Lecture 07 (2 25-21) soils
0 likes126 views
The document outlines a lecture on the diversity of soils and sediments, focusing on defining the concepts, contrasting microbes within each, and explaining biogeochemical cycles. It details the metabolic diversity and habitats of the five classes of proteobacteria and gram-positive bacteria, along with their ecological roles and significance in nutrient cycling. Key examples include nitrogen-fixing bacteria, pathogens, and antibiotic producers, illustrating the complex interactions within soil ecosystems.
Lecture 07 (2 25-21) soils
- 1. SOILS & SEDIMENTS Unit 07, 2.25.2021 Reading for today: Brown Ch. 10 & 11 Reading for next class: Brown Ch. 13 & 14 Dr. Kristen DeAngelis Office Hours by appointment deangelis@microbio.umass.edu
- 2. Unit 7: Diversity of Soils & Sediments LECTURE LEARNING GOALS 1. Define soils and sediment, and contrast the microbes living in each. Explain biogeochemical cycles. 2. Describe the diversity, metabolism & habitat of the five classes of the phylum Proteobacteria, including some common example species. 3. Describe the diversity, metabolism & habitat of the Gram-positive bacteria (phylua Firmicutes & Actinobacteria). 2
- 3. Unit 7: Diversity of Soils & Sediments LECTURE LEARNING GOALS 1. Define soils and sediment, and contrast the microbes living in each. Explain biogeochemical cycles. 2. Describe the diversity, metabolism & habitat of the five classes of the phylum Proteobacteria, including some common example species. 3. Describe the diversity, metabolism & habitat of the Gram-positive bacteria (phylua Firmicutes & Actinobacteria). 3
- 4. What is soil? • A solid matrix that supports plant growth • Minerals, organic matter & microbes
- 5. What is soil? • "Soils are a medium for plant growth" • Soil can be divided into two broad groups: – Mineral soils = Derived from rock weathering – Organic soils = Derived from sedimentation in bogs and marshes • Soils change with time, sun, water, wind, ice, and living creatures • Soils take thousands to millions of years to form
- 6. Rhizosphere • The soil directly influenced by plant roots • Rhizosphere soils have more water, nutrients, stable pH, microbial biomass and activity compared to bulk soil
- 7. Rhizosphere • Roots change chemical and physical properties of soils, so are also a route of soil formation or transformation • Root exudates (sugars and amino acids), secretions (waste), sloughed root cells, and lysates
- 8. Rhizosphere-specific microbes • Plant growth promoting rhizobacteria – diverse, functionally cryptic other than promoting plant growth • Mycorrhizal fungi (shown at right) – not all plants are capable of making mycorrhizal associations, but these also tend to be specific • Root nodule forming bacteria – N fixation in symbiosis with plants; can be specific associations (e.g., the filamentous Actinobacteria Frankia which forms nodules on alder trees), or or non-specific associations 8
- 9. Rhizobium etli Class Alphaproteobacteria • N-fixing plant symbiont – informally known as rhizobia – Photo shows root N-fixing nodules, which are terminally differentiated symbiotic associations with plants
- 10. Microbial N cycling in soils • There are 5 movements in the nitrogen cycle, all accomplished by microbes – Fixation – Uptake – Mineralization – Nitrification – Denitrification* 10 Industrial N2 fixation
- 11. Microbial N cycling in soils • Biogeochemical cycles map the transformations and movements of an element or compound through the environment. • Microbes are responsible for all soil N cycling – Microbes make soil N available to plants – Plants get ALL of their nutrients (except C) from soils • N fixation happens naturally by bacteria, but right now we are industrially fixing N using the Haber- Bosch process – As much N enters the atmosphere through industrial fixation as through biotic routes 11
- 12. Maritan Soils • There is evidence of water on Mars • There are iron minerals like on Earth • No microbes or evidence of them found on Mars… yet! 12
- 13. Sediments • Soil transported by water (fluvial processes), wind (aeolian processes) and ice (glaciers) – deposition on land forms soil, which takes thousands to millions of years per centimeter depth. – may eventually become sedimentary rock.
- 14. Activity for Review of Unit 07.1 • How are soil and sediment related? • What is the name for soil influenced by plant roots? 14
- 15. Unit 7: Diversity of Soils & Sediments LECTURE LEARNING GOALS 1. Define soils and sediment, and contrast the microbes living in each. Explain biogeochemical cycles. 2. Describe the diversity, metabolism & habitat of the five classes of the phylum Proteobacteria, including some common example species. 3. Describe the diversity, metabolism & habitat of the Gram-positive bacteria (phylua Firmicutes & Actinobacteria). 15
- 18. Phylum Proteobacteria • Most of the familiar gram-negative bacteria are proteobacteria • This is a “very successful” phylum because of the tremendous phylogenetic diversity of its members. – Each of the five classes of proteobacteria (alpha, beta, gamma, delta and epsilon) is as diverse as any other bacterial phyla. • They have a wide range of phenotypes scattered across the phylogenetic tree. • They are named for the shape-shifting sea god Proteus, because these organisms have evolved so many phenotypes.
- 19. Class Alphaproteobacteria • wide diversity of organisms, including – Purple non-sulfur phototrophic bacteria – Heterotrophs – Pathogens – Autotrophic methane oxidizers (methylotrophs) • Metabolism: Autotrophs fix C by the Calvin cycle • Habitat of this class ranges extensively, but these organisms dominate in soils and sediments • Examples – Caulobacter crescentus – Wolbachia spp. – Rhizobium etli – Mitochondria
- 20. Wolbachia pipientis Class Alphaproteobacteria • Common intracellular symbiont of arthropods and nematodes – Up to 60% of all insects are infected with Wolbachia – Maternally transmitted – tends to not naturally infect Aedes aegypti, the mosquito that carries infectious diseases like dengue virus • Mosquitos infected with Wolbachia have a reduced ability to carry viruses. Fig 10.7. wasp egg infected with Wolbachia, which are the white dots at the bottom of the image
- 21. Mitochondria Class Alphaproteobacteria • Order Rickettsiales • Has DNA, performs respiration, has an electron transport system that occurs across membranes, and produces ATP • endosymbiotic theory – once was a bacterial cell that colonized a eukaryote – Mitochondria originated as a symbiosis between separate single-celled organisms
- 22. Class Betaproteobacteria • Large and diverse • Metabolism – Chemolithoautotrophs or heterotrophs, and some pathogens – Aerobic or facultative anaerobic – Members can degrade compounds involved in “waste management,” including lignin and phenol • Habitat: most environments, especially organic-rich soils, sediments, wastewater, and eutrophic aquatic systems
- 23. Ralstonia solanacearum Class Betaproteobacteria • Plant pathogen – Bacterial wilt disease in crops – tobacco, potato, tomato, pepper, and bananas • Obligately anaerobic motile rods • Infects through the root hairs, grows, and is transported around the plant through the xylem – This pathogen grows in such abundance that the diagnostic test is to dip the cut end of an infected plant in water – the infection can be seen as a milky stream flowing out of the xylem (shown at right)
- 24. Class Gammaproteobacteria • A very large and diverse class • Metabolism – obligate aerobes, facultative anaerobes, microaerophiles, and obligate anaerobes – Heterotrophs, chemoautotrophs and photoautotrophs • Habitat – Pathogens, opportunistic pathogens, and symbionts – Cryophiles, mesophiles, and moderate thermophiles • Examples – Escherichia coli – Chromatium spp.
- 25. Escherichia coli Class Gammaproteobacteria • Facultative anaerobe • Common in animal feces, lower intestines of mammals, and even on the edge of hot springs – Routinely used as a fecal indicator for contamination in food and water • Opportunistic pathogen – E. coli O157:H7 is a strain of the bacterium E. coli that produces Shiga-like toxins – Toxin catalytically inactivates the ribosome of most eukaryotic cells – enterohemorrhagic
- 26. Chromatium spp. Class Gammaproteobacteria • Purple sulfur bacteria – microbial mats • Motile by polar flagella and grow alone or in small groups • May use H2 or sulfide (H2S) as an electron donor for reverse electron flow to gain energy (NADH) • The product of H2S oxidation is elemental sulfur, which accumulates in granules inside of the cell
- 27. Class Deltaproteobacteria • Diversity – most are anaerobic sulfate reducers • Metabolism: – syntrophic hydrogen-generating heterotrophs – Also some aerobic heterotrophs • Habitat: anaerobic sediments and parasites of other bacteria • Example species – Myxococcus xanthus – Bdellovibrio bacteriovorans
- 28. Myxococcus xanthus Class Deltaproteobacteria • Gliders with complex life cycles, usually found on bark or decomposing leaves or wood • Produces simple spheroid fruiting bodies on short stalks • Is able to swarm and excrete lytic and digestive enzymes that lyse bacteria
- 29. Class Epsilonproteobacteria • Diversity: narrow phylogenetic group • Habitat: Intestinal symbionts, parasites of other bacteria, and deep-sea environments, especially hydrothermal vents • Metabolism: – Microaerophilic or anaerobic heterotrophs – Generally cannot eat carbohydrates • Example species – Helicobacter pylori
- 30. Helicobacter pylori Class Epsilonproteobacteria • Microaerophilic curved rod with sheathed flagella • Common symbiont of the stomach, colonizing ~70% of humans • Sometimes can cause stomach ulcers, but may also help modulate stomach acidity so important to the human microbiome
- 31. Helicobacter pylori • Barry Marshall & Robin Warren won the Nobel prize in 2005 for establishing the role of H. pylori in stomach ulcers. • In 1985, Marshall showed that self administration of Helicobacter pylori causes acute gastritis, and suggested that chronic colonisation directly leads to peptic ulceration. • They showed that antibiotic and bismuth salt killed H. pylori and cured duodenal ulcers. • This was the first evidence that gastric disorders could be due to infectious disease. 31
- 32. Activity for Review of Unit 07.2 • What microbe is an environmental biocontrol agent for mosquito-transmitted viral pathogens? • What microbe is the ancestor of the mitochondria? • What microbe is responsible for ulcers? • What phylum and class do the purple sulfur bacteria belong to? 32
- 33. Unit 7: Diversity of Soils & Sediments LECTURE LEARNING GOALS 1. Define soils and sediment, and contrast the microbes living in each. Explain biogeochemical cycles. 2. Describe the diversity, metabolism & habitat of the five classes of the phylum Proteobacteria, including some common example species. 3. Describe the diversity, metabolism & habitat of the Gram-positive bacteria (phylua Firmicutes & Actinobacteria). 33
- 35. Phylum Firmicutes • Large & diverse phylum – aka low G+C Gram positive bacteria • Metabolism – Almost all Heterotrophs – Anaerobes use substrate-level phosphorylation rather than anaerobic respiration • Habitat: abundant in soils, also colonize the skin, mucous membranes & gut
- 36. Bacillus cereus Phylum Firmicutes • Close relative of B. anthracus • Soils & guts • Produces endospores, stress-resistant asexual spore that develops inside mother cells Fig. 11.3. Bacillus cereus
- 37. Phylum Actinobacteria • Diversity spans a small phylogenetic range but includes a large number of families & species • Metabolism – Aerobic mesophilic heterotrophs – Known antibiotic producers – These plus Bacillus are the most common bacterial source of antibiotics • Habitat – Common in soils & guts – Few animal symbionts and pathogens Fig. 11.11. Mycobacterium ulcerans Fig. 11.12. Thermoleophilium album
- 38. Streptomyces antibioticus Phylum Actinobacteria • Filamentous growth with specific spatial arrangements • Used in the industrial production of antibiotics Fig 11.10. Phase-contrast image overlaid with red (DNA) and green (sporulation septa) fluorescence
- 39. Mycobacterium tuberculosis Phylum Actinobacteria • M. tuberculosis complex (MTC) – M. africanum, M. bovis, M. canettii, M. microti, M. tuberculosis (TB). • Obligate human pathogens with no environmental reservoir – One third of people have TB – Aerosol transmitted – Treatable with 6 months course of antibiotics • MTC’s unique ability to utilize cholesterol, which is a common component of human cell membranes, plays a role in its persistence
- 40. Activity for Review of Unit 07.3 Gram positive bacteria • For each microbe listed, name the phylum it belongs to, and match it to its function. _ Bacillus cereus _ Mycobacterium tuberculosis _ Streptomyces antibioticus a. Most common source of industrial antibiotics b. Animal pathogen with no known environmental reservoir c. Soil microbe that produces endospores 40
- 41. Unit 7: Soils & Sediments LECTURE LEARNING GOALS 1. Define soils and sediment, and contrast the microbes living in each. Explain biogeochemical cycles. 2. Describe the diversity, metabolism & habitat of the five classes of the phylum Proteobacteria, including some common example species. 3. Describe the diversity, metabolism & habitat of the Gram-positive bacteria (phylua Firmicutes & Actinobacteria). Next class is Unit 8: Rare & uncultured microbes Reading for next class: Brown Ch. 13 & 14 41