Environmental; Biogeochemical Cycles

oligotrophic

low nutrient, specifically low in fixed N, P, and Fe

mixed culture

several species living together

environment in which most microbes live

biofilms

reversible attachment

microbe reacts with a surface - 1st step of biofilm formation

irreversible attachment

microbe attaches to surface via fimbriae or pili - 2nd step of biofilm formation

proliferation

multiple microbes clump together and build an extracellular matrix forms around them - 3rd step of biofilm formation

maturation

colonization by others, pieces begin to slough off - 4th step of biofilm formation

eutrophication

nutrient runoff causes the overgrowth and then death of aquatic algae

process that follows the initial algal bloom in eutrophication

the algae die/bust and release fixed carbon

process that follows algae death in eutrophication

a bloom of bacterial heterotrophs forms

process that follows bacterial heterotroph bloom in eutrophication

the bacteria use up the oxygen, and the system becomes anaerobic

process that follows the anaerobic environment in eutrophication

fish and other organisms die, the water begins to stink

organisms classified based on carbon source

autotrophs and heterotrophs

autotrophs

fix carbon from CO₂ to organic carbon

heterotrophs

use organic carbon sources

organisms classified based on energy source

phototrophs, chemotrophs (organotrophs, lithotrophs)

phototrophs

use light energy

chemotrophs

use chemical energy

organotrophs

use electrons from organic compounds

lithotrophs 

use electrons from minerals (nonorganic sources)

anaerobic respiration

O₂ is NOT the terminal electron acceptor

oxidants

SO₄, NO₃, Fe³⁺, CO₂

carbon fixation (carbon cycle)

CO₂ → CH₂O (reduction)

respiration (carbon cycle)

CH₂O → CO₂ (oxidation)

methane oxidation (carbon cycle)

CH₄ → CO₂ (oxidation)

methanogenesis (carbon cycle)

CO₂ → CH₄ (reduction)

nitrification (nitrogen cycle)

NH₃ → NO₂ → NO₃ (oxidation)

ammonia oxidation (nitrogen cycle)

NH₃ → NO₂

nitrite oxidation (nitrogen cycle)

NO₂ → NO₃

denitrification (nitrogen cycle)

NO₃ → N₂O → N₂ (reduction)

diazotrophs

nitrogen fixers

nitrogen fixation (nitrogen cycle)

N₂ → NH₃

assimilation (nitrogen cycle)

NH₃ / NO₃ → amino acids

sulfate reduction (sulfur cycle)

SO₄ → H₂S (dissimilatory)

assimilatory (sulfur cycle)

SO₄ → protein

oxidation reaction (sulfur cycle)

H₂S → S^○ →SO₄

vadose zone

aerobic area underground, reaching the water table

pump and treat

water is pumped into the ground (plume), and the dirty water that comes back out is treated at the surface

enhanced bioremediation

water, air, and nutrients are pumped into the ground, causing a redox reaction, and water and VOCs come out for treatment

in situ

treat in place

ex situ

dig it up and treat it elsewhere

composting

pile it up and let it degrade naturally

bioremediation technique that exhibits succession of species

composting