Board, and the Association of 

Official Seed Certification Agencies. The procedures are designed to meet fundamental standards of 

quality but to be flexible enough to accommodate commonly-used practices. 

Field diagnostic aids are developed by plant pathologists with expertise in symptomatology of diseases 

in each crop. 
45

PHYTOSANITARY INSPECTION PROCEDURES

EQUIPMENT REQUIREMENTS

1. Field maps

2. 10x hand lens

3. Pocket knife/scissors

4. Tape measure

5. Sampling bags or envelopes (paper)

6. Labels

7. Ice chest

8. Hand counter

9. Diagnostic illustrations

10. Report forms

FIELD INSPECTION STRATEGY

Field overview

Find a point near the field that allows the best opportunity to look the field over. This overview enables: 

a. Verification that the field is correct by comparison between the map or information provided and 

the observed field.

b. Identification of special areas or micro-climates in the field that appear different enough to warrant 

special attention when inspected. These would include:

Locations in which high moisture levels may be retained such as proximity to: 

Rivers and streams

Drainage areas

Low spots

Weedy areas

Areas of the field affected by borders, such as: 

Field edges

Tree lines in the field

Adjacent fields of a similar crop

Presence of buildings or bins

Drought stress areas, such as:

High spots

Light textured soils

Margins or overhead irrigation areas
46

Establish the seed field inspection pattern

1. The seed field inspection pattern should ensure that all parts of the field are adequately and 

proportionately represented in the plants inspected within the various usual micro-climates of the field.

2. As long as these requirements are met, the pattern of field inspection can vary. 

3. Examples of established inspection patterns are as follows. Other formats may, however, be 

acceptable.

Stagger “X” pattern. (CDFA Phytosanitary Certification Manual, 1985)

This is used for cereal crops and requires examination of plants along one side of the field, then 

diagonally in a stagger pattern across rows to the far corner, across the far side, and diagonally back to 

starting corner (Figure 1). Additional examinations may be necessary for field environments not covered 

by the inspection pattern. 

Equidistant passes pattern. (CDFA Phytosanitary Certification Manual, 1985)

This system is used for crops other than cereals. Table 1 lists the minimum number of field passes 

(Figure 2) in relation to field size to give a minimum of 95% confidence level in detecting an infection 

level of 0.1%. 

Table 1. Minimum field passes per acre.

Field size (acres) Minimum # passes

0 - 1 6

1 - 5 9

5 - 10 11

10 - 20 13

20 - 50 17

50 - 100 20

100 - 200 24

200 - 500 30

500 – 1000 36

1000 + 42
47

Figure 1 “X” Field Inspection Pattern
48

10 feet

10 feet

Start

Finish

Figure 2 - Equidistant Pass Pattern
49

Customized field inspection pattern.

This system allocates appropriate numbers of plants to be inspected in the various environments in a 

field. An example is shown in Figure 3. 

Disease Diagnosis in the Field

1. The presence or absence of diseases relevant to the inspection requirements is first determined by 

visual examination of plants in the field. Descriptions of signs and symptoms are provided in this manual 

for the individual diseases of the major seed crops. Other established aids to identification may also be 

used.

2. Inspections have to be made at crop growth stage when signs or symptoms of a disease are evident. 

Appropriate inspection times for particular pests or diseases are indicated in this manual. 

3. An appropriate number of plant samples, representative of diseases in the field, should be taken for 

laboratory confirmation of the visual diagnosis. More extensive sampling should be carried out when 

visual symptoms are insufficient to ensure to accurate diagnosis. Samples of suspected disease tissue 

should be kept flat in paper envelopes or towels in a plastic bag in ice chest. All samples should be 

correctly labeled to indicate date, time, locations, crop, and plant part. 

Disease Diagnosis in the Laboratory

1. Samples should be processed systematically in a laboratory facility with demonstrated proficiency in 

diagnosing plant diseases. 

2. Information on diagnostic tests for particular diseases is provided in this manual. 

Reports

Inspection reports should be made on a standard form that is indicated below.
50

Figure 3 - Example of field inspection by customized pattern
51

PHYTOSANITARY GROWING SEASON INSPECTION REPORT

Crop _______________________________________

___________________________________

Accredited Entity

PLEASE PRINT

_______________________________________________________________ ___________________________

Company Name Variety

_______________________________________________________________ ___________________________

Company Contact Official Field # Acres

_______________________________________________________________

Address TYPE OF FIELD:

 Increase/Production

_______________________________________________________________

Telephone Number

_______________________________________________________________ ___________________________

Contract Grower Phone County

Growth Stage & Date: _____________________ ___________________________ 

________________________

 1

st Insp. 2nd Insp. 3rd Insp. 

INSPECTION DATA

(Refer to list of plant diseases/pests on separate pages)

 Severity Lab Sample Lab Confirmation

Code (Optional ) Submitted Field Diagnosis Additional Lab

Low, Moderate, High Confirmed Pathogens Identified Sample

 L, M, H Yes No Yes/No Code Number

____ ___________________ [ ] [ ] [ ] _________

_____________ 

____ ___________________ [ ] [ ] [ ] _________ _____________

____ ___________________ [ ] [ ] [ ] _________ _____________

____ ___________________ [ ] [ ] [ ] _________ _____________

____ ___________________ [ ] [ ] [ ] _________ _____________

____ ___________________ [ ] [ ] [ ] _________ _____________

____ ___________________ [ ] [ ] [ ] _________ _____________

____ ___________________ [ ] [ ] [ ] _________ _____________

 No Other Diseases Noted.

I inspected these fields during active growth and determined the above diseases/pests were found as indicated.

Remarks

INSPECTOR_______________________________________________ID 

NUMBER:____________________DATE:__________

LAB MANAGER_(If sample submitted)________________________ID 

NUMBER:____________________DATE:___________
52
53

DIAGNOSTIC AIDS
54

Pantoea stewartii (syn. Erwinia stewartii)

Time of inspection:

Corn plants in early flowering stage

Field symptoms:

Leaf: Leaves show linear, pale-green to yellow streaks with irregular or wavy margins that run parallel 

to veins and may extend the length of the leaf (Figure 1). These streaks soon become dry and brown. 

Masses of bacteria may also stream from the cut edges of infected leaf tissue. When diseased tissue was 

placed near the edge of a water drop, the drop quickly became cloudy.

Stalk: Conducting vessels become plugged with bright-yellow slime. If infected stems are cut in cross 

section, the yellow slime will often exude. Cavities form in the stalk near the soil line in severely infected 

plants.

Whole plant: Plants infected early in the season may show wilting and stunting (Figure 2).

Indicators of disease presence: 

The corn flea beetle, Chaetocnema pulicaria, is generally recognized as the most important carrier of 

inoculum for E. stewartii in the USA (Pepper, 1967). The pathogen overwinters in the alimentary tract 

of this insect, which emerges from hibernation and feeds on young maize. The occurrence of substantial 

numbers of the corn flea beetle at the beginning of the growing season (Figure 3) and subsequent 

feeding scars of this insect on leaves of the growing corn plant are strong indictors of infection by E. 

stewartii. 

In the US Corn Belt, survival of the corn flea beetle is greatly reduced by low winter temperatures. 

Severity of Stewart’s wilt can be forecast on the basis of the average temperatures during December, 

January, and February.

Laboratory diagnosis:

Leaf sections with suspect Stewart’s wilt lesions may be cut across veins and observed under the 

microscope for bacterial streaming from the vascular tissue. 

Suspect colonies of E. stewartii on culture medium can be tested for pathogenicity on susceptible 

seedlings.

The presence of the E. stewartii in plant tissue can also be detected with an ELISA test kit (Agdia. 

Elkhart, Indiana). This kit is adapted from the method of Lamka et al, 1991). The method, described in 

Method 2.1 in Section 1 of this manual for detection of seedborne E. stewartii, can also be used to 

detect the pathogen in leaf or stalk tissue and in insects. 
55

References:

Lamka GL, Hill JH, McGee DC, and Braun, EJ. 1991. Development of an immunosorbent assay for 

seed-borne Erwinia stewartii. Phytopathology 81:839-846.

Pepper EH, 1967. Stewart's Bacterial Wilt of Corn. Monogr. 4. St. Paul, Minnesota, USA: American 

Phytopathological Society.
56

Alternaria dauci

Time of inspection:

Buds on carrot plants are just beginning to flower and tops still green

Field symptoms:

Leaf: Lesions produced on leaf and petiole tissues are generally dark-brown to black, and chlorosis of 

surrounding tissues is observed. Gradually, the spots increase in size and become confluent. Finally, the 

whole leaf becomes grayish-black, while the leaflets become curly and convolute. The older leaves are 

more heavily infected than the young ones (Figure 2).

Stalk: The stem bark is discolored.

Root: Root lesions are irregular in shape, dark-brown to black. The decay is dark-brown to black, firm 

and shallow.

Floral structures: Alternaria dauci causes dark, longitudinal spots on flower-stalks and umbels, and 

attacks flowers and immature seeds, causing them to be discolored (Figures 3 & 4).

Whole plant:

When infection is severe, the top part of the may be killed (Figure 1).

Indicators of disease presence:

The pathogen requires the presence of moisture for infection. Heavy dews and rains are favorable for 

this process. The optimum temperature for infection is 82oF.

Laboratory diagnosis:

For lesions on plant parts, incubation in a moist chamber on blotters at 20-25°C or on agar media will 

lead to the production of conidiophores and conidia for final identification (Figures 5 & 6). The methods 

of isolation of A. dauci from diseased carrot leaves, seedlings and seeds and the ways to achieve 

abundant sporulation are described in detail by Strandberg (1987).

References:

Strandberg JO. 1987. Isolation, storage, and, inoculum production methods for Alternaria dauci. 

Phytopathology. 77(7):1008-1012.