2. BIOLOGY ECOLOGY GENETICS of FOREST FUNGI Lesson 1 of BEG Spring 2011 Taught by Dr. Matteo Garbelotto –Matteog@berkeley.eduMatteog@berkeley.edu –Office: 338 Hilgard Hall –Office hours: WEDNESDAYS at 3 pm, THURSDAYS at 1 pm

3. Course info One two hour lecture per week One quiz every week on previous lecture and reading assignments NO syllabus, but…. Some readings will be emailed to students Web site: www.matteolab.orgwww.matteolab.org »Link to UCB course »POWERPOINT LECTURES, assigned readings »Posted on Fridays

4. Course info One final quiz (3 questions out of 9) One short Powerpoint presentation Possibility to improve grade by writing paper (5 pages) on same topic as oral presentation One computer lab: use of software for genetic analyses Participation in SOD blitz mandatory

5. GRADING 25% class participation 25% weekly quizzes 25% final quiz 25% oral presentation

6. COURSE PROGRAM-1 What is an emergent disease ? What do plant diseases exactly do? How do plant and pathogens interact? What are the evolutionary consequences of emergent diseases? What causes plant diseases How can we use genetic information to identify a pathogen? DNA, chromosomes and loci

7. COURSE PROGRAM-2 DNA used to identify a species DNA used to identify an individual within a species Following an individual pathogen to understand infection process Using genes to tag individuals; how far does an individual go? Identify populations and migration among populations

8. COURSE PROGRAM-3 Identify source of a pathogen and phylogeography Determine whether a population is introduced or native Rapid evolutionary changes linked to introductions Epigenetics of disease

9. EMERGENT FOREST DISEASES: ARE THEY A THREAT TO NATIVE ECOSYSTEMS? Matteo Garbelotto U.C.Berkeley

10. “Native diseases”: Indigenous microbesIndigenous microbes Plant ecosystems have co-evolved to resistancePlant ecosystems have co-evolved to resistance Native diseases are an important component of forest ecosystemsNative diseases are an important component of forest ecosystems

11. “Roles of native diseases”: Thin natural populations of treesThin natural populations of trees Optimal allocation of resourcesOptimal allocation of resources Selection for a genetically diverse host populationSelection for a genetically diverse host population Maintain tree rangesMaintain tree ranges Succession: nutrient cyclingSuccession: nutrient cycling

12. “Emergent diseases”: diseases on the rise New introduced, exotic, organismsNew introduced, exotic, organisms Good gone bad: e.g. climate change or human activities trigger excessive pathogenicity of native organismGood gone bad: e.g. climate change or human activities trigger excessive pathogenicity of native organism

13. DISEASE TRIANGLE Pathogen Host Environment

14. Pathogen Host Environment HIGH DISEASE

15. Pathogen Does it need a wound to infect a host? Can it survive in the environment without a host? soil, water on alternate host How does it move around? airborne/waterborne animal vectors humans

16. Host Must be physically present with pathogen Must be physically compatible with pathogen Must provide window of opportunity for infection Genetic resistance? often lack of resistance if disease is introduced What type of resistance? simple= one gene complex=several genes

17. Environment Climatic As modified per human management Species composition Plant density

18. “Emergent diseases”: 1: host New host-pathogen combinations:New host-pathogen combinations: exotic hosts hosts planted off site

19. Cypress canker by Seiridium cardinale Pathogen was first described in California in the 20s. Later it was described in Italy where it started a serous epidemic of Italian cypress Belief that pathogen is native to California: is that true and why is it then causing a significant disease in our state?

20. Conidia of Seiridium cardinale observed by optical microscope and SEM

21. Use of molecular genetics to resolve issue of origin of pathogen Use of molecular genetics to resolve issue of origin of pathogen Used a technique similar to the one used in human forensics Native populations should comprise many different individuals genetically Introduced populations should be genetically simpler because of bottleneck related to introduction events

22. RESULTS: CA vs. Europe oCalifornia population diverse genetically= native to the state oEuropean population show no diversity=introduced

23. Symptoms caused by Seiridium cardinale on Cupressus macrocarpa (above) and xCupressocyparis leylandii (right) Fig. 3

24. Why a disease in CA? If pathogen is native to California, why is it causing such a serious disease? We observed that disease incidence is variable with: –cypress species, –location,

25. Range of susceptibility Leyland cypress, Italian, monterey are listed as most susceptible Arizona and McKnob are regarded as more resistant

26. Range of susceptibility 90% of Leyland are heavily infected 10% of monterey LEYLAND CYPRESS IS AN ORNAMENTAL CROSS, NOT NATIVE

27. Range of susceptibility Monterey is more susceptible in inland areas where it is NOT NATIVE: we believe that colder temperatures cause more wounds that lead to infection

28. CONCLUSIONS Cypress canker is a serious disease in Europe because pathogen was introduced Cypress canker is a serious disease in California because hosts were introduced either through planting off range (Monterey cypress) or because host is artificial creation (Leyland cypress); extinction of LEYLAND is most likely

29. “Emergent diseases”: 2: environmental changes Forestry and intensive forest use:Forestry and intensive forest use: timber production tree felling and creation of stumps fire exclusion and increase in density oversimplified forest composition changes in forest composition changes in forest structure

30. Heterobasidion root disease Heterobasidion (a bracket or shelf mushroom) infects trees through wounds and stumps, then it spreads through the roots to neighboring trees With tree felling,stumps and wounds are created, suddenly exponentially increasing infection levels

31. Heterobasidion shelf fruit-body

34. Use of molecular genetics Use of molecular genetics: Differentiate Heterobasidion on fir/sequoias (H. occidentalis) from that on pine/junipers (H.irregularis) Show that airborne meiospores are responsible for most infection of Heterobasidion Show that in pines most infections start on stumps and that in true firs most infections on wounds

35. True firs Pines Each spore is a genetically different individual: In pines we found the same genetic individual in stumps and adjacent trees indicating direct contagion between the two In true firs and true firs/sequoias we find same individual in adjacent standing trees indicating infection not linked to stumps but to wounds on standing trees

36. CONCLUSIONS: Logging activities increase Heterobasidion infection because of stump creation in pines and because of wounding in true firs sequoias We have shown that in pine stumps H. irregularis and H. occidentalis can both be present and create a new hybrid entity We have shown that in the past these hybridization events have lead to sharing of genes among these two species (Horizontal gene transfers)

37. Armillaria root diseases Armillaria, the honey mushroom, normally infects the roots of trees. It can be a saprobe and a pathogen and is common amongst oaks If woodland composition shifts to pine/oak, pines become the target of attacks and gaps in canopy enlarge over time. Stress (e.g. flooding) exacerbates susceptibility

38. Clusters of Armillaria

39. How Does it Infect? SOURCE: http://www.forestpathology.org/dis_arm.htm l Two means of dispersal to other trees: 1.Mycelium can grow through direct root contacts and grafts with uninfected trees. 2.Rhizomorphs can grow through soil to contact uninfected trees. DEAD OAK OAK or PINE

40. What are Rhizomorphs? …“conglomerations of differentiated parallel hyphae with a protective melanized black rind on the outside.” Rhizomorphs are able to transport food and nutrients long distances which allows the fungus to grow through nutrient poor areas located between large food sources such as stumps. SOURCE: http://www.nifg.org.uk/armillaria.htm SOURCE: http://botit.botany.wisc.edu/toms_fungi/apr2002.html

41. Humongous Fungus It’s One of U-HAUL’s “Bizarre Roadside Attractions” http://botit.botany.wisc.edu/toms_fungi/apr2002.html

42. CONCLUSIONS Human activities shifting from oak woodlands to mixed oak-pine lead to large mortality gaps in pines around oaks if honey mushroom is present CHANGING SPECIES COMPOSITION LEADS TO SEVERE DISEASE

43. Many gaps with very little regeneration and have not closed in

44. Change in gap area 1972- 1999

45. “Emergent diseases”: 3: exotic pathogens 99% of times human responsible for their introduction99% of times human responsible for their introduction

46. Like the conquistadores brought diseases that were lethal to those who had never been exposed to them, so do exotic diseases cause true devastation in plant communities because of lack of coevolution between hosts and microbes

47. California invaded: 1849 A.D. New hybrid root pathogen 1990s White pine blister rust 1930s Port Orford Cedar Root Disease 1950s Pitch canker disease 1980s Dutch Elm Disease 1960s Sudden Oak Death 1990s Oak root canker 2000 Manzanita/madrone die-back Canker-stain of Sycamores 1980’s

48. How can people transport pathogens By transporting plants and plant parts –Crops, and seeds –Raw food –Ornamental plants Untreated lumber Soil Insects vectoring fungi Military activity

49. The Irish Potato Famine From 1845 to 1850 Phytophthora infestans Resulted in the death of 750,000 Emigration of over 2 million, mainly to the United States.

51. Is it exotic? Our studies have indicated that California population is extremely simplified, basically two strains reproducing clonally as expected of an introduced organism Many hosts appear to have no resistance at all Limited geographic distribution

52. Where does it come from? It is unknown where pathogen originally comes from, but previous studies have shown that California forest population is derived from a relatively genetically diversified US nursery population, indicating ornamental nurseries were the most likely avenue for pathogen introduction

53. Where was it introduced? First reports mid 90’s Pathogen identified in 2000 By then, the pathogen was widespread CLUES: severity of symptoms and anedoctal stories Positive isolation P. ramorum

54. We found same genotypes in nurseries and forests proving origin of wild outbreak

55. nurseries Introduction phase 1- Escape of pathogen from Infected nursery plants at two locations: Mount Tamalpais (Marin County), and Scott’s Valley (Santa Cruz County) 2- Nurseries and two sites have identical strain composition, but distance between sites is impossible for natural spread of organism

56. What favors invasion of exotic fungi ? –Density of host increases severity of disease –Corridors linking natural habitats –Synchronicity between host susceptibility and pathogen life cycle –Ecological and environmental conditions

57. Bay/Oak association Bleeding canker Canker margin in phloem Bay Coast Live Oak (no sporulation) Sporangia

59. Synchrony pathogen-host Susceptibility of oaks (lesion size)

60. Wetness > 12 h Temp >19 C

61. Bay Laurel / Tanoak SOD Spore Survey Date Temp (C) Rain (mm)

62. How to control emergent exotic diseases PREVENT THEIR INTRODUCTION LIMIT THE HUMAN-SPREAD OF PATHOGENS (infected plants, plant parts, dirty tools) EMPLOY HOST RESISTANCE CHEMICAL AND OTHER MITIGATION STRATEGIES

63. Forest pathogens can never be eradicated

65. PREVENT: Diagnose Symptoms relatively generic, very variable, and pathogen not always culturable LAB CULTURES DNA TESTS

67. AgriFos and PentraBark Topical Application +

68. Agrifos vs. Azomite Treatments (efficacy 1 - 24 months) Canker Size (mm) a a b

69. Why emphasis on molecular analyses? As a way to identify and quantify microbes in the environment As a way to understand microbial biology: how do microbes reproduce and infect hosts As a way to determine epidemiology: follow the movement of a strain

70. Why emphasis on molecular analyses? As a way to determine potential for spread: use genes as markers for individuals As a way to determine whether population of microbes is exotic or native As a way to identify source of a pathogen and migration patterns

71. Why emphasis on molecular analyses? As a way to determine the size of the gene pool of a pathogen, Important to scale management options As a way to determine rapid evolutionary changes linked to an introduction As a way to determine epigenetic effects