Microbial physiology, Nutrient Cycles, and Biogeochemistry Flashcards
What are energy sources
Light, organic chemical, and inorganic chemicals
What is electron source
Inorganic or organic
What is a carbon source
CO2 or organic
What is an electron acceptor
Aerobic or anaerobic
What are nutrient sources
N2 fixation and Iron acquisition
What are some lifestyles
Free-living vs. Attached/Biofilm
Sporulation
Saprotrophic, parasitic, mutualistic fungi
What are the Carbon, Hydrogen, Nitrogen, Phosphorus, and Sulphur macronutrients
The building blocks of the cell: proteins, lipids, and nucleic acids
What are the potassium and sodium macronutrients
Important in membrane transport
What are the calcium and magnesium macronutrients
Constituents of cell wall polymers
What is magnesium macronutrients
Important in enzymatic functions
What is iron in macronutrients
Constituent of cytochromes and iron-sulfur proteins
What is Nitrification
Oxidation of NH3 to NO2- then to NO3
What is sulfur oxidation
Oxidation of H2S to SO4 via multiple intermediate steps. Produces large amounts of acid
What is iron oxidation
Oxidation of Fe2+ to Fe3+. Changes the solubility of iron, can lead to formation of oxygen radials.
What are the kinds of anaerobic respiration
Nitrate reduction (denitrification, anammox)
Metal reduction
Sulfate reduction
CO2 reduction (methanogenesis or homoacetogenesis)
What is necessary for nitrogen fixation
- Reduction of nitrogen gas (N2) to ammonia (NH3) by the enzyme nitrogenase - very O2 sensitive
- Life as we know it depends on the rapid cycling of nitrogen into biologically available forms
- Only prokaryotes do it: Free-living aerobes, free-living anaerobes and symbiotic bacteria
When does aerobic N2 fixation occur
Under low O2, no slime layer
Under high O2, big slime layer
Slime retards diffusion of O2 into cell. Nitrogenase will not inactivated.
What are the steps of the carbon cycle
- Entry of Carbon into the Atmosphere
- Carbon Dioxide Absorption by Producers
- Passing of the Carbon Compounds in the Food Chain
- Return of the Carbon to the Atmosphere
What are the types of phototrophy
Oxygenic and Anoxygenic
What is oxygenic phototrophy
Produces O2 and electrons from the electron transport chain comes from water
What is anoxygenic phototrophy
No O2 production and the electrons come from sources other than water
What is photosynthesis
The light-dependent transfer of a proton from a donor (H2A) to carbon dioxide - that donor other than water (H2S) can be used in this process
What is analogous in evolutionary genomics terms
Similar function, different descent
What is homologous in evolutionary genomics terms
Descended from the same ancestor
What is orthologous in evolutionary genomics terms
Diverged after speciation - usually similar function
What is paralogous in evolutionary genomics terms
Diverged after speciation - usually different function
What is (Super)Family in evolutionary genomics terms
Group of proteins or genes that are homologous - often have some shared function
What is fold in evolutionary genomics terms
Aspect of protein tertiary structure
What is domain in evolutionary genomics term
Functional section of protein
What does oxygenic photosynthesis do
Creates oxygen and takes electrons from water. Essentially the two anoxygenic pathways put together.
How does the iron cycle work
Bacteria thrive when they couple a reduced fuel source and they produce a powerful oxidant.
What are biofilms
Complex, slime enclosed colonies attached the the surfaces. When biofilms form on medical devices can often lead to illness. They can form on any conditioned surface.
What is biofilm formation
Microbes reversibly attach to a surface and release polysaccharides, proteins, and DNA. There are complex interactions occur among attached organisms in a population.
How do gram-positive endospores work
Occurs as bacteria age due to nutrient deprivation. They are NOT triggered in response to environmental stress. They are extremely to environmental stress. With few exceptions, all spore-forming bacteria are Gram-positive.
How can you get endospores to return to vegetative state
- Activation: heat endospore to sublethal temperature
- Place in nutrient broth
- Germination: very rapid; synthesizes RNA, protein, DNA, and breaks and discards spore coat.
During Microorganisms and Climate Change, what are microbial processes in regards to world around us
Microbial processes have a central role in the global fluxes of the key biogenic green house gases and are likely to respond to climate change.
During Microorganisms and Climate Change, how can we improve climate models
To improve the prediction of climate models, it is important to understand the mechanisms by which microorganisms regulate terrestrial greenhouse gas flux.
During Microorganisms and Climate Change, what is radiative forcing
A measure of the influence that a factor has an altering the balance of incoming and outgoing energy in the Earth-atmosphere system. It is an index of the factor as a potential climate change mechanism
During Microorganisms and Climate Change, what is the debate taking place
What is more open to debate is the part that they will play in the coming decades and centuries the climate feedbacks that will be important, and how humankind might harness microbial processes to manage climate change
During Microorganisms and Climate Change, what is heterotrophic
An organism that can use organic compounds as nutrients to produce energy for growth
During Microorganisms and Climate Change, define autotrophic
An organism that can synthesize carbon from the fixation of inorganic carbon
During Microorganisms and Climate Change, define dissolved inorganic carbon pool
The sum of inorganic carbon in solution
During Microorganisms and Climate Change, define net primary production
The part of the total energy fixed by autotrophic organisms that remains after the losses through autotrophic respiration
During Microorganisms and Climate Change, define methanogenesis
The process by which methane is produced by microorganisms
During Microorganisms and Climate Change, define methanotrophic
An organism that can use methane as a nutrient to produce energy for growth
During Microorganisms and Climate Change, define nitrification
The conversion of NH3 into more oxidized form such as nitrate or nitrite
During Microorganisms and Climate Change, define denitrification
The reduction of oxidized forms of nitrogen to N2O and dinitrogen
During Microorganisms and Climate Change, define reactive nitrogen
Nitrogen in a form that can undergo biological transformations, such as nitrite and nitrate
During Microorganisms and Climate Change, what are the terrestrial emissions of carbon dioxide
For terrestrial ecosystems, the uptake of carbon dioxide from the atmosphere by net primary production dominated by higher plants, but microorganisms contribute greatly to net carbon exchange through processes of decomposition and heterotrophic respiration.
During Microorganisms and Climate Change, what are the terrestrial emissions of methane
Natural emissions of methane are dominated by microbial methanogenesis, a process that is carried out by a group of anaerobic archaea in wetlands, oceans, rumens, and termite guts.
During Microorganisms and Climate Change, what is the emission of dinitrogen oxide
Most dinitrogen oxide produced by nitrification is a result of the activity of autotrophic ammonia oxidizing bacteria belonging to the class of Betaproteobacteria.
During Microorganisms and Climate Change, define permafrost
Soil that remains permanently frozen
During Microorganisms and Climate Change, define recalcitrant carbon
A form of carbon that is resistant to microbial decomposition owing to its chemical structure and composition
During Microorganisms and Climate Change, define peatland
An area dominated by deep organic soils
During Microorganisms and Climate Change, define water table
The level at which the groundwater pressure is the same as the atmospheric pressure.
During Microorganisms and Climate Change, how does increase carbon dioxide levels impact the environment
Increased levels of carbon dioxide quantitatively and qualitatively alter the release of labile sugars, organic acids, and amino acids from plant roots, and this can stimulate microbial growth and activity. They can then change the carbon dioxide flux depending on the availability of nutrients.
During Microorganisms and Climate Change, how can increased carbon dioxide levels impact methane
Increased carbon dioxide levels may affect methane emissions indirectly through their effects on microbial activity and physiology, and it is possible that plant-mediated increases in soil moisture in the presence of increased carbon dioxide levels in the soil will lead to more anoxic conditions, thereby increasing methanogenesis and reduce methanotrophy.
During Microorganisms and Climate Change, define arable land
Land that is used for growing crops
During Microorganisms and Climate Change, define mineralization
The conversion of organic carbon into organic forms, mainly carbon dioxide.
During Microorganisms and Climate Change, define grassland
Land that has grass as the dominant vegetation
During Microorganisms and Climate Change, how can we reduce carbon dioxide emissions
The conversion of croplands to permanent grassland, which causes a build-up of organic matter at the soil surface, could also increases carbon sequestration.
During Microorganisms and Climate Change, how can we reduce methane emissions
It is well established that conversions of arable land or grassland to forest results in a substantial reduction in methane flux, and it is evident that both the type and abundance of methanotrophs are important for predicting methane flux.
During Microorganisms and Climate Change, how can we reduce dinitrogen oxide
Potential strategies that include reducing the amount of fertilizer and applying it at an appropriate time, using slow-release fertilizer, and avoiding nitrogen forms that are likely to produce large emissions or leaching losses.
During Microorganisms and Climate Change, what must we do to ensure that we don’t suffer from the changing climate
First, we need to better understand and quantify microbial responses to climate change to comprehend future ecosystem functioning. Second, we need to classify microbial taxa in terms of their functional and physiological capabilities and to link this information to the level of ecosystem function. Third, we need to improve our mechanistic understanding of microbial control of greenhouse gas emission and microbial responses. Fourth, we need to develop a framework to incorporate data into climate models to reduce uncertainty and to improve estimation and prediction. Fifth, we need to better understand the effect of climate change on above-ground and below-ground interactions and nutrient cycling. Sixth, we need to develop a framework around the five points listed above to enhance carbon sequestration and/or reduce greenhouse gas emissions
