Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Organic matter decomposition / Enzymatic depolymerization of plant polymers / Enzyme kinetics: Michaelis-Menten rates and temperature response
Enzyme kinetics: Michaelis-Menten rates and temperature response
How extracellular enzyme rates follow Michaelis-Menten saturation with substrate and Arrhenius-type rise with temperature. Sets the speed at which polymers are cut into units microbes can absorb.
Boundary: where this process starts
Starts with: Enzyme binds substrate and releases product at rate V = Vmax[S]/(Km+[S])
Boundary: where it ends
Ends after: Ecoenzymatic stoichiometry: matching enzymes to nutrient limitation
Line thickness = size of impact (1 to 5)% on a line = chance a fork takes that branch📄 = pieces of evidence on a stepNegative effectLoops backHypothesisResource used up (arrow into the step)Resource used, not used upResource made or released (arrow out of the step)
What am I looking at? The concepts on every map
- Participant
- Someone or something that takes part in a process or influences it: a plant, a microbe, a river, a machine, a force. Participants are the rows of a map.
- Resource
- Something a step uses or uses up: water, oxygen, sunlight, a tool. Each step has an arrow down to the resources it uses.
- Step
- One thing that happens in a process. Every step has at least one participant and carries evidence.
- Decision fork
- A step where the process can go several ways. Every outcome is labeled with a percentage, and the percentages add up to 100%. It is not limited to yes or no.
- Loop
- A line that carries the process back to an earlier step. We record whether it reinforces or balances, how strong it is (weak, moderate, strong), and its gain (0 to 1): the share of the effect that returns on each pass.
- Size of impact
- Every line says how much the earlier step affects the next one (1 to 5), in which direction (+, -, 0), and why. Thicker lines mean bigger impact.
- Evidence
- The support for a claim: a source and what it shows. Every step, line, change and vote needs it. Click any step or line to read its evidence.
- Boundary
- Where a process starts and where it ends. Every process, and every subprocess, has a start and an end.
- Subprocess
- A step that is itself a whole process, with its own boundary, steps and lines. Click a step marked ↘ to open it. Subprocesses nest as deep as the evidence goes.
- Description
- A plain-language summary of what a process is and what it covers.
- Hypothesis
- A proposed new connection between two parts of the map that nobody has linked. It carries a prediction, a way to test it, and a count of papers on each topic and on both. It is an unverified idea until someone tests it.
Inside this process
Every step, with its evidence
The same information as the map, as a list you can search and share. Click a participant or resource to see everywhere it appears.
Enzyme binds substrate and releases product at rate V = Vmax[S]/(Km+[S])
Evidence (1) · added by Ember
- German et al. 2011, Optimization of hydrolytic and oxidative enzyme methods for ecosystem studies, Soil Biol Biochem 43:1387-1397: Soil hydrolase assays fit this relation; Km of beta-glucosidase and phosphatase in the micromolar to hundreds of micromolar range (confidence 0.7)
⑂ Substrate concentration relative to Km
Evidence (1) · added by Ember
- German, Marcelo, Stone & Allison 2012, The Michaelis-Menten kinetics of soil extracellular enzymes in response to temperature, Global Change Biology 18:1468-1479: Soil substrate near enzymes is often below Km so rate is substrate-limited; shares are estimates (confidence 0.45)
Substrate-limited: rate rises roughly in proportion to substrate or enzyme density
Evidence (1) · added by Ember
- Burns et al. 2013, Soil enzymes in a changing environment: current knowledge and future directions, Soil Biol Biochem 58:216-234: Review: enzyme activity in soil is usually limited by substrate access, not by enzyme quantity (confidence 0.6)
Near Km: rate rises with substrate but with diminishing return
Evidence (1) · added by Ember
- German et al. 2011, Optimization of hydrolytic and oxidative enzyme methods for ecosystem studies, Soil Biol Biochem 43:1387-1397: Michaelis-Menten curve between linear and saturated regions (confidence 0.6)
Saturated: rate capped at Vmax, extra substrate has no effect
Evidence (1) · added by Ember
- German et al. 2011, Optimization of hydrolytic and oxidative enzyme methods for ecosystem studies, Soil Biol Biochem 43:1387-1397: Vmax is the ceiling rate at saturating substrate (confidence 0.7)
Warming raises Vmax (Q10 about 1.5-2.5 for hydrolases) and also raises Km
Evidence (2) · added by Ember
- German, Marcelo, Stone & Allison 2012, The Michaelis-Menten kinetics of soil extracellular enzymes in response to temperature, Global Change Biology 18:1468-1479: Vmax and Km of soil enzymes both increased with temperature, Km increases partly offset gains (confidence 0.8)
- Davidson & Janssens 2006, Temperature sensitivity of soil carbon decomposition and feedbacks to climate change, Nature 440:165-173: Decomposition Q10 near 2 typical but varies with substrate quality (confidence 0.7)
At low substrate, higher Km reduces the warming gain so temperature sensitivity of decomposition falls
Evidence (2) · added by Ember
- German, Marcelo, Stone & Allison 2012, The Michaelis-Menten kinetics of soil extracellular enzymes in response to temperature, Global Change Biology 18:1468-1479: Km rise offsets Vmax rise at low substrate concentrations (confidence 0.65)
- Allison, Wallenstein & Bradford 2010, Soil-carbon response to warming dependent on microbial physiology, Nature Geoscience 3:336-340: Models with enzyme kinetics predict only transient soil carbon loss under warming (confidence 0.6)
Sorption to clay and organic coatings raises apparent Km and lowers apparent Vmax
Evidence (1) · added by Ember
- Burns et al. 2013, Soil enzymes in a changing environment: current knowledge and future directions, Soil Biol Biochem 58:216-234: Immobilized enzymes show changed kinetic parameters and extended persistence (confidence 0.65)
Hydrolysis products accumulate and repress further enzyme synthesis (catabolite repression)
Evidence (2) · added by Ember
- Schimel & Weintraub 2003, The implications of exoenzyme activity on microbial carbon and nitrogen limitation in soil, Soil Biol Biochem 35:549-563: Model: microbes regulate enzyme production according to product availability (confidence 0.6)
- Allison & Vitousek 2005, Responses of extracellular enzymes to simple and complex nutrient inputs, Soil Biol Biochem 37:937-944: Simple nutrient additions repress some enzyme activities (confidence 0.55)
↘ Ecoenzymatic stoichiometry: matching enzymes to nutrient limitation
Evidence (1) · added by Ember
- Sinsabaugh et al. 2008, Stoichiometry of soil enzyme activity at global scale, Ecology Letters 11:1252-1264: Global analysis of soil enzyme activity ratios relative to C:N:P of microbial biomass (confidence 0.9)