Ecology and Plant-Microbe Interactions

Class Information

• Final lecture: Tuesday, 5/13
• Final exam review/Q&A: Thursday, 5/15 in Sci-108 (12 PM), bring food.
• C-fern group paper due: Thursday, 5/15 at midnight.
• Allelopathy lab due: Friday, 5/16 at midnight.
• No late assignments or resubmissions after Saturday 5/17.
• Final exam covers Unit 4 and class's big picture themes.
• Final exam: 12:45 PM on 5/20 in room 108. Bring a laptop and charger.

Introduction to Ecology

Ecology is the study of the interactions between organisms and their environment. This study ranges in scale from single organisms to the entire planet.

• Key questions in ecology:
  • What factors affect what species we find and where?
  • How do species interact with other organisms and the environment (good, bad, neutral)?
  • How many people can the Earth support?

Levels of Ecological Study

• Individual (Organism): A single organism.
• Population: All the individuals of the same species in an environment.
• Community: All the populations in an environment combined.
• Ecosystem: Community + environment (abiotic factors).
• Landscape: Ecosystems in an area and the in-between spaces.
• Biosphere: Every ecosystem on Earth.

Global Climate Factors and Species Distribution

• Similar environments lead to convergent evolution.
• Global climate factors like temperature and precipitation determine plant life, which forms the foundation of ecosystems.
• Common biomes produce similar forms of life.
• Species distribution can be limited by:
  • Dispersal: Insufficient time to disperse.
  • Biotic Factors: Interactions with other species.
  • Abiotic Factors: Physical/chemical environmental factors.

Ecological and Evolutionary Change

Ecological and evolutionary change go hand in hand:

• Ecological change alters selective pressures in a population.
• Evolutionary change alters the outcome of ecological interactions.

Ecology and Natural Selection

Example: Beak depth in finches.

• In 1976 (before drought), the average beak depth was 9.5 mm.
• In 1978 (after drought), the average beak depth was 10.5 mm, and the population size decreased from 1,200 to 180 individuals.

Another example: Peppered moths during the Industrial Revolution.

• Light-colored moths were better camouflaged in pristine environments; dark-colored moths were better camouflaged in sooty environments.
• As the Industrial Revolution progressed, the moth population shifted from light to dark.

Upcoming Topics in Ecology

• Plant-microbe interactions
• Building communities and ecosystems

Ecology Subfields

• Organismal ecology
• Population ecology
• Community ecology
• Ecosystem ecology
• Landscape ecology
• Global ecology

Plant Symbioses

• Nitrogen Fixation:
  • Nitrogen-fixing bacteria in the soil convert atmospheric nitrogen (N2) into ammonia (NH3).
  • Ammonia gains a proton (H^+) from the soil, becoming ammonium (NH_4^+).
  • Nitrifying bacteria convert ammonium to nitrite (NO2^-) and then to nitrate (NO3^-).
  • Plants can then absorb nitrate from the soil.
  • Denitrifying bacteria convert nitrate back to atmospheric nitrogen.
  • Rhizobacteria form nodules on plant roots and provide fixed nitrogen to the plant in exchange for photosynthate (sugars) and a stable environment.

Crop Rotation and Legumes

• Crop rotation naturally enriches the soil without fertilizer.
  • Legume-based cropping systems:
  • Involves biological nitrogen fixation, where atmospheric nitrogen (N_2) is converted into mineral nitrogen.
  • Crop residue decomposition contributes to mineral nitrogen levels.
• Example crop rotation:
  • Year 1: Potatoes/Tomatoes (Potato Family)
  • Year 2: Brassicas (Brussels sprouts, cabbage, cauliflower, kale, kohlrabi, oriental greens, radish, swede, turnips)
  • Year 3: Legumes (Peas, broad beans, french beans, runner beans)
  • Year 4: Root crops (Alliums, beetroot, carrot, celeriac, celery, florence fennel, parsley, parsnip, etc.)

Plant Symbioses: Recognition and Infection

• The process of recognition and infection is a complex instance of co-evolution.
• Passive process: Bacteria get sugars from the plant, so mutations that harm the plant are harmful to the bacterium.
• "Symbiosome": Bacterium acts differently inside plant cell. Could this become a new organelle?

Nitroplast

• Nitroplast – the newest potential organelle, represents the fourth instance of primary endosymbiosis observed.
• This is the first time a eukaryote has gained N (Nitrogen)-fixation ability.
• Applications are being explored to engineer plants with nitroplasts.
• Evidence of the nitroplast’s identity as an organelle was found in alga Braarudosphaera bigelowii.

Mycorrhizae

• Mycorrhizae: A convergent phenotype.
  • Arbuscular mycorrhizae: Penetrate cortex cells with arbuscules (feeding structures).
  • Ectomycorrhizae: Stay between cells (apoplast).
• AM fungi are needed for growth in over 85% of land plant species.
• About 10% of land plant species, mostly woody plants, form ectomycorrhizal associations.
• Seeds planted in non-native soils may be missing their fungal partner.

Parasitic Plants and Plant Diseases

• Plants may live on other plants as parasites.
• Plants have defenses against parasites, pathogens, and herbivores.

Plant Diseases

• Plants can get diseases from fungi, bacteria, viruses, and nematodes.
• Tobacco mosaic virus was the first virus ever discovered.
• Plant diseases are sometimes visually indistinguishable from abiotic symptoms (physical damage, nutrient deficiencies).
• Diagnosis requires more information and tests.

Disease Triangle

• Having a pathogen does not mean you have a disease.
• Need a susceptible host, pathogen, and right environmental conditions.
• Management of diseases can involve minimizing one or more of these three factors.
  • Reduce the amount of pathogen present through sterile practice or using resistant hosts.

Importance of Crop Diversity

• Lack of diversity is a serious danger.
• Maintaining crop biodiversity helps bolster resistance.
• Allows us to create new crop varieties by breeding existing varieties with wild varieties.
• Late blight (a fungal disease) and political oppression from the British Empire led to the Irish potato famine of the mid-19th century.
• Svalbard Global Seed Vault: A backup in case of apocalypse.

Plant Defenses

• Structural defenses: Pre-formed physical barriers.

• Chemical defenses: Toxins, pathogen inhibitors, and lack of recognition.

• Pre-formed defenses:

  • Toxins, pathogen inhibitors, lack of recognition

• Induced defenses:

  • Callose deposition: Reinforces cell walls.
  • Suberized cork layers: Seal off infected parts.
  • Tougher new organs.
  • Defense compounds/hormones.
  • Hypersensitive response.

Hypersensitive Response (HR)

• HR: Plant cells undergo programmed cell death to stop the spread of the pathogen.
• Can boost Systemic Acquired Resistance (SAR) in the rest of the plant, allowing it to respond more rapidly to subsequent infections.

Plant Defense at the Cellular Level

• Complex back-and-forth recognition between plant and invader.

• PAMP-Triggered Immunity (PTI):

  • Receptors on the surface of plant cells detect the presence of a pathogen outside.
  • Flagellin (protein in flagellum) is a Pathogen-Associated Molecular Pattern (PAMP) or MAMP.
  • Activation of PTI genes produces antimicrobials, reactive oxygen species, and strengthens cell walls. Functions as the plant’s innate immune system.

• Effector-Triggered Susceptibility (ETS):

  • Pathogens have developed effectors to circumvent PTI by targeting the PAMP receptors or the downstream response.
  • Pathogenic bacteria inject effectors, which suppress the host’s PTI.

• Effector-Triggered Immunity (ETI):

  • Plant R-proteins detect effector activity and trigger HR.
  • R-protein recognizes effector, triggers ETI.

Zigzag Model of Plant Defense

The zigzag model illustrates the evolutionary arms race between host and pathogen:

• PTI: Pattern-Triggered Immunity
• ETS: Effector-Triggered Susceptibility
• ETI: Effector-Triggered Immunity

R Proteins and the Guard Hypothesis

• Originally, R proteins were thought to directly bind effectors and trigger a plant systemic response (HR).
• Now, it is known that most R proteins recognize effector activity indirectly (“guard” hypothesis).
• Avr = effector
• P/HP = host protein (target of effector)
• R = R protein

Plant Defenses at All Levels

• Whole organisms may change their behavior (e.g., flowering time) for defense.
• Populations may coordinate behavior by signaling (e.g., they all produce seeds at the same time).
• Community: Corn plants recruit insects to defend them.