PAV – collection of plant pathogen microorganisms: fungi ... · EPPO- Q collection Rome 2015. The PAV-collection of phytopathogenic microorganisms includes fungi, oomycetes, bacteria,

PAV – collection of plant pathogen microorganisms:fungi, oomyctes, bacteria, viruses, and viroids

Council for Agricultural Research and Economics - Plant Pathology Research Center of Rome, Italy

EPPO- Q collection Rome 2015


Before talking about the PAV-collection of living microorganisms just few words on the historical scientific roots of our Institute which harbors several Herbaria:The most famous is:the Herbarium of fungi of citrus of Otto Penzig a famous German mycologist

Herbarium Mycologicum RomanicumMycotheca Italica (of Saccardo)

Herbarium Crittogamico Italiano (of Anzi, Arcangeli, Carestia, Passerini, Spegazzini)

Herbarium of parasitic fungi of cultivated plants (of Cavara, Briosi, Pollacci).

Herbaria


The PAV-collection of phytopathogenic microorganisms includes fungi, oomycetes, bacteria, viruses and viroids

It is a working collection and the microorganisms or infective entities here preserved derived from research or diagnostic activities

A group of core isolates have been included in a national collection project named COLMIA

Consultable on the web at:

www.colmia.it

This National project included 11 working units each with its in-situcollection of microorganisms associated with agricultural research fields (soil, diseases, entomopathogenic activity) or transformation processes (wine, cheese, table-olives)

http://www.colmia.it/


Specimens listed in COLMIA are just few among hundreds of single-cell strains conserved in PAV

Most of them are characterized and subjected to phylogenetic and molecular studies

Table 1. List of main species or genera of the plant pathogen microorganisms or infective entities included in COLMIA (www.COLMIA.it) Microorganism or entity

N. of strains

Fungi 251 Alternaria spp. 7 Ascochyta rabiei 19 Bipolaris spp. (Of which 14 Bipolaris oryzae) 16 Drechslera teres 12 Drechslera graminea 23 Fusarium spp. 51 Fusarium lateritium 54 Marssonina juglandis 5 Monilia spp. 13 Monilia fructicola quarantine organism 6 Neotyphodium spp. 14 Phomopsis 4 Pyrenochaeta lycopersici 22 Tubakia dryina 5 Oomycetes 11 Phytophthora cactorum 1 Phytophthora cinnamomi 4 Phytophthora hedraiandra 2 Phytophthora megasperma 1 Phytophthora niederhauserii 3 Bacteria 62 Brenneria nigrifluens 4 Erwinia carotovora 5 Pseudomonas avellanae 10 Pseudomonas syringae 11 Xanhomonas arboricola 16 Xanthomonas campestris 6 Virus and viroids 35 Apple scar skin viroid 1 Hop stunt viroid 2 Peach latent mosaic viroid 3 Pear blister canker viroid 1 Beet pseudo yellow virus 1 Caper latent virus 2 Cucumber mosaic virus 1 Cucurbit aphid-borne yellows virus 2 Plum pox virus quarantine organism 23

Table 1. List of main species or genera of the plant pathogen microorganisms or infective entities included in COLMIA (www.COLMIA.it)

Microorganism or entity

N. of strains

Fungi

251

Alternaria spp.

7

Ascochyta rabiei

19

Bipolaris spp. (Of which 14 Bipolaris oryzae)

16

Drechslera teres

12

Drechslera graminea

23

Fusarium spp.

51

Fusarium lateritium

54

Marssonina juglandis

5

Monilia spp.

13

Monilia fructicola quarantine organism

6

Neotyphodium spp.

14

Phomopsis

4

Pyrenochaeta lycopersici

22

Tubakia dryina

5

Oomycetes

11

Phytophthora cactorum

1

Phytophthora cinnamomi

4

Phytophthora hedraiandra

2

Phytophthora megasperma

1

Phytophthora niederhauserii

3

Bacteria

62

Brenneria nigrifluens

4

Erwinia carotovora

5

Pseudomonas avellanae

10

Pseudomonas syringae

11

Xanhomonas arboricola

16

Xanthomonas campestris

6

Virus and viroids

35

Apple scar skin viroid

1

Hop stunt viroid

2

Peach latent mosaic viroid

3

Pear blister canker viroid

1

Beet pseudo yellow virus

1

Caper latent virus

2

Cucumber mosaic virus

1

Cucurbit aphid-borne yellows virus

2

Plum pox virus quarantine organism

23


In our Institute are stored approximately:2500 Fungi130 Phytophthoras860 Bacteria300 Virus & viroids


One of the purpose of a collection is to preserve biodiversity. In PAV-collection are maintained isolates of the same pathogenic species for preserving the variability within the population in terms of virulence, metabolite/toxin production, pesticide resistance, etc.

We have numerous strains that are used as reference in pathogenic tests

I will be giving some examples about fungi, bacteria, and viruses showing the information provided on the web site catalogue of COLMIA


Fungi


Bacteria


Viruses


Alternaria alternata complex or “small-spored catenulate A. alternata species groups pathogenic on nuts (walnut & hazelnut)

NGN

A. alternata complex strains

A. alternata A. tenuissima A. arborescensBAN

AFLP, ISSR, H4 polyphasic classification

Hong S. G., Maccaroni M., Figuli P. J., Pryor B. M., Belisario A., 2006. Polyphasic classification of Alternaria spp. isolated from hazelnut and walnut in Europe. Mycological Research, 110: 1290-1300.

A. infectoriaA. alternataalter ISPaVe1769 alter ISPaVe1796 alter ISPaVe1781 tenui ISPaVe1792 tenui ISPaVe1770 tenui ISPaVe1783 tenui ISPaVe1788 tenui ISPaVe1789 tenui ISPaVe1790 tenui ISPaVe1798 tenui ISPaVe1786 tenui ISPaVe1773 alter ISPaVe1779 A. tenuissimaalter ISPaVe1782 A. arborescensarbor ISPaVe1793 arbor ISPaVe1768 arbor ISPaVe1778 arbor ISPaVe1771 arbor ISPaVe1772 arbor ISPaVe1794 arbor ISPaVe1780 arbor ISPaVe1791 arbor ISPaVe1784 arbor ISPaVe1787 arbor ISPaVe1776 arbor ISPaVe1774 arbor ISPaVe1722 arbor ISPaVe1795 arbor ISPaVe1797 arbor ISPaVe1775

Coefficient0.00 0.25 0.50 0.75 1.00

Hong et al., Mycological Research

A. infectoriaA. alternataalter ISPaVe1769 alter ISPaVe1796 alter ISPaVe1781 tenui ISPaVe1792 tenui ISPaVe1770 tenui ISPaVe1783 tenui ISPaVe1788 tenui ISPaVe1789 tenui ISPaVe1790 tenui ISPaVe1798 tenui ISPaVe1786 tenui ISPaVe1773 alter ISPaVe1779 A. tenuissimaalter ISPaVe1782 A. arborescensarbor ISPaVe1793 arbor ISPaVe1768 arbor ISPaVe1778 arbor ISPaVe1771 arbor ISPaVe1772 arbor ISPaVe1794 arbor ISPaVe1780 arbor ISPaVe1791 arbor ISPaVe1784 arbor ISPaVe1787 arbor ISPaVe1776 arbor ISPaVe1774 arbor ISPaVe1722 arbor ISPaVe1795 arbor ISPaVe1797 arbor ISPaVe1775

Coefficient0.00 0.25 0.50 0.75 1.00

Hong et al., Mycological Research


TEF-1α

RAPDForty (40) strains of Fusarium oxysporum f. sp. melonis (FOM) characterized by race, RAPD profile and phylogeny to distinguish the 4 races by UPGMA with the Neighbor-joining analysis

Luongo L., Ferrarini A., Haegi A., Vitale S., Polverari A., Belisario A., 2015. Genetic Diversity and Pathogenicity of Fusarium oxysporum f. sp. melonis Races from different areas of Italy. Journal of Phytopathology, 163: 73–83. doi: 10.1111/jph.12280. ISSN: 1439-0434.


Neighbor-joining analysis of Simple

Sequence Repeats (SSR) of 315 Italian

Fusarium fujikuroi isolates

Valente M.T., Infantino A., Desiderio F., Aragona M., 2013 Analysis of Fusarium fujikuroi genetic structure by SSR markers. Proceedings of the 12th European Conference on fungal genetics, Seville, March 23-27, 2014, Poster 414, page 277


SA

12_T

2SA

15_T

2SA

11_T

2

83

SA19

_T2

SA23

_T2

SA13

_T2

61

SA24

_T2

63

SA9_

T2SA

10_T

2

99

SA25

_T2

SA26

_T2

98

SA20

_T2

SA14

_T2

I19_

T2SA

1_T2

SA2_

T2

75

SA3_

T2SA

4_T2

76

I16_T

2

I4_T2

I5_T2

I20_T

2

I1_T2

I6_T2

I10_T2

70 I11_T2

I13_T259

RB16_T

2

RB17_T2

95RB13

_T2

RB1_T2

RB2_T2

RB3_T2RB4_T2RB5_T2RB6_T2RB7_T2RB8_T2RB9_T2RB10_T2RB11_T2RB12_T2

61

51

RB15_T2RA16_T2RA17_T2RA15_T2RA14_T2

99

RA1_T2RA10_T2RA11_T2

RA12_T2RA9_T2

RA8_T2RA2_T2

RA3_T2

RA4_T2

RA6_T2

RA7_T2

RA13_T2

52

87

76

R3-18_T2

Is1361_T1

Is1447_T1

Is1448_T1

Is1362_T1

Is1363_T1

71Is1347_T1

Is1360_T1

Is1364_T1

Is1346_T1

Is1384_T1Is1449_T1Is1385_T1Is1446_T1Is1444_T1Is1445_T1

52SD

7_T2

SD8_

T2SD

9_T2

SD14

_T2

SD15

_T2

SD10

_T2

SD13

_T2

SD21

_T2

SD24

_T2

SD25

_T2

SD6_

T2

SD12

_T2

SD1_

T2

SD2_

T255

SD4_

T2

R3-20

_T2

R3-11

_T2

R3-14

_T1

R3-5_

T2R3

-6_T2

R3-2_

T2R3

-9_T2R3-

3_T2

R3-12_

T2 52R3-1_T

2R3-1

3_T2 59R3-1

6_T2R3-7_T2R

3-8_T2R3-15_

T1SB2_T1P

11_T2R3-10_T2R3-17_T2 63

SD3_T1SD5_T1

57

SD11_T1

88

RB14_T1I18_T1

RA18_T1

SB10_T1

SB17_T1

SB16_T1

SB4_T1

SB9_T1

84

SB15_T1

SB8_T1

SB7_T1

SB13_T1

5469

SA8_T1

I14_T1

P16_T1

P17_T1

89

P10_T1SB3_T1

P12_T1P13_T1

93

P4_T1P3_T1

P15_T1P9_T1

P7_T1P8_T1

P14_T165

81

0

2

4

6

8

10

Evolutionary relationships of 139 Pyrenochaeta lycopersiciisolates inferred using the Neighbor-joining method after AFLP analyses

Infantino A., Pucci N., Aragona M., De Felice S., Rau D. Genetic structure of Italian populations of Pyrenochaeta lycopersici causal agent of corky root rot of tomato. Plant Pathology 64, 941–950

AFLP analysis of Xanthomonas arboricola pv. juglandis pathogenic on walnut

(104 strains in PAV-collection)

Loreti S., Gallelli A., Belisario A., Wajnberg E. and Corazza L., 2001. Investigation of genomic variability of Xanthomonas arboricola pv. juglandis by AFLP analysis. European Journal of Plant Pathology, 107, 583-591


Gene-sequence analysis of genes involved in plant - pathogen interaction for developing a diagnostic method ofPseudomonas syringae pv. actinidiae (241 strains in PAV-collection)

Gallelli A., L’Aurora A. and Loreti S. , 2011. Gene sequence analysis for the molecular detection of Pseudomonas syringae pv. actinidiae: developing diagnostic protocols. Journal of Plant Pathology 93 (2): 425-435


More than 300 isolates of 70 viruses, viroids and phytoplasmas are collected in our Institute since the 90’s

These species are pathogens of the major agricultural crops: vegetables, fruit trees, grapevine

PAV viruses, viroids and phytoplasmas collection


Plum Pox Virus: M, D, EA, Rec, C strains

Peach Latent Mosaic Viroid: severe, mild and calico isolates

Flavescence Dorée: C and D isolates

Potato Spindle Tuber Viroid: tomato, Solanum jasminoides, Cestrum spp. isolates

Potato Virus Y: O, N, NTN, W strains

Viral pathogens of particular interest



Strains are preserved following several methods suitable to the type of organism

For fungi:

Tubes with agarized medium (slants)Mineral oilWaterLiquid nitrogenFilter paper

For bacteria:

Maintenance at -80°C in glycerolFreeze-drying


For phytoplasmas:

DNA extract maintained at -80°C Plant tissue freeze-drying

For viruses and viroids:

RNA/DNA extract maintained at -80°CPlant tissue freeze-dryingPreservation on plants


To develop a PAV-collection catalogue on the web

To reach a continuity in maintenance and implementation of the collection

To have a curator fully dedicated to PAV-collection

Last but not least to have stable funding to support all the activities

About the future

Thank you for your

attention!!


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PAV – collection of plant pathogen microorganisms: fungi ... · EPPO- Q collection Rome 2015. The PAV-collection of phytopathogenic microorganisms includes fungi, oomycetes, bacteria,