Lecture 06 (2 23-2021) microbial mats
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This document covers the diversity of microbial mats, including the definitions and characteristics of microbial mats, their layers, and functional guilds of microbes. It also contrasts the carbon fixation methods and energy acquisition strategies of three photosynthetic bacterial phyla and describes adaptations of two thermophilic bacterial phyla. The learning goals are aimed at understanding how these microbial communities interact and the implications for early life on Earth.
Lecture 06 (2 23-2021) microbial mats
- 1. DIVERSITY OF MICROBIAL MATS Unit 06, 2.23.2021 Reading for today: Brown Ch. 8 & 9 Reading for next class: Brown Ch. 10 & 11 Dr. Kristen DeAngelis Office Hours by appointment deangelis@microbio.umass.edu 1
- 2. Introducing the Microbial Zoo • 13 Bacterial Phyla, Archaea, Eukaryotes and Acellular life • General characteristics of the phyla with 1-2 example species 2
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- 4. Unit 6: Diversity of Microbial Mats LECTURE LEARNING GOALS 1. Define microbial mats. Describe the functional guilds of microbes in the different layers, and how they interact. 2. For each of the three phyla of photosynthetic bacteria, contrast how each fixes C and gains energy and reducing equivalents from light. 3. For the two thermophilic bacterial phyla, describe their adaptations to life at high temperature. Explain how they are primitive and deeply-branching. 4
- 5. Unit 6: Diversity of Microbial Mats LECTURE LEARNING GOALS 1. Define microbial mats. Describe the functional guilds of microbes in the different layers, and how they interact. 2. For each of the three phyla of photosynthetic bacteria, contrast how each fixes C and gains energy and reducing equivalents from light. 3. For the two thermophilic bacterial phyla, describe their adaptations to life at high temperature. Explain how they are primitive and deeply-branching. 5
- 8. Microbial mat • Bacteria, archaea & microbial eukaryotes – The first life on earth existed as photosynthetic mats – Mats are food and encouraged evolution of “higher” life • Multi-layered, stratified sheet of microbes – Usually a few centimeters thick at most – a wide range of internal chemical environments – Close physical proximity of microbes facilitates interspecies transfers, sometimes known as cross-feeding • Microbial mats are a biofilm that you can see – the three kinds of biofilm (simple monolayer, stratified, and complex) are also found in mats – held together by “slime” or EPS and filamentous microorganisms – Usually prefer interfaces e.g., liquid-air or solid-air
- 9. Biological soil crusts • Cyanobacteria, mosses, and lichens • Can cover all soil spaces not occupied by vascular plants – hold soils in place, preventing erosion – Blowing sand can bury and kill crusts • Crusts grow very slowly, so walking on them can kill them and take decades to recover
- 10. Stromatolites
- 11. Stromatolites • Network of syntrophic relationships – cyanobacteria, other photosynthetic bacteria – anaerobic heterotrophs (including fermenters) – sulfate reducers and sulfur-oxidizers • grow through sediment and sand, bound by EPS, & new layers grow up towards the sun • Over time, layers harden to form rock – This process is called lithification. • Stromatolites built reefs in the first least three- quarters of the earth's history = “molecular fossils”
- 12. Lithification in Stromatolites • Extracellular polysaccharides (EPS) have carboxyl groups that can bind divalent cations, including calcium (Ca++) • Biofilms have cation binding capacity
- 13. Lithification in Stromatolites • Lithification = when precipitation of minerals outweighs dissolution. • Carbonate precipitation is possibly the most important process that impacts global carbon cycling • Microbes determine precipitation – EPS production – pH
- 15. Photoautotrophy • There are several types of chlorophyll (L), but all share the chlorin magnesium ligand (R) • Water is a natural attenuator of light, absorbing most of the infrared wavelengths within the first meter • Longer wavelengths penetrate further into water sediments
- 16. Photosynthetic microbial mat from top to bottom 1. macro- and micro- green algae – Fix C by photosynthesis – Filter light, exude some extra sugars 2. cyanobacteria & diatom species – Cyanobacteria fix C – Diatoms are heterotrophs or photosynthetic 3. purple sulfur bacteria – Photosynthetic C fixers – Use reduced sulfur to oxidize to S or SO4 4. Spirochaetes – Microaerophilic heterotrophs 5. green sulfur bacteria – Photsynthetic – Oxidize sulfide 6. sulfate reducers – Reduce SO4 to H2S (“rotten egg” smell) 7. Iron sulfide-rich sediments and remnants of decaying mats – Below the mat
- 17. Activity for Review of Unit 06.1 Microbial mats 1. A new phototrophic microbe you’ve discovered was isolated from low in the water column. What light- harvesting pigments is it likely to have, and why? 17
- 18. Unit 6: Diversity of Microbial Mats LECTURE LEARNING GOALS 1. Define microbial mats. Describe the functional guilds of microbes in the different layers, and how they interact. 2. For each of the three phyla of photosynthetic bacteria, contrast how each fixes C and gains energy and reducing equivalents from light. 3. For the two thermophilic bacterial phyla, describe their adaptations to life at high temperature. Explain how they are primitive and deeply-branching. 18
- 19. Green phototrophic bacteria • … 19 Chlorobi Chloroflexi (“blue-green algae”)
- 20. Phylum Chlorobi (green sulfur bacteria) Fig. 9.9 Chlorobium tempidum Fig. 9.10 Chlorobium limicola
- 21. Phylum Chlorobi (green sulfur bacteria) • Small number of closely related species, most are poorly characterized • All are strict photolithoautotrophs • Hydrogen or sulfur are electron donors for reverse TCA cycle to fix C • Energy via cyclic photophosphorylation • Most can fix N • Chlorosomes are inclusion bodies with high concentrations of accessory photopigments e.g. bacteriochlorophylls or carotenoids
- 22. Carbon fixation mechanism: Reverse (reductive) TCA cycle • Used by Chlorobi (green sulfur bacteria) • It consumes CO2, ATP, NADH/NADPH, and reduced ferredoxin to produce pyruvate
- 23. Obtaining ATP from light: Cyclic photophosphorylation • Most common way for bacteria to convert light into energy (ATP) – Chlorobi – Chloroflexi • Single photosystem • ATP produced via proton motive force (PMF) generated by the electron transport chain (ETC) RC, reaction center Bph, bacteriopheophytin Q, quinone ETC, electron transport chain CytC, cytochrome c
- 24. Reducing equivalents for C fixation: sulfur-dependent photosynthesis • Chlorobi have strongly reducing RCs • Electrons passed from Chl a to FeS proteins are able to generate reducing power as Fdred • External sources of reductant (sulfide etc) replace the electrons removed from the ETC to generate ATP via PMF Chl a, chlorophyll a FeS, iron-sulfur proteins Fd, ferredoxin S=, sulfide SO, elemental sulfur
- 25. Symbiotic consortia Chlorobium (seen) encapsulating a flagellated betaproteobacterium (unseen) Fig 9.10 Chlorobium symbiotic consortium
- 26. Symbiotic consortia Chlorobium (seen) encapsulating a flagellated betaproteobacterium (unseen) • The heterotroph (inside) is provided resources by the Chlorobi • The Chlorobi are provided motility by the heterotroph • The two cell types divide synchronously • The symbiont can swim phototactically (towards light)
- 27. Phylum Cyanobacteria (blue-green algae) Fig. 9.17 Fig. 9.16 Fig. 9.15 Fig 9.15 Dermocarpa violacea, Fig. 9.16 Oscillatoria, Fig. 9.17 Anabaena, freshwater species in the family Nostoc
- 28. Phylum Cyanobacteria (blue-green algae) • Not “algae,” these bacteria are functionally diverse but phylogenetically closely related – All do oxygenic photosynthesis with two photosystems to get energy and reducing power for fixing CO2 via the Calvin cycle – Chl-a as their only chlorophyll, but many also have phycobillins as accessory photopigments • Most can fix N – remember the NanoSIMS where we mapped the C fixation in vegetative cells of anabaena and N fixation to the heterocysts
- 29. ATP & reducing equivalents from light: Oxygenic photosynthesis • Cyanobacteria (including chloroplasts in plant cells) carry out oxygenic photosynthesis • Light activates the RC and reducing power is generated with ferredoxin reduction • A second reaction center (PS II) transfers electrons to the ETC to generate ATP via PMF Fdox, oxidized ferredoxin Fdred, reduced ferredoxin PSII, Photosystem II
- 30. Carbon fixation mechanism: Calvin cycle • Used by Cyanobacteria • Rubisco is the key enzyme in this pathway (ribulose bis-phosphate carboxylase/oxidase) • Rubisco carboxylates ribulose 1,5- bisphosphate to make two molecules of 3- phosphoglycerate • Rubisco is the most abundant enzyme on Earth
- 31. Chloroplasts
- 32. Chloroplasts • Found only in plant cells to provide energy from light • Derived from endosymbiosis of a cyanobacteria of the Prochlorales • Primary chloroplasts have 2 membranes • Secondary chloroplasts have 3 or 4 membranes
- 33. Phylum Chloroflexi (green nonsulfur bacteria) Fig 9.3 Chloroflexus aurantiacus Fig 9.4 Roseiflexus castenholzii Fig 9.5 Herpetosiphon aurantiacus
- 34. Phylum Chloroflexi • Generally include thermophilic phototrophs and heterotrophs which are sometimes thermophilic • Single type of photosystem & carry out Cyclic photophosphorylation to get energy (ATP) from light • Need to use reverse electron flow for NADH • Most can fix C via the unusual hydroxypropionate pathway
- 35. Reducing equivalents for C fixation: reverse electron flow • Purple non-sulfur bacteria & Chloroflexi get their NADH from this pathway • Requires a strong chemical reductant: sulfide, thiosulfate, elemental sulfur, a ferrous cation or H2 • Running the ETC in reverse drains the proton gradient & costs ATP Q, quinone ETC, electron transport chain CytC, cytochrome c S=, sulfide S0, elemental sulfur
- 36. Carbon fixation mechanism: Hydroxypropionate pathway • Used by Chloroflexi • Some of the same reactions as the TCA cycle, but generates glyoxylate
- 38. Chloroflexus-rich microbial mat • in the outflow of Excelsior Geyser, Yellowstone NP. • C. aurantiacus was isolated here & seems to be the primary producer. • You can see some patches of green cyanobacteria interspersed with the orange Chloroflexi 38
- 39. Green phototrophic bacteria Chlorobi (aka green sulfur bacteria) Cyanobacteria (aka blue-green algae) Chloroflexi (aka green non-sulfur bacteria) lifestyle Photo- lithoautotrophs, some are N-fixers Oxygenic phototrophs, some are N-fixers Anoxic phototrophs & photo- heterotrophs C-fixation Reverse TCA cycle Calvin cycle Hydroxypropionate pathway Energy (ATP) Cyclic photo- phosphorylation Oxygenic photosynthesis Cyclic photo- phosphorylation Reducing equivalents (NADH) Ferridoxin from the ETC (aka sulfur- dependent photosynthesis Oxygenic photosynthesis (two PS “Z-scheme”) Reverse electron flow via S2- or H2 oxidation 39 Chlorobi Chloroflexi (“blue-green algae”)
- 40. Activity for Review of Unit 06.2: Phototrophic bacteria 1. Chloroplasts are derived from an ancient endosymbiotic event, and have genomes. To what phylogenetic group to they belong? a. Phylum Chloroflexi (green nonsulfur bacteria) b. Phylum Chlorobi (green sulfur bacteria) c. Phylum Cyanobacteria (blue-green algae) 2. Based on the phylum that chloroplasts belong to, how do they a. gain energy from light? b. make reducing equivalents from light? c. fix carbon? 40
- 41. Unit 6: Diversity of Microbial Mats LECTURE LEARNING GOALS 1. Define microbial mats. Describe the functional guilds of microbes in the different layers, and how they interact. 2. For each of the three phyla of photosynthetic bacteria, contrast how each fixes C and gains energy and reducing equivalents from light. 3. For the two thermophilic bacterial phyla, describe their adaptations to life at high temperature. Explain how they are primitive and deeply-branching. 41
- 43. Thermophilic bacteria • Primitive – have changed less than other organisms since their common ancestry – They are NOT ancestors of other bacteria – They are NOT less complex • Deeply branching – branches connect closer to the root compared to other branches – This is a reflection of when this phylum (assumed to be a distinct group) emerged or evolved 43
- 44. Phylum Aquifex Fig. 8.3 Aquifex pyrophilus Fig. 8.4 Thermocrinus ruber
- 45. Phylum Aquifex • Phylogenetic relationships between representative members of the Aquifex • There are only a few dozen species in total • All are thermophilic or extremely thermophilic 45
- 46. Phylum Thermotoga Fig 8.7 Thermotoga maritima Fig 8.8 Thermosipho melanesiense Fig 8.9 Fervidobacterium islandicum Fig 8.7 Fig 8.8 Fig 8.9
- 47. Phylum Thermotoga • Fewer than three dozen species are described • All are thermophilic, anaerobic fermentative organisms • Their distinguishing feature is a loose sheath (or “toga”) snug over the sides but protruding at one or both ends • The toga is an outer membrane, rich in porin-like proteins, full of periplasm, with function otherwise unknown
- 48. Obsidian pool is an acidic, boiling spring
- 49. Life at high temperatures 1. Membrane fluidity: the membrane lipids have higher melting points 2. DNA structure: most organisms negatively supercoil their DNA but extreme thermophiles positively supercoil their DNA; there is actually no GC enrichment at high temp 3. RNA structure: some RNAs are GC rich, but enhanced stability comes from folding 4. Protein structure: we cannot predict how proteins are stabilized at high temp, but enzymes do function well under high temp conditions 5. Small molecule stability: many small molecules (e.g., GTP or NAD) are not heat resistant, so it is thought that they are consumed as they are produced
- 50. Activity for Review of Unit 06.3 Thermophilic bacteria • The Aquificae and Thermotogae are both primitive and deep-branching phyla. Can you draw a tree with deep branches that are not primitive, and with primitive branches that are not deep? Do you know of any examples of either? 50
- 51. Unit 6: Diversity of Microbial Mats LECTURE LEARNING GOALS 1. Define microbial mats. Describe the functional guilds of microbes in the different layers, and how they interact. 2. For each of the three phyla of photosynthetic bacteria, contrast how each fixes C and gains energy and reducing equivalents from light. 3. For the two thermophilic bacterial phyla, describe their adaptations to life at high temperature. Explain how they are primitive and deeply- branching. Next class is Unit 7: Diversity soils and sediments Reading for next class: Brown Ch. 10 & 11 51