THE ECOLOGY OF PLANT-ASSOCIATED MICROBES
Classroom: 201C Kottman Hall, 203 Selby Hall / video linked
Lectures: TR 10-11:48
Recitation: to be arranged with student schedules 1 hr/week
Credit: 5 credit hours Prerequisites: Plant Pathology 602, or consent of instructor
Instructors: B. McSpadden Gardener, 214 Selby Hall, 330 202-3565, bbmg+@osu.edu
P. (Enrico) Bonello, 483C Kottman Hall, 614 688-5401, bonello.2@osu.edu
Office hours: by appointment
Course Structure:
This is an advanced seminar course with two weekly lectures and a 1-hr recitation section for discussion of assigned primary literature. The purpose of these discussions is to expand on lecture material and instruct students in approaches to critically reviewing manuscripts. Some lectures will be taught by outside experts. Assignments will consist of required readings, participation in paper discussions, and a critical review of one selected paper. Paper critiques will consist of a 2-3 page written review, due by the 8th week of class, and a 20-30 minute period where the student will present their critique to the class for discussion in the 10th week of class.
Rationale for the course:
Plant-associated microbes dynamically mediate numerous processes that affect plant health. Such processes include facilitation of nutrient uptake, infection and destruction of host tissues, suppression of plant diseases, and recycling of plant biomass. A thorough knowledge of the diversity, dynamics, and effects of plant-associated microbial populations is a prerequisite for effective disease control in the field. This course builds upon the material covered in PLNT PTH P602, and complements topics related to molecular plant-microbe interactions that are presented in PLNT PTH 841 and 844.
Course Objectives: Upon completion of the course, students should be able to:
Þ Describe the diversity of plant-associated microbes and the methods used to define microbial taxa
Þ Use various taxonomic keys and web-based resources to identify diverse microbes
Þ Understand the timing and composition of nutrient pools available for growth of microbial epiphytes and endophytes
Þ Describe the different types of plant-microbe interactions that occur on and in plant tissues and the environmental constraints that affect those interactions
Þ Define several key unanswered question about the contributions of plant-associated microbes to plant health and fecundity
Þ Critically evaluate the literature on the ecology of plant-associated microbes
Þ Know how to use the literature to write, synthesize, and present to an audience a critical review of a manuscript related to course content (but different from any the student may be working directly with in their thesis or dissertation work)
Required Textbook: No specific textbook required. Readings will be taken from selected book chapters (see bibliography), journal articles, and online resources.
Number
Microbial Diversity in the Phytosphere
03/xx 1 Techniques & resources for studying microbial diversity BMG
2 Prokaryotes BMG
3 Eukaryotes 1: Oomycets and other non-fungi EB
4 Eukaryotes 2: Fungi EB
5 Viruses and other subcellular microbes FQ
Plants as Dynamic Habitats
6 Nutrient availability in the phytosphere BMG
7 Factors affecting colonization and population size BMG
8 Organic matter composition and nutrient cycling EB
9 Reproduction and dispersal of microbes L Madden
MIDTERM EXAM
Microbes in context
10 Soil food webs: Agroecosystems BMG
11 Soil food webs: Forest ecosystems EB
12 Insect-microbe interactions EB
13 Nematode-microbe interactions PG
Modulation of plant growth, health, and fecundity
14 Plant responses to colonization and infection EB
15 N and P assimilation and mutualisms EB
16 Biological control and plant growth promotion BMG
17 Significance of plant diseases in different ecosystems BMG&EB
Paper Critiques
Paper Critiques
FINAL EXAM
Methods of Evaluation:
Exams will include questions relating to both lecture and discussion sessions. Course grades will be determined as follows:
Midterm exam 30%
Paper critique 15%
Presentation 15% (50% instructor, 50% audience)1
Total 100%
1The student audience will be asked to give the presenter a numerical grade evaluation based on the grading scale below. The mean grade from the audience will be weighed as 50% of the final grade on presentation.
All assignments, examinations, etc. are due on the dates that will be indicated below. Exceptions can be made only in the case of extenuating circumstances, such as the death of a close family member, serious illness, etc. Evidence to support such occurrences will be required.
A 92.5%
A- 88.5%
B+ 86.5%
B 82.5%
B- 78.5%
C+ 76.5%
C 72.5%
C- 68.5%
D+ 66.5%
D 62.5%
E <62.5%
Academic Misconduct: Academic misconduct erodes the integrity of the University and is unacceptable. Suspected cases will be forwarded to the University’s Committee on Academic Misconduct for action as outlined in the OSU Student Resource Guide / Code of Student Conduct which is available online at http://studentaffairs.osu.edu/resource_csc.asp.
Students with disabilities: If you have a disability, please tell one or both instructors about it. We will work with any student who desires an accommodation based on the impact of a disability but you need to let us know before we can accommodate your specific needs. Additional assistance is also available through the Office for Disability Services - Room 150 Pomerene Hall or by calling 614-292-3307.
Bibliography:
Note: Material presented in class will be derived from the following references. Portions of other texts and additional research papers will also be used during the course.
General Reference Texts:
CABI Publishing: Cambridge MA
Academic Press: London
ASM Press: Washington DC
Sina M. Adl ed. 2004
CABI Publishing: Cambridge MA
J.B. Halborne 1993
Academic Press: London
Part I: Microbial Diversity
THE ECOLOGY AND GENETICS OF MICROBIAL DIVERSITY
Rees Kassen, Paul B. Rainey
Annual Review of Microbiology 2004 58, 207-231
THE UNCULTURED MICROBIAL MAJORITY
Michael S. Rappé, Stephen J. Giovannoni
Annual Review of Microbiology 2003 57, 369-394
METAGENOMICS: Genomic Analysis of Microbial Communities
Christian S. Riesenfeld, Patrick D. Schloss, Jo Handelsman
Annual Review of Genetics 2004 38, 525-552
LATERAL GENE TRANSFER AND THE ORIGINS OF PROKARYOTIC GROUPS
Yan Boucher, Christophe J. Douady, R. Thane Papke, David A. Walsh, Mary Ellen R. Boudreau, Camilla L. Nesbø, Rebecca J. Case, W. Ford Doolittle
Annual Review of Genetics 2003 37, 283-328
WHAT ARE BACTERIAL SPECIES?
Frederick M. Cohan
Annual Review of Microbiology 2002 56, 457-487
COMPARATIVE GENOMIC ANALYSIS OF PLANT-ASSOCIATED BACTERIA
M. A. Van Sluys, C. B. Monteiro-Vitorello, L. E. A. Camargo, C. F. M. Menck, A. C. R. da Silva, J. A. Ferro, M. C. Oliveira, J. C. Setubal, J. P. Kitajima, A. J. Simpson
Annual Review of Phytopathology 2002 40, 169-189
AMMONIA-OXIDIZING BACTERIA: A Model for Molecular Microbial Ecology
George A. Kowalchuk, John R. Stephen
Annual Review of Microbiology 2001 55, 485-529
THE EVOLUTION OF ASEXUAL FUNGI: Reproduction, Speciation and Classification
JW Taylor, DJ Jacobson, MC Fisher
Annual Review of Phytopathology 1999 37, 197-246
METABOLIC DIVERSITY IN AROMATIC COMPOUND UTILIZATION BY ANAEROBIC MICROBES
Jane Gibson, Caroline S. Harwood
Annual Review of Microbiology 2002 56, 345-369
THE CLASS MESOMYCETOZOEA: A Heterogeneous Group of Microorganisms at the Animal-Fungal Boundary
Leonel Mendoza, John W. Taylor, Libero Ajello
Annual Review of Microbiology 2002 56, 315-344
Part II: Dynamics
MICROBIAL POPULATION DYNAMICS ON LEAVES
Linda L. Kinkel
Annual Review of Phytopathology 1997 35, 327-347
MICROBIAL DYNAMICS AND INTERACTIONS IN THE SPERMOSPHERE
Eric B. Nelson
Annual Review of Phytopathology 2004 42, 271-309
QUORUM SENSING IN BACTERIA
Melissa B. Miller, Bonnie L. Bassler
Annual Review of Microbiology 2001 55, 165-199
QUORUM SENSING IN PLANT-PATHOGENIC BACTERIA
Susanne B. von Bodman, W. Dietz Bauer, David L. Coplin
Annual Review of Phytopathology 2003 41, 455-482
CIRCADIAN RHYTHMS IN MICROORGANISMS: New Complexities
Patricia L. Lakin-Thomas, Stuart Brody
Annual Review of Microbiology 2004 58, 489-519
OXYGEN DEFICIENCY AND ROOT METABOLISM: Injury and Acclimation Under Hypoxia and Anoxia
Malcolm C. Drew
Annual Review of Plant Physiology and Plant Molecular Biology 1997 48, 223-250
CHEMICAL BIOLOGY OF MULTI-HOST/PATHOGEN INTERACTIONS: Chemical Perception and Metabolic Complementation
Andrew G. Palmer, Rong Gao, Justin Maresh, W. Kaya Erbil, David G. Lynn
Annual Review of Phytopathology 2004 42, 439-464
Part III: Context
MOLECULAR PHYSIOLOGY OF LEGUME SEED DEVELOPMENT
Hans Weber, Ljudmilla Borisjuk, Ulrich Wobus
Annual Review of Plant Biology 2005 56, 253-279
RISING ATMOSPHERIC CARBON DIOXIDE: Plants FACE the Future
Stephen P. Long, Elizabeth A. Ainsworth, Alistair Rogers, Donald R. Ort
Annual Review of Plant Biology 2004 55, 591-628
FUNCTION AND MECHANISM OF ORGANIC ANION EXUDATION FROM PLANT ROOTS
PR Ryan, E Delhaize, DL Jones
Annual Review of Plant Physiology and Plant Molecular Biology 2001 52, 527-560
MACRONUTRIENT UTILIZATION BY PHOTOSYNTHETIC EUKARYOTES AND THE FABRIC OF INTERACTIONS
Arthur Grossman, Hideki Takahashi
Annual Review of Plant Physiology and Plant Molecular Biology 2001 52, 163-210
THE IMPACT OF REDUCED TILLAGE ON SOILBORNE PLANT PATHOGENS
W. W. Bockus, J. P. Shroyer
Annual Review of Phytopathology 1998 36, 485-500
MICROBIAL COMMUNITIES AND THEIR INTERACTIONS IN SOIL AND RHIZOSPHERE ECOSYSTEMS
Angela D. Kent, Eric W. Triplett
Annual Review of Microbiology 2002 56, 211-236
THE ECOLOGY AND BIOGEOGRAPHY OF MICROORGANISMS ON PLANT SURFACES
John H. Andrews, Robin F. Harris
Annual Review of Phytopathology 2000 38, 145-180
MICROBIAL DIVERSITY IN SOIL: Selection Microbial Populations by Plant and Soil Type and Implications for Disease Suppressiveness
P. Garbeva, J.A. van Veen, J.D. van Elsas
Annual Review of Phytopathology 2004 42, 243-270
EFFECTS OF PLANTS ON NEMATODE COMMUNITY STRUCTURE
GW Yeates
Annual Review of Phytopathology 1999 37, 127-149
Part IV: Modulation of Plant Health and Fecundity
ROOT NODULATION AND INFECTION FACTORS PRODUCED BY RHIZOBIAL BACTERIA
Herman P. Spaink
Annual Review of Microbiology 2000 54, 257-288
ECOLOGY OF MYCORRHIZAE: A Conceptual Framework for Complex Interactions Among Plants and Fungi
M.F. Allen, W. Swenson, J.I. Querejeta, L.M. Egerton-Warburton, K.K. Treseder
Annual Review of Phytopathology 2003 41, 271-303
MOLECULAR AND CELLULAR ASPECTS OF THE ARBUSCULAR MYCORRHIZAL SYMBIOSIS
Maria J. Harrison
Annual Review of Plant Physiology and Plant Molecular Biology 1999 50, 361-389
SYMBIOSES OF GRASSES WITH SEEDBORNE FUNGAL ENDOPHYTES
Christopher L. Schardl, Adrian Leuchtmann, Martin J. Spiering
Annual Review of Plant Biology 2004 55, 315-340
EVOLUTIONARY ECOLOGY OF PLANT DISEASES IN NATURAL ECOSYSTEMS
Annual Review of Phytopathology 2002 40, 13-43
BIOFILMS AS COMPLEX DIFFERENTIATED COMMUNITIES
P. Stoodley, K. Sauer, D. G. Davies, J. W. Costerton
Annual Review of Microbiology 2002 56, 187-209
THE ECOLOGICAL SIGNIFICANCE OF BIOFILM FORMATION BY PLANT-ASSOCIATED BACTERIA
Cindy E. Morris, Jean-Michel Monier
Annual Review of Phytopathology 2003 41, 429-453
SYSTEMIC RESISTANCE INDUCED BY RHIZOSPHERE BACTERIA
L. C. van Loon, P. A. H. M. Bakker, C. M. J. Pieterse
Annual Review of Phytopathology 1998 36, 453-483
PATHOGEN SELF-DEFENSE: Mechanisms to Counteract Microbial Antagonism
Brion Duffy, Alexander Schouten, Jos M. Raaijmakers
Annual Review of Phytopathology 2003 41, 501-538
MICROBIAL POPULATIONS RESPONSIBLE FOR SPECIFIC SOIL SUPPRESSIVENESS TO PLANT PATHOGENS
David M. Weller, Jos M. Raaijmakers, Brian B. McSpadden Gardener, Linda S. Thomashow
Annual Review of Phytopathology 2002 40, 309-348
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