MICB 301: Anaerobic Food Web

Anaerobic food web (Definition)

A model for understanding nutritional interactions typical in anaerobic environments

Nutritional mutualism

Interactions within the anaerobic food web based on syntrophy (feeding-together)

Fermentation (Industrial meaning)

Refers to industrial fermentations, in which microorganisms are used for a chemical transformation; may involve aerobic or anaerobic metabolism and can include anabolism (e.g., antibiotic production)

Fermentation (Pasteur's definition)

"Life in the absence of oxygen"

Fermentation (Brock's definition)

Anaerobic catabolism of an organic compound in which the compound serves as both an electron donor and an electron acceptor and in which ATP is produced by substrate-level phosphorylation (SLP)

Fermentation (Essential elements)

Balanced overall equation and redox balance; both oxidation and reduction of substrate; substrate is not mineralized (not all substrate carbon converted to $CO_2$); some mechanism yields biologically useful energy (ATP or PMF)

Fermentation (Frequent but non-essential elements)

Often an organic disproportionation (a branched pathway with both oxidized and reduced products)

oxidative processes often form high-energy compounds that support SLP

reductive processes often balance oxidative processes

$\text{NADH/NAD}$ is often cycled between oxidative and reductive parts, with the reductive parts regenerating $\text{NAD}$

Substrate-level phosphorylation (SLP)

Occurs in many, but not all, fermentations

often the major mechanism of energy conservation in a fermentation

Energy coupling

A key process using exergonic reactions to drive endergonic reactions, making the overall process exergonic

SLP (Classical example)

The PEP kinase reaction in glycolysis: $PEP + ADP \rightarrow Pyr + ATP$ ($\Delta G'_{0} = -27~kJ/mole$)

Growth yield (Definition)

Biomass produced / substrate consumed (e.g., g of cellular dry weigh per g of substrate)

Fermentation (Low growth yield characteristics)

Involves a smaller free energy change than respiratory processes

yields far less energy than glucose oxidation coupled to oxygen respiration

organic products contain available chemical energy not conserved by the fermentative organism

Fermentation (Ecology/Environments)

Anaerobic (oxygen demand exceeds supply)

often eutrophic (abundant organic matter, depleted respiratory TEAs)

Syntrophy is common

typical environments include sediments, mouth, gut, urogenital tract, skin, waste digesters, spoiled food, and decomposing vegetation

Glycolysis (Stage I: Preparatory rxns - activation)

Phosphorylation by kinases using ATP (energy invested via energy coupling); aldolase splits fructose-1,6-bisP (6-C) to two 3-C units (glyceraldehyde-3-P)

Glycolysis (Stage II: Oxidation - making ATP, energy conservation)

Oxidation of G3P coupled to reduction of NAD by dehydrogenase ($\text{NADH}$ produced)

oxidation forms 1,3-bisP glycerate (a high-energy compound)

hydrolysis coupled to $\text{ADP}$ phosphorylation (SLP)

later, another high-energy compound, PEP, is hydrolyzed, yielding more ATP via SLP (net of 2 ATP/glucose synthesized)

Glycolysis (Stage III: Reduction - completes fermentative process)

Achieves redox balance

yields fermentation products

regenerates $\text{NAD}$ consumed in the oxidation stage

Three fermentation possibilities shown in Stage III

If only ethanol is produced, then alcohol fermentation

if only lactate is produced, then homolactic acid fermentation

if some or all products are produced, then mixed acid fermentation

Alcohol Fermentation (Applications)

Baking (leavens bread, EtOH evaporates)

alcoholic beverages (huge industry, preserves nutrition)

fuel ethanol

Ethanol Fuel Production (Feedstocks/Economics)

Corn is commonly used (but is not economical without subsidies, and its production has negative environmental consequences)

woody biomass (lignocellulose) is arguably the preferable feedstock

Homolactic fermentation (Ecology)

Mainly used by Lactic acid bacteria (LAB) (Order Lactobacillales, Phylum Firmicutes)

they are specialists that lack ETC (so not capable of respiration) and are obligately fermentative

Lactate/H symport (Mechanism)

Driven by a concentration gradient of lactate to increase the PMF, which can then drive ATP synthesis

Mixed Acid Fermentation (Ecology/Habitats)

Many are facultative aerobes adapted to transitioning between aerobic and anaerobic environments (e.g., from water to gut)

Habitats include gut environments, plants, water, and soil

Anaerobic Food Web (Environments/Significance)

Occurs in sediments and guts, and engineered environments like anaerobic digesters

These are typically eutrophic environments depleted of respiratory electron acceptors

It is an important part of the global C cycle

Main products ($CO2 + CH4$) are important greenhouse gasses.

Guilds (Definition)

Groups of organisms with a common function within the food web, which do not necessarily comprise closely related organisms

Secondary Fermenters (Role/Substrates)

Substrates include VFAs, ethanol and benzoate (all but the latter are products of primary fermentations)

they catalyze secondary fermentation (e.g., converting VFAs to $H_2$ and acetate)

if inhibited, the whole anaerobic food web will stop functioning

Secondary Fermenters (Substrate difficulty)

The carbon in their substrates (VFAs, etc.) is relatively reduced, making them thermodynamically unfavourable for fermentation

Secondary Fermenters (Energy Conservation)

Energy is conserved via a sodium-motive force (analogous to a PMF)

mechanism typically involves membrane-associated decarboxylases that couple a decarboxylation reaction to pumping a sodium ion out of the cell

Secondary Fermenters (Research Difficulty)

Can only be grown in co-cultures and are thus very difficult to study and not yet well understood

Direct Interspecies Electron Transfer (DIET)

An alternative to interspecies $H_2$ transfer

Homoacetogens (Defining characteristics)

Ferment glucose to acetate as the sole product

have the characteristic capacity to grow on only $CO2 + H2$

Homoacetogens (Classification)

They are facultative chemolithoautotrophs because they can grow on $H2 + CO2$ (chemolithotrophy) and use $CO_2$ as their sole $C$ source (autotrophs)

Homoacetogens (Ecological significance)

Often the main $H_2$ consumers in certain environments (e.g., the gut of certain termites)

acetogenic termites emit less greenhouse gases than methanogenic termites

Homoacetogenesis (Net reaction from glucose)

$\text{C}6\text{H}{12}\text{O}6 \rightarrow 3\text{CH}3\text{COOH}$ (Glucose $\rightarrow$ 3 Acetate)

Wood-Ljungdahl pathway (Key facts)

An important pathway for many anaerobic prokaryotes (Bacteria & Archaea)

the reaction is reversible (in some organisms, it proceeds in reverse, oxidizing acetate to $CO_2$)

functions in both catabolism (chemolithotrophy) and anabolism (autotrophy).

Methanogens (Phylum: Archaea)

Obligate anaerobes that produce methane ($\text{CH}_4$) from a narrow range of substrates

Methanogenesis (Definition/Net Reaction)

The process of methane production, often summarized as $\text{CO}2 + 4\text{H}2 \rightarrow \text{CH}4 + 2\text{H}2\text{O}$

Methanogenesis (Ecological Significance)

The main products of the anaerobic food web ($\text{CO}2 + \text{CH}4$) are important greenhouse gases

accumulation of flammable methane in landfills can be a fire hazard

food production poses a major challenge to meeting climate change targets due to methane release

Methanogens (Substrates)

Use a narrow range of substrates, mainly including just three classes of relatively simple compounds (Table 5.2 in notes)

Hydrogenotrophic Methanogenesis (Key Processes)

The reduction of $\text{CO}_2$ to a bound methyl group is analogous to homoacetogenesis but involves different catalysts

Energy conservation is believed to occur via sodium translocation coupled to transfer of a methyl group (chemiosmotic mechanism)

the methyl reductase complex is a key component, defining all methanogens (produces methane and is important for energy conservation)

Acetoclastic Methanogenesis (Key Points)

Involves the Wood-Ljungdahl pathway but in the reversed direction compared to homoacetogenesis

acetate is disproportionated, being oxidized to $\text{CO}2$ and reduced to $\text{CH}4$

the methyl reductase complex is again present

energy conservation is again believed to occur via sodium translocation coupled to transfer of a methyl group (chemiosmotic mechanism)

proposed that the transfer of $2\text{H}$ from $\text{CODH/ACS}$ to the methyl reductase complex may support PMF/chemiosmotic energy conservation

Methanogens (vs. Homoacetogens)

Both compete for $\text{H}_2$

Methanogens are obligate chemolithoautotrophs

Anaerobic Digester Souring (Cause)

A rapid increase in degradable organic matter in the digester influent, overloading the system and disrupting the food web

Anaerobic Digester Souring (Consequence)

Leads to an accumulation of VFAs (Volatile Fatty Acids), which causes a drop in $\text{pH}$ that inhibits methanogens (which are sensitive to low $\text{pH}$), causing the whole system to fail

Rumen (Definition)

A highly specialized anaerobic digester in the first stomach compartment of ruminants

Rumen (Function)

Catalyzes anaerobic mineralization of plant polysaccharides (cellulose, hemicellulose, pectin) to Volatile Fatty Acids (VFAs) and $\text{CH}_4$

Rumen (Products/Benefits to Host)

VFAs (acetate, propionate, butyrate) are absorbed by the host and serve as the primary $\text{C}$ source for energy282828; $\text{CO}2$ and $\text{H}2$ are used by methanogens to form $\text{CH}_4$

Rumen (Microbial Groups/Function)

Primary fermenters (use sugars/polysaccharides $\rightarrow \text{VFAs}$, $\text{CO}2$, $\text{H}2$)

Methanogens (use $\text{H}2/\text{CO}2 \rightarrow \text{CH}_4$)

there are strong syntrophic interactions between the guilds

Rumen (Ecology/Adaptation)

Organisms are typically obligate anaerobes

the host provides constant temperature, constant $\text{pH}$, nutrients, and protection from predators

Acidosis (Rumen)

A nutritional disease caused by a sudden dietary change to high amounts of fermentable starch/sugars, resulting in excess production of lactic acid (a stronger acid than VFAs)

causes a rapid decrease in $\text{pH}$ that inhibits cellulolytic bacteria and methanogens

Rumen Engineering (Mimosine)

Mimosine, a toxic compound in tropical legumes, was degraded by a microbial community, and transplants of the microbial communities from resistant Hawaiian cattle to Australian cattle made the latter resistant to the toxin .

Rumen Engineering (Fluoroacetate)

Fluoroacetate, a toxic plant compound, was targeted; rumen bacteria were genetically engineered to degrade it (not commercially permitted) ; current efforts focus on selecting for sufficient populations of native rumen bacteria capable of degradation.