University of Texas BIO 330 Microbial Ecology Exam 1 review topics/Guide

University of Texas BIO 330 Microbial Ecology Exam 1 review topics/Guide Microbial Ecology 2024 – Exam 1 review topics/guide What is microbial dark matter? A type of microbial matter that is hypothesized to account for a large part of the microbial data missing. It cannot be seen directly, but it’s properties are inferred. What are archaea? How were they discovered? Archaea are single celled organisms that were originally classified with bacteria. However, they were separated due to unique characteristics found in their rRNA. How are phylogenetic trees made? DNA sequences are aligned and compared in order to make inferences about relationships and timeline. What are the parts of a phylogenetic tree? Root, internal branches, internal nodes (represent hypothetical ancestral taxa), terminal taxa, terminal branches How are microbes characterized based on temperature regimes? Psychrophiles: 0-20 C Psychrotrophs: 0-35 C Mesophiles: 20-45 C Thermophiles: 45-85 C Hyperthermophiles: 85-100 CWhat does mean to be monophyletic? They have the same most recent common ancestor and all descendants. Includes a node and everything arising from it. - Inherited set of common traits How are phylogenetic trees tested/supported? Bootstrapping - Assigns accuracy to sample estimates - Random sampling with replacement - Compare quality of inference from resample data to “true” sample - Node has support when >80 via 16s rRNA or ribosomal protein How did Carl Woese discover archaea? He developed a new evolutionary marker, SSU rRNA that led to the discovery of archaea as theirs was distinct from other bacteria. What is a pangenome, core and accessory genes? Pangenome – the complete set of genes in a species or clade. Made up of the core and accessory genes. Core Genes – genes that are present in all individuals in a species. Accessory – genes that are present in only some individuals or strains. What are some things that cause genomes to evolve? For example, why do some genomes get small? Smaller genome - More stable habitat - Specialist - “dumber” Larger genome- More dynamic habitat - Generalist - “smarter” What is the great plate anomaly? the difference between the number of microbial cells in an environmental sample and the number of colonies that can be grown from a sample in a lab. Demonstrates that only a small fraction of microbial diversity can be assessed with standard cultivation techniques Why did Carl Woese choose rRNA to make the first trees of life, or what makes it a good gene for making the tree of life? He chose rRNA to make the first trees of life because it is highly conserved across all organisms and evolves very slowly. Allowing it to be used for comparison across even distantly related species and serving as a reliable “molecular clock” to trace deep evolutionary relationships. What are the limitations and advantages of the different techniques we covered in lecture? Microscopy and FISH Can provide high resolution details of cells for research! However, may be lengthy/expensive process and cells can be killed in the process. Using geochemistry to study microbial communities Can allow us to detect microbial diversity by detecting their chemical products like oxygen and hydrogen sulfide. How we detected life on mars. However, sampling areas are limited and there is uncertainty when identifying distinct populations. DNA-SIP Can help us separate different microbial species within an environmental sample. However, takes a long time and is not suitable for every sample as there is a chance that none would respond to the substrate.Culturing Can give us a really clean look at how microbes grow with the chance to analyze them. However, can only sample small fractions of real microbial communities. Cultivation and sequencing biases. Diversity surveys of nature (using PCR to amplify 16S rRNA genes and make trees) Provides insight into the nature of biological systems, can help us recognize previously unknown information, gives us a starting point for generating hypotheses about functional roles in environment. Unfortunately, it takes a very long time and was pretty inaccessible until recently. Single-cell genomics The use of cell-sorting techniques and random PCR amplification of single cells results in genome amplification provides new information on microbial species and advances knowledge of genomic diversity in a population. Disadvantages include that there can be a lot of noise with low input material, amplification bias and heterogeneity that it can be hard to focus on the target. Metagenomics Shotgun sequencing of microbial community DNA provides an in-depth look at genotypic richness within populations. It is a very sensitive process that can be easily messed up, large volumes of data make it very hard to sort through, and it can be very costly to carry out efficiently. What is the microbial rare biosphere? A term used to describe a group of microorganisms that are present in low number in microbial communities but are genetically diverse. What’s the difference between a microbial generalist vs a specialist? The main difference is the range of environments they can survive in. Generalists can survive in many different environments. They have broad environmental tolerances and can acquire more habitats. Specialists can only survive in onetype of environment. They have a narrower rand of habitats and specific adaptations to survive in them. How has metagenomics altered our view of the tree of life? It made it possible for us to generate trees based on multiple genes and not just 16S rRNA gene. How have SAR11 bacteria adapted to life in low nutrient Open Ocean? Streamlined a genome with minimal complexity. Small cell size so not much energy was required. Slow growth rate. What are the CPR bacteria and DPANN archaea, what do we know about them? Small-celled symbionts that are often found in groundwater and play important roles in the microbial community such as expanding the bacterial and archaeal domains, helping ecosystems cope with antibiotic resistance, pushing back the LUCA of bacteria and archaea, and disobeying what we thought to be core features of life. What genomic binning, what is the advantage of doing it? Genomic binning is the process of taking contigs, which are overlapping sequencing reads that represent a segment of a genome and grouping them based on similarity. This suggests that they belong to the same organism and can make sequencing a microbial system faster. How is it thought that the first eukaryotic cells were formed? What is endosymbiosis theory and how does it relate to the origin of eukaryotes? It is thought that eukaryotes evolved from prokaryotes combining together during endosymbiosis. How do we know that mitochondria came for bacteria? There is a lot of evidence. Membranes – have double cell membranes DNA – have circular DNA, like bacterial genome Reproduction – via budding, just like bacteria Size – similar size to bacteria Also, mitochondria have their own genomes that looks like bacteriaWhat is the hydrogen hypothesis? An interaction based on hydrogen exchange led to the first mitochondrial containing eukaryotic cell. How has the discovery of Asgard archaea (Lokiarchaeota) impact our understanding of the origin of eukaryotes? It is thought that Asgard archaea was the original “body” of a eukaryotic cell and absorbed the other prokaryotes. What evidence is there that Asgard archaea are related to eukaryotes Their metabolic systems. Microbial ecology Exam 2 – review topics Basic terminology: Oxic/anoxic = an environment with/without oxygen present Aerobic/anaerobic = specifically refers to a metabolism or organisms with/without oxygen How are microbes named based on they metabolisms? What is a heterotroph, chemotroph, autotroph, phototroph, etc… Given the metabolism of an organisms you should be able to name it, for example, chemoorganoheterotroph, photolithoautotroph, etc. Chemotrophy a) Energy coming from chemicals b) Respiration (aerobic or anaerobic) Redox reaction between external electron donor and acceptor c) Fermentation Phototrophy a) Energy coming from light b) Oxygenic (with oxygen) c) Anoxygenic (without oxygen)Heterotroph – cannot produce its own food and mut obtain nutrients by consuming other organisms, consumes organic carbon Autotroph – can produce its own food, fix its own CO2 (inorganic) Mixotroph – can derive energy from both sources Organotroph – obtain energy from organic compounds Lithotroph – get energy from inorganic compounds Energy source (photo or chemo) + electron source (litho or organo) + carbon source (auto or hetero) What is chemosynthesis and why is it important? Chemosynthesis is where organisms produce food by using chemical energy from inorganic compounds like sulfur. Bacteria that can do this are the primary source of life in deep hydrothermal vents because there’s no light. Why are microbial communities ordered in nature? For example, in sediments there are layers from top to bottom: respiration, nitrate/nitrite reduction (denitrification), sulfate reduction, methanogenesis. Why are things in order this way? They are ordered because of the redox tower. In any redox reaction you have an electron donor and electron acceptor and E’ determines whether the reaction requires energy or gives it off. Certain reactions where you get more energy than others. Redox tower. - Aerobic respiration is the most energetically favorable (positive E’ = 0.82) - Organic matter degradation least energetically favorable (negative E’ = -0.48)This Redox tower then determines the order in which you find organisms. Because aerobic respiration is first, these organisms will come first. Once oxygen is depleted then the next most favorable metabolism takes place (nitrate respiration), and so on. What is the reason that this order is not always found in nature, aka what causes this to not always be in order of energetics? The variable organic matter supply can lead to the disruption of the redox tower. If the supply of organic matter is disrupted it can cause the steps to be out of order. This can also happen if there’s diffusion of electron acceptors. Pollution also can alter redox conditions. Be familiar with the key steps in carbon cycling – methanogenesis, methanotrophy, carbon fixation, aerobic respiration. Methanogenesis – production of methane. By-product of fermentation. Complete breakdown of carbon in nature (by microbes) results in methane production. Carbon Dioxide turning into methane. Takes a bunch of genes to do. Chain of fermentation- Polymers → monomers → Acetolactic and autotrophic methanogens → CH4, CO2 DIAUXIC RELATIONSHIP W SULFUR – sulfur used first, then methane used. If sulfate present → the sulfate reducers will use those to reduce sulfate to sulfide. Without sulfate → sulfate must be used up and then methane can be produced What is syntrophy? For example, ANME and their partners, be familiar with this. Syntropy is a mutualistic relationship between different microbial species that work together to degrade compounds that neither could break down alone. A well-knownexample of syntrophy is ANME and their partners SRB. ANME want to oxidize methane anaerobically, which requires the removal of electrons. However, they cannot do this. So, SRB accepts the electrons from the methane and uses them to reduce sulfate to hydrogen sulfide. This results in mutual benefits because ANME gets to oxidize methane and SRB gains energy from sulfate reduction. Together, this partnership helps to reduce greenhouse gas emissions. When and where (it is common in sediments, why?) does methanogenesis occur in nature? Methanogenesis can happen in a multitude of places in nature. However, it commonly occurs in sediments because the sulfate presence is low meaning that methane can be produced by the breakdown of carbon from microbes. How do microbes generate ATP/energy? ATP is generated through multiple pathways. Phototrophy and chemotroph both release ATP. In Phototrophy, electron transport chain drives proton motive force, ATP generation. Can be done oxically or anoxically. In autotrophy, ATP is generated through substrate level phosphorylation as a by product of glycolysis. One glucose creates 2 ATP. What are the two types of photosynthesis and how do they differ? Oxygenic photosynthesis – PRODUCES OXYGEN. H2O is split into hydrogen and oxygen, incorporating electrons of hydrogen into sugar molecules. Cyanobacteria (and chloroplast descendants) are only known to do this. Anoxygenic photosynthesis – DOES NOT PRODUCE OXYGEN. Instead of using H2O - H2S, H2, and Fe2+ are used. Produces SO4 2-, H+, or Fe-3 instead of oxygen. Purple and green sulfur bacteria use this.What is the different between catabolism and anabolism, dissimilatory vs. assimilatory metabolism? Catabolism – the breaking down of large molecules into smaller ones for the release of energy. EX: release of ATP from glucose being broken down (cellular respiration) Anabolism – the use of energy to assemble large molecules from smaller ones. EX: protein synthesis. Amino acids are being assembled into proteins. Work together to allow organisms to break down nutrients to gain energy and then use that energy to build necessary cellular components. Dissimilatory Metabolism – when organisms use inorganic molecules for energy without incorporating them into biomass. EX: nitrate reduction uses nitrate as an electron acceptor to gain energy but its not incorporated into the cell’s structure. It is released as waste Assimilatory Metabolism – when inorganic molecules are incorporated into the organisms biomass for building cellular components. EX: a different side to nitrate reduction is when the nitrate is taken up and converted into amino acids and nucleotides. Which are then used in the cells structure rather than being released. What is the biological carbon pump? How is it important in global carbon cycling and climate change? The biological carbon pump is the process where CO2 taken from the atmosphere is transported from the surface ocean to the deep ocean (microbial loop). It plays a crucial role in the global carbon cycle by helping the Earth regulate the concentration of CO2 in the atmosphere. What is fermentation? Is a way to generate energy from carbon. Heterotrophy. Takes glucose or other organic compounds and reduces them to create ATP. Makes alcohol, acetate, and lactic acid.Important because there’s organisms that create the energy from fermentation and organisms that use the energy created from fermentation. Polymers → Monomers → formate/acetate → sulfate reducers use acetate to do sulfate reduction. Why to Thaumarchaeota outcompete bacteria for ammonia oxidation in the oceans? It is the dominant organism. It takes ammonia and converts it to nitrite. How do they outcompete? Enzyme kinetics. How quickly things can be done based on the concentration of substrate. Did the enzyme kinetics of the ammonia oxidizing archaea. Found a low Km. Which means they can do ammonia oxidation with really low amounts of ammonia present. Whereas most bacteria in these environments had a high Km meaning that they need high concentrations of ammonia in order to perform the oxidation efficiently. Big discovery. Can convert urea to ammonia and then oxidize this. How might ocean acidification impact carbon cycling? Some phytoplankton have cell walls made out of carbonates. At normal ocean pH, 90% of the carbon is bicarbonate, 9% is carbonate, and 1% is CO2. Ocean acidification – If CO2 is increased in the ocean (by the increasing amount of CO2 in the atmosphere) the pH is shifted to more acidic. If you decrease the pH of the ocean, it is harder to precipitate carbonate so organisms that have carbonate cell walls (phytoplankton) have a harder time surviving. They can’t make cell walls. What are oxygen minimum zones (OMZ), areas in the water columns of lakes and oceans where oxygen is deplete, and how are they formed? OMZ’s are regions in the water column of oceans and some lakes where oxygen is extremely low. Either hypoxic or anoxic. They are formed from a combination of factors:1. High Biological Activity and Oxygen Consumption – microbial decomposition consumes oxygen. When this is done at high rates, it depletes the oxygen. 2. Limited Oxygen replenishment – where oxygen from surface does not easily mix down to mid-deep layers of the ocean. This is mainly due to water stratification where waters with different temperatures and densities prevent the mixing of oxygen-rich surface water. 3. Slow ocean currents : less mixing due to lack of currents. Hold an importance when coming to nutrient cycling because they can perform chemical transformations not possible in oxygen rich waters. For example, anaerobic ammonium oxidation. Why is iron such an important nutrient in the oceans? Why might iron fertilization not be such a good approach to slowing climate change? Iron is a vital nutrient to phytoplankton as they require it to perform photosynthesis. It is shown that in low iron areas of the ocean, phytoplankton growth is scarce. Meaning that the microbial loop is not taking place. Iron fertilization involves adding iron to the ocean in order to stimulate phytoplankton growth and the uptake of CO2. However, it’s benefits may be limited because of some key factors: 1. Not all carbon fixed by phytoplankton goes into the deep sea. A lot of it is released back into the atmosphere which makes the net impact negligent 2. Studies have shown that only a fraction of carbon from iron induced phytoplankton actually makes it to the deep ocean (not effectively sequestered) 3. Greenhouse gas pollution like methane and nitrous oxide have the chance to be increased. 4. Ecosystem disruptions 5. Ocean acidification. Any remaining CO2 in the ocean would contribute to ocean acidification. 6. Oxygen depletion. With a high amount of phytoplankton degrading organic matter, oxygen could become depleted which would result in OMZs. What are the major microbial processes in the nitrogen cycle and where do they occur? Make sure you know what each of these processes do for example; denitrification reducesnitrate to N2. Comamox converts ammonia to nitrate. Anammox converts ammonia and nitrite to N2. Anammox, denitrification, nitrification, ammonia oxidation, N fixation, and Comamox 1. Nitrogen fixation. a. Converts nitrogen gas (NH2) to ammonia (NH3) where it can be used by plants and other organisms b. Occurs in soil and aquatic environments. Often within plant root nodules or symbiotic relationships. As well as free living nitrogen fixers in soil and water. 2. Nitrification a. Two step aerobic process that converts ammonia to nitrate. b. Step 1 – ammonia oxidation. Conversion of ammonia into nitrite. Occurs in soils, sediments, and upper layers of the ocean. c. Steo 2 – nitrite oxidation. The conversion of nitrite into nitrate. Occurs in same areas above. Needs supply of nitrite and oxygen 3. Comammox a. Recently discovered process where a single organism can convert ammonia (NH3) directly to nitrate without needing to go through nitrification described above. b. Has been observed in soils, wastewater, treatment plants, and other environments with low nitrogen concentrations. 4. Denitrification a. Reduction of nitrate to nitrogen gas or nitrous oxide which is released back into the atmosphere. b. Occurs in anaerobic environments like waterlogged soils, wet lands, sediments, and OMZ’s 5. Anammox a. Anaerobic process that converts ammonia and nitrite directly into nitrogen gas and water. Bypasses nitrate production and is a significant nitrogen removal pathway b. Occurs in oxygen limited environments like marine sediments, OMZs, and wastewater treatment plants How are the carbon and nitrogen cycling linked in the ocean water column AND in anoxic environments? 1. Ocean water column – oxic conditions a. Photosynthesis by phytoplankton. Take up dissolved CO2 and nitrate, ammonium, or nitrate to produce organic matters essential for the marine food web b. Decomposition and respiration. When organisms die, CO2 is released, and inorganic nitrogen is released back into water. Termed “remineralization” – when carbon and nitrogen are returned to their dissolved inorganic formsc. Nitrification and carbon fixation. Nitrification releases small amounts of Co2. d. Denitrification in low oxygen zones. In OMZs, microbes use nitrate as an alternative electron acceptor to break down organic carbon. 2. Anoxic environments a. Anammox. Anammox use CO2 for carbon fixation and the bacteria then converts ammonium and nitrite directly into nitrogen gas. b. Anaerobic Decomposition (fermentation and methanogenesis). In anoxic environments, organic carbon is broken down without oxygen using fermentation and methanogenesis. Formation produces Co2 and methanogens then use CO2 to produce methane c. In anoxic environments, sulfate reducing bacteria uses sulfate as an electron acceptor which competes with methanogenesis. The suldate reduction affects nitrogen by creatin a low oxygen environment d. Denitrification coupled with carbon decomposition. In low oxygen areas, organic carbon is used as an electron donor for denitrification. Bacteria reduce nitrate to nitrogen gas. What is eutrophication and what are the causes of it? Eutrophication is the process by which a body of water becomes overly enriched with nutrients, primarily nitrogen and phosphorus, which leads to excessive growth of algae and other aquatic plants. Can be caused by agricultural runoff, sewage and waste water, industrial discharge, detergents and household products, atmospheric deposition (fossil fuel combustion), natural processes like weathering of rocks (less harmful). How do microbes accelerate cave formation? - Microbially induced carbonate dissolution. Sulfur oxidizing bacteria produces sulfuric acid as a byproduct which dissolves carbonate rocks, accelerating cave formation. How are DMS and Roseobacter so important? - When released into the atmosphere, DMS oxidizes to form sulfate aerosols, which contribute to cloud formation and cool the environment. - Roseobacter is a group of marine bacteria that specialize in producing DMS by breaking down DMSP. What are siderophores?- Siderophores are organic molecules produced by certain bacteria and fungi to scavenge iron from their surroundings. Crucial for microbial growth in ironlimited environments. How are Fe cycling and C cycling linked in sediments? - Iron reducing bacteria use organic carbon as an electron donor to reduce Fe3 to Fe2 under anoxic conditions. - The reduced iron created can react with sulfides produced by sulfate reducing bacteria to form iron sulfide minerals that trap carbon within the sediment. What are magnetosome and what is their function? - Magnetosomes are intracellular structures containing magnetic materials produced by certain bacteria called magnetotactic bacteria. - They allow the bacteria to orient themselves on the Earth’s magnetic lines, a behavior known as magnetotaxis. - Help bacteria navigate vertically within the water column or sediments. Why do rate of denitrification and sulfate reduction vary on the sea floor? What makes them increase? Both denitrification and sulfate reduction are forms of anaerobic respiration where microbes use either nitrate or sulfate to break down organic matter. Factors determining the rates of this: - Availability of organic matter. Both require organic carbon as an electron donor and availability of this may vary - Electron acceptor availability. Nitrate and sulfate have to be present to accept the electron from carbon and become reduced. Availability of this may vary. Things that may make this increase is high organic matter deposition (high carbon), limited oxygen availability, high nitrate and sulfate levels, and optimal temperatures. How to viruses benefit microbial communities? - Viruses benefit microbial communities by regulating populations, promoting diversity, and contributing to nutrient cycling.How do they influence diversity, and evolution? - They often influence diversity through horizontal gene transfer. This is where genes are carried between different microbial species which confer beneficial traits like antibiotic resistance or metabolic abilities. Overall, this leads to evolution. What’s is “kill-the-winner” and how is it important? - The kill the winner hypothesis suggests that viruses help maintain microbial diversity by preferentially infecting and killing the most abundant species. Basically, the viruses keep the dominant species in check by not allowing them to overpopulate and monopolize the resources. What are AMGs and why are they important? - AMG’s are genes carried by viruses that encode enzymes and other proteins involved in the metabolism of their host microbes. Are beneficial because they can enhance the metabolic capacity of the host cell and participate in nutrient cycling by facilitating the degradation of organic compounds. What is the microbial loop and how are viruses involved? - The microbial loop describes the nutrient transfer between primary producers and higher trophic levels. Helps to get carbon into deeper levels of the ocean. - Viruses contribute to this by killing microbes and releasing their nutrients back into the water for cycling. Final portion of microbial ecology class review (this is just a review for the lectures since exam 2, the final is comprehensive) What is a plant symbiosis in which the plant acquires its symbionts every generation and how do these symbionts contribute to their hosts? (could be either rhizobia or mycorrhizae) This process is called horizontal symbiosis or horizontal transmission of symbionts. This means the plant does not inherit the symbionts from the parent, but instead acquires them from the environment in each new generation. Rhizobia-Legume Symbiosis- Legumes form a mutualistic relationship with nitrogen-fixing bacteria called rhizobia - Legumes acquire rhizobia via signal molecules, when rhizobia enter they induce the formation of root nodules. The nodules convert atmospheric N2 into ammonia NH3, providing the Legume with a usable nitrogen source. - In return, the plant supplies rhizobia with carbohydrates and protection. Mycorrhizal Fungi-Plant Symbiosis - Fungi are inherited from parent plants, but are acquired from the soil - The fungi colonize plant roots and create arbuscules, which increase nutrient and water absorption - The plant supplies the fungi with carbohydrates produced via photosynthesis. Both of these are mutualistic, but the plants must acquire these microbes from the soil for each generation. So, soil health and microbial diversity is essential in the formation/strength of this relationship. What are the functions of the gut microbiota in cows (and/or in termites?) Ruminants in Cows Cows rely on microbial fermentation in their rumen to break down plant material. The rumen microbiota help to: - Break down cellulose into simpler sugars - Ferment plant material to VFAs which energize the cow - Produce methane - Produce vitamins - And support the immune system Termite Microbiota Termites feed on wood, high in lignocellulose but nutrient poor. Their gut microbiota is essential for survival. Their microbiota can: - Breakdown cellulose and lignin - Convert sugars into acetate (energy source) - Fix nitrogen - Produce methane - What is rumen fermentation and what are some consequences for atmospheric composition?Rumen fermentation is the microbial breakdown of plant material in the rumen, the largest chamber of a ruminant’s stomach. It allows cows, sheep, and other plant consumers to digest compounds like cellulose that cannot be broken down on their own. Atmospheric effect: - Methane emissions are increased through rumen fermentation. Every cow emits 100-200 liters of methane per day via burping or gas. Methane is a big contributor to climate change. - Manure from ruminants can contribute to Nitrous Oxide emissions. What is the basis of primary production for communities around hydrothermal vents? In other words, how is CO2 fixed there without light? Microorganisms that grow on inorganic energy sources and fix carbon via chemosynthesis. This is similar to photosynthesis, but the energy is derived from chemical reactions and not sunlight. - Overall, it was found that photosynthesis is still used as Oxygen, a by-product of photosynthesis was needed in a lot of the chemical reactions. - It was found that there are photosynthetic, deep sea hydrothermal bacteria. These bacteria capture geothermal radiation as sunlight, using pigments, chlorosome, and a photosynthetic antennae complex. - This geothermal energy is utilized by animals in vents via symbiosis, consumption of bacteria, and predators that feed on the above. What is the importance of mycorrhizal fungi in Earth ecosystems, and when did these symbioses first originate? Mycorrhizal Fungi enhance plant nutrient uptake via hyphal networks, improve soil structure with glomalin, and promote biodiversity by reducing plant competition by sharing resources through CMNs. - These relationships are thought to originate back 500 million years ago. - Fossil evidence suggests that the earliest land plants formed symbiotic relationships with Glomeromycota fungi which allowed them to colonize terrestrial environments by providing essential nutrients. How do hydrothermal vents impact the chemistry of the oceans?Deep sea hydrothermal plumes are the interface for chemical exchange between the lithosphere and ocean. - Chemistry of the oceans previously unbalanced as excess Mg would enter them through rivers but there would not be enough Mg output (sediment). However, vents allow additional exchange of minerals that increased the chemical output of the ocean floor. - Hydrothermal vents are rich in: iron, manganese, sulfide, hydrogen, methane, and toxic heavy metals - The chemical characteristics come from reactions between sea water and basalt (rock from cooled lava) What is the source of microbes in hydrothermal plumes? How do plumes impact the water column? Deep sea hydrothermal plumes are a significant source of Fe & Mn to the oceans. When these minerals are introduced to deep-sea environments, it can cause “background” bacteria on the sea floor to become more activated and create “plume” communities. These plume communities then facilitate chemosynthesis which becomes an important source of iron to the surrounding water column. What is the chemical/physiological basis for the symbiosis between tube worms (Riftia) and bacteria in their troposphere? Symbionts in Riftia are internal = endosymbiosis - Their troposphere (feeding body) is packed with sulfur-oxidizing and carbon fixing bacteria that provide organic matter to the host - The host provides oxygen, sulfur, and CO2 to the symbionts What is a meromictic lake and how does this impact microbial community structures of lakes and biogeochemisitry in the different seasons? A meromictic lake is a lake in permanent stratification, meaning its layers do not fully mix. Unlike other lakes that undergo seasonal turnover and mixes, meromictic lakes have a deep, isolated later that remains anoxic all year round. Because of the layer stratification, each layer is known to have it’s own distinct microbial communities that drive unique biogeochemical cycles:- Mixolimnion layer (surface): dominated by aerobic bacteria, where photosynthesis occurs. Undergoes freezing in colder months that may reduce surface oxygen exchange - Chemocline layer (middle): supports anaerobic and microaerophilic bacteria. Sulfurreducing bacteria thrives here. During colder months, may have lower photosynthetic activity but sulfur cycling is still active - Monimolimnion layer (deep): dominated by strict anaerobes like methanogens, sulfate-reducing bacteria, and fermentative bacteria. Seasons do not affect its activity. CO2 and methane build up on the bottom due to lack of mixing. What are the most dominant bacteria in lakes? Actinobacteria What are the “killer lakes” and how have they been treated to avoid issues in the future? A killer lake is a meromictic lake that undergoes a rare explosion event that releases all of the methane and carbon dioxide that built up in the bottom layers. The release of these gases cause displacement of air and mass suffocation to people/animals in the area. In order to treat this, pressure from the bottom layer is released from man made pumps tat safely flushes out carbon dioxide and decreases the risk of an explosion. What are the limitations to life in the subsurface? There is low biological activity in the subsurface due to temperature and low energy flux. Relatively small concentrations of electron donors/acceptors and other key nutrients which leads to very slow reaction rates. Overall, there is a slow decline in energy. Rather than turning over biomass in hours to days, it takes centuries to millennia.