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Fungi Soil Soil
I. Classification, morphology.. II. Fungi distribution in soil III. Survival and propagation IV. Important roles of fungi in soil
1. Organic matter degradation 2. Importance in soil foodwebs 3. Parasites and pathogens 4. production of mycotoxins 5. Mutualistic associations 5. Soil aggregation
IV. Application of soil fungi
1. Fermentation 2. production of antibiotics 3. Biological control 4. Bioremediation
Reading: Textbook: Sylvia et al., 2004. Chapter 6, pages 141-161.
Eukaryotes
Fungi Eukaryote Nuclearmembrane Multiplechromosomes Mitochondria,organelles Polysaccharidetypewall(cellulose, chitin) Twotypesofribosomes(80S,70S) Multicellularanddifferentiated Sexualreproduction Cells>5 mindiameter Structuraldiversity
From Coyne, Soil Microbiology
Bacteria Prokaryote Nonuclearmembrane Singlechromosome Fewinternalstructures Peptidoglycanwalls 70Sribosomesonly Usuallyunicellular Asexualreproduction Cells<5 mindiameter Metabolicdiversity
Heterotrophs
Saprotroph
Parasite
Symbiont
Hyphae
Filaments: 3-10 m in
Mycelium
Nature 356(2) 428-431, 1992
2003: Armillaria ostoyae, Oregon
- 0.15 km2 (37 acres) - 1500 years old
- 8.9 km2 (2,200 acres) - 2000-8650 years old
Filamentous Fungi Single-cell yeasts
Fungal cell wall
Eukaryotes Heterotrophs Almost all aerobic 80.000 species described but much more exist
Fungal distribution
Organism Plantroots Fungi Bacteria Actinomycetes Protozoa Nematodes Earthworms Biomass(kgper hectare) 20,00090,000 2,500 1,0002,000 02,000 0500 0200 02,500
Relative contribution of soil organisms to the biomass of a temperate grassland soil
Fungal distribution
Determined by: - Availability of organic C (most are saprobes) - Vegetation composition - pH (tolerant to acid pH) - Temperature (mesophile) - Water - Oxygen (most are strictly aerobes in top 15
cm of soils)
Fungal distribution: mutualism
Endophytic association
Neotyphodium coenophialum in Festuca arundinacea
Mycorrhizal association
(see next lecture)
Survival and propagation
- sexual and asexual spores - survival from weeks to years in soil
conidia: asexual spores ascospores: result of sexual fusion
sclerotia: aggregated hyphae, easily dispersed
Survival and propagation
Active dispersion
Fairy rings
Survival and propagation
2.5 m
Pilobolus (ballistospores) Ascomycetes
Survival and propagation
ascus
Max 0.5 m
ascospores
Ascomycetes
Survival and propagation
spore
basidia
0.5-1 mm
Basidiomycetes
Survival and propagation
Passive dispersion by wind or water
Earthstar
Puffball spore dispersal
dry
wet
Survival and propagation
Passive dispersion by animals Truffle
Stinkhorn
From Van Elsas et al., Modern Soil Microbiology, 2007
1. Organic matter decay
Role of Fungi in soils
Role of Fungi in soils
2. Importance in soil foodwebs
Food source for invertebrates Predators of nematodes
SEM of a nematode caught in the constricting rings of Arthrobotrys anchonia
Adhesive net
nematodes by trapped the adhesive nets of the predatory fungus Arthrobotrys oligospora
Role of Fungi in soils
3. Parasites and pathogens
70% of crop diseases are caused by fungi
Sudden Oak Death (Phytophthora ramorum)
From Van Elsas et al., Modern Soil Microbiology, 2007
Role of Fungi in soils
4. Production of mycotoxins (reported as early as 1861)
Poisonous mushrooms
responsible for 95 % of the fatal cases of mushroom poisoning throughout the world
Amanita muscaria
Amanita phalloides
Role of Fungi in soils
4. Production of mycotoxins (reported as early as 1861)
Ergot (Claviceps purpurea) Ergotism (St Anthonys fire)
Role of Fungi in soils
5. Mutualistic associations Mycorrhizae (cf next lecture) Lichens
Role of Fungi in soils
6. Enhanced soil aggregation
Applications of soil Fungi
1. Fermentation (yeasts)
Penicillium species yeasts
Saccharomyces cerevisiae and S. carlsbergensis
Aspergillus oryzae
Applications of soil Fungi
2. Production of antibiotics
Penicillin discovered in 1928 by Alexander Fleming Isolated from a mold, Penicillium notatum First drug against syphilis and Staphylococcus 1945 Nobel prize Staphylococcus
aureus
Penicillium
Applications of soil Fungi
3. Biological control
About 20 fungal products sold commercially Competition for space and for nutrients, predation and antibiotics
Myrothecium verrucaria as biocontrol of weed species
Applications of soil Fungi
3. Biological control
Fungi to Control Plant Diseases: Root rot of Conifers
Root rot of pine caused by the bracket fungus Heterobasidium annosum
Phlebiopsis gigantea prevents invasion by the pathogen Heterobasidium annosum
Applications of soil Fungi
3. Biological control
Fungi to Control Plant Diseases: Post-harvest rot of citrus fruits
Fruit rot of citrus showing the effectiveness of biocontrol with Pichia guillermondii (U.S.-7)
Applications of soil Fungi
3. Biological control
Biocontrol of insects:
Control of cabbage loopers with Noumorea rileyi Control of coakroach with Metarrhizium
body cavity full of spores
Applications of soil Fungi
3. Biological control
Biocontrol of Nematodes:
a) Nematode-trapping fungi: Arthrobotrys irregularis, Dactylella spp. Monacrosporium spp.
Dactylella drechsleri
Monacrosporium robustum Anthrobotrys dactyloides
Applications of soil Fungi
3. Biological control
Biocontrol of Nematodes:
b) Endoparasitic fungi: Drechmeria coniospora, Catenary anguillulae, Hirsutella rhossiliensis
sinuous fungal hyphae inside the nematode
conidia
Drechmeria coniospora
Applications of soil Fungi
3. Biological control
Biocontrol of Nematodes:
c) Parasitic fungi attacking sedentary stages of nematodes: Pochonia chlamydosporia, Paecilomyces lilacinus
P. chlamydosporia infected Meloidogyne incognita egg
Applications of soil Fungi
4. Bioremediation - White-rot fungi - PAHs - Chlorophenols - Nitrotoluenes - Polychlorinated biphenyls - Azo dyes
Applications of soil Fungi
5. They are delicious

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Berkeley - ESPM - 131

Mycorrhizal Symbioses MycorrhizalI. Introduction and history II. Types and distribution of mycorrhizae1. Endomycorrhizae: Arbuscular 2. Ectomycorrhizae 3. Orchidaceous mycorrhizae 4. Ericaceous mycorrhizae 5. Changes of mycorrhizal types with latitude/a

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Rediscovering the original methods of soil microbiologyCatherine OsborneBeijerinck, the first environmental microbiologist1888Conn, the first soil microbial ecologistThe microscopicallydetermined size of the soil bacterial population is at least 20 t

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Molecular analysis of soil microbial communities1. Diversity, structure and quantity Eoin BrodieLawrence Berkeley National Lab elbrodie@lbl.gov 510-486-6584Complexity of soil Physical heterogeneityParticle size distribution And aggregate formation Re

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Molecular analysis of soil microbial communitiesII. Function of soil microbial communities Eoin Brodie, LBNL elbrodie@lbl.govSummary Whos there? Biomarkers: DNA extraction PCR amplification clone libraries / microarrays How many? Relative abundance:

Berkeley - ESPM - 131

Soil FaunaI. Classification II. Groups of soil fauna 1. Macrofauna: earthworms 2. Mesofauna: collembolans and nematodes 3. Microfauna: protozoa III. Effects of soil fauna on soil and soil microorganisms 1. Grazing 2. Fragmentation of soil organic matter

Berkeley - ESPM - 131

Viruses in soilViruses are molecular sharks, a motive without a mind. Richard Preston I. Introduction II. General properties of viruses 1. Size and morphology 2. Types of viruses 3. The structure of viruses 4. General features of virus replication III. V

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Applications of Ecological ConceptsJennifer Pett-RidgeS curve of population growth # of animalstimeEcology & Microbial Ecology Historical disconnect between ecologists and microbiologists Microbes difficult to observe in nature Tools and disciplines

Berkeley - ESPM - 131

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Soil Organic Matter Soil3: Humification and CompostingI. Humus formation and characteristics 1. Humus formation 2. Humus characteristics a. Composition b. Chemical fractionation c. Humus-clay complexes b. Adsorptive properties 3. Beneficial properties i

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Berkeley - ESPM - 131

Degradation of xenobiotics Degradation(part 2)I. Xenobiotics 1. Definition 2. Types of compounds 3. Pesticides II. Processes affecting xenobiotics cycle in soils 1. Volatilization 2. Adsorption/desorption 3. Leaching/runoff 4. Abiotic transformations 5.

University of Phoenix - FIN - 324

Week 3Individual Quiz (Albrecht et al, chapters 14; and Brealey et al, chapter 17) Directions: Choose the correct answer by highlighting the answer with yellow marker from the MS Word program (You can also use a separate sheet, but make sure to number you

MIT - CS - 6.841

6.841 Advanced Complexity TheoryFeb 4, 2009Lecture 1Lecturer: Madhu Sudan Scribe: Mergen Nachin1Administrative Information Lecturer: Madhu Sudan (madhu@mit.edu) TA: Brenden Juba (bjuba@mit.edu) Website: http:/courses.csail.mit.edu/6.841/ The grading

MIT - CS - 6.841

6.841 Advanced Complexity TheoryFebruary 9, 2009Lecture 2Lecturer: Madhu Sudan Scribe: Sam McVeetyToday, we will study diagonalization and Ladners Theorem, which states roughly that: P = NP NP-intermediate Problem Later, we will look at relativization

MIT - CS - 6.841

6.841 Advanced Complexity TheoryFeb 11, 2009Lecture 3Lecturer: Madhu Sudan Scribe: Debmalya PanigrahiIn todays lecture, we will focus on non-uniform models of computation. In non-uniform computation, we have a dierent gadget/program/machine for each i

MIT - CS - 6.841

6.841 Advanced Complexity TheoryFeb 17, 2009Lecture 4Lecturer: Madhu Sudan Scribe: Adam Spanbauer1IntroductionTodays lecture will focus on the proof of Barringtons Theorem: Barringtons Theorem: All polynomial-size formulas have an O(1) width brachin

MIT - CS - 6.841

6.841 Advanced Complexity TheoryFeb 18, 2009Lecture 5Lecturer: Madhu Sudan Scribe: Yang Cai1Overview P ARIT Y AC 0 . / Random Restriction Switching Lemma DN F CN F2Introduction AC k : Class of functions computable by polynomial size and O(log n)k

MIT - CS - 6.841

6.841 Advanced Complexity TheoryFeb 23, 2009Lecture 6Lecturer: Madhu Sudan Scribe: Michael ForbesThe goal of this lecture is to give alternate proof of PARITY AC0 , following the outline of Razborov / and Smolensky.0.1Probability ReviewProbability

MIT - CS - 6.841

6.841 Advanced Complexity TheoryFeb 7, 2005Lecture 7: Communication Complexity and Lower BoundsLecturer: Madhu Sudan Scribe: David ChenThis lecture gives an introduction to Communication Complexity. We go over the properties and examples of Communicat

MIT - CS - 6.841

6.841 Advanced Complexity TheoryMar 02, 2009Lecture 08Lecturer: Madhu Sudan Scribe: Vartika Singh1AlternationIt is a notion which tries to capture languages in N P and CoN P in a unifying way. It denes the time-vs-space relation and hence Alternatin

MIT - CS - 6.841

6.841 Advanced Complexity TheoryMar 04, 2009Lecture 09Lecturer: Madhu Sudan Scribe: Jeremy HurwitzIn this lecture, we introduce a new model of computation and a set of corresponding complexity classes which sit between N P and P SP ACE . This model is

MIT - CS - 6.841

6.841 Advanced Complexity TheoryMarch 9, 2009Lecture 10Lecturer: Madhu Sudan Scribe: Asilata BapatMeeting to talk about nal projects on Wednesday, 11 March 2009, from 5pm to 7pm. Location: TBA. Includes food.1Overview of todays lecture Randomized c

MIT - CS - 6.841

6.841 Advanced Complexity TheoryMar 11, 2009Lecture 11Lecturer: Madhu Sudan Scribe: Colin Jia Zheng1RecapWe dened RP as the class of languages accepted by PPT machine with one-sided error bounded below 1/3, BPP with two-sided error with gap 1/3. RP

MIT - CS - 6.841

6.841 Advanced Complexity TheoryMarch 18, 2009Lecture 13Lecturer: Madhu Sudan Scribe: Alex Cornejo1Overview of todays lecture Todas Theorem: PH :=k N P k P#P , steps: Prove some properties concerning C , C , C , BP C Do some operator calculus to

MIT - CS - 6.841

6.841 Advanced Complexity TheoryMar 30, 2009Lecture 14Lecturer: Madhu Sudan Scribe: Huy Nguyen1Admin Interactive proofs The complexity classes IP and AMThe topics for today are:Please see Madhu if you have not been assigned a project.2Theorems v

MIT - CS - 6.841

6.841 Advanced Complexity TheoryApril 1, 2009Lecture 15Lecturer: Madhu Sudan Scribe: Rotem Oshman1Todays topics Private coins public coins (that is, IP[k ] AM) Goldwasser-Sipser approximate counting protocol Towards protocols for the Permanent, in t

MIT - CS - 6.841

6.841 Advanced Complexity TheoryApril 7, 2009Lecture 16Lecturer: Madhu Sudan Scribe: Paul Christiano1Worst-Case vs. Average-Case ComplexitySo far we have dealt mostly with the worst-case complexity of problems. We might also wonder aobut the average

MIT - CS - 6.841

6.841 Advanced Complexity TheoryApril 8, 2009Lecture 17Lecturer: Madhu Sudan Scribe: Jean Yang1OverviewLast lecture we showed P ERM IP #P IP by constructing an IP protocol involving verifying a polynomial using a curve. In this lecture we review the

MIT - CS - 6.841

6.841 Advanced Complexity TheoryApr 13, 2009Lecture 18Lecturer: Madhu Sudan Scribe: Jinwoo ShinIn this lecture, we will discuss about P CP (probabilistically checkable proof). We rst overview the history followed by the formal denition of P CP and the

MIT - CS - 6.841

6.841 Advanced Complexity TheoryLecture 19Lecturer: Madhu SudanApril 15, 2009Scribe: Alex Arkhipov1. Review of Last Class Last class we gave a formulation of Probabilistically Checkable Proofs as a coloring of a graph that satises certain constraints

MIT - CS - 6.841

6.841 Advanced Complexity TheoryApril 22, 2009Lecture 20Lecturer: Madhu Sudan Scribe: Kristian Brander1IntroductionThe purpose of todays lecture is to explore the landscape of PCPs. In particular three constructions of Dinur, Raz and H astad will be

MIT - CS - 6.841

6.841 Advanced Complexity TheoryApr 27, 2009Lecture 21Lecturer: Jakob Nordstrom Scribe: Rishi GuptaToday and Thursday we will give an (extremely) selective overview of Proof Complexity. We will cover some major concepts, give an overview of the area,

MIT - CS - 6.841

6.841 Advanced Complexity TheoryApr 29, 2009Lecture 22Lecturer: Madhu Sudan Scribe: Jessica Yuan1Last TimeLast time, we talked about what a propositional proof system is. Its a way of proving that a formula is a tautology (i.e., its always true). Ve

MIT - CS - 6.841

6.841 Advanced Complexity TheoryMay 4, 2009Lecture 23Lecturer: Madhu Sudan Scribe: Rishi GuptaProject PresentationsPresentations are this Wednesday 9am-12pm and Thursday 9am-1pm. Slots may be moved around to space them out/ensure we dont run up again

MIT - CS - 6.841

6.841 Advanced Complexity TheoryMay 11, 2009Lecture 25Lecturer: Madhu Sudan Scribe: Rishi GuptaWrite your feedback for the course at https:/sixweb.mit.edu/student/evaluate/6.841-s2009. It will help future students decide whether they should take the c

MIT - CS - 6.841

MIT - CS - 6.841

MIT - CS - 6.841

MIT - CS - 6.841

MIT - CS - 6.841

MIT - CS - 6.841

MIT - CS - 6.841

MIT - CS - 6.841

MIT - CS - 6.841

MIT - CS - 6.841

MIT - CS - 6.841

MIT - CS - 6.841

6.841 Advanced Complexity TheoryMarch 19, 2007Lecture 12Lecturer: Madhu Sudan Scribe: Suho Oh, Jose Soto1Overview Randomized Reductions. Valiant-Vazirani: SAT RP U nique-SAT . Todas Theorem: P H P #P .2The Theorem of Valiant-Vazirani.To state thi

MIT - CS - 6.841

MIT - CS - 6.841

MIT - CS - 6.841

MIT - CS - 6.841

6.841 Advanced Complexity TheoryApril 9, 2007Lecture 16Lecturer: Madhu Sudan Scribe: Amanda Redlich, Shubhangi Saraf1Overview Permanent: worst case average case Permanent IP towards IP PSPACEIn todays lecture we will cover the following2The Perma

MIT - CS - 6.841

MIT - CS - 6.841

6.841 Advanced Complexity TheoryApril 18, 2007Lecture 18Lecturer: Madhu Sudan Scribe: Nadia Benbernou1Probabilistically Checkable Proofs (PCP)The goal of a probabilistically checkable proof is to verify a proof by looking at only a small number of b

MIT - CS - 6.841

MIT - CS - 6.841

MIT - CS - 6.841

MIT - CS - 6.841

MIT - CS - 6.841

6.841 Advanced Complexity TheoryMay 7, 2007Lecture 23Lecturer: Madhu Sudan Scribe: Alex Andoni, Anastasios Sidiropoulos1Overview Continue the discussion on Average-Case analysis (as opposed to Worst Case); Present Impagliazzos ve possible worldsl Ad

MIT - CS - 6.896

MIT - CS - 6.896

6.896 Sublinear Time AlgorithmsSeptember 14, 2004Lecture 2Lecturer: Ronitt Rubinfeld Scribe: Akshay Patil1Last Time Optimization problems - standard (saw the notion of -additive and -multiplicative relative approximations). Decision problems - saw e