Microbial Carbon, Nitrogen, and Sulfur Cycles

• All organisms must have carbon, nitrogen, and sulfur.
• Assimilative and dissimilative activities by microbes are essential in sustaining life on Earth.
• Carbon, nitrogen, and sulfur cycles are well studied.

Lithotrophic vs Phototrophic Sulfide Oxidation

• Thiobacillus is a lithoautotroph.
• Thiobacillus uses O2 or another oxidant to oxidize H2S or S°.
• Oxidizing H2S or S° by Thiobacillus produces energy and electrons needed to make reduced carbon from CO2.
• Phototrophic purple sulfur bacterium Chromatium are involved in phototrophic sulfide oxidation.
• Anoxygenic photosynthesis involving Chromatium gets energy from light and electrons from H2S.

The Carbon Cycle

• Autotrophs are dominant in fixing carbon into organic matter.
• Plants are the main photoautotrophs in terrestrial settings, performing the Calvin Cycle.
• Algae, bacteria, and archaea are the main photoautotrophs in aquatic environments.
• Calvin cycle and rTCA are key processes and also consider chemolithotrophs.
• Organotrophs return carbon to abiotic reservoirs.

Nitrogen Redox Cycle

• Nitrification: NH4+ is converted to NO2- by Comammox (Nitrospira species) or Nitrosomonas, then NO2- to NO3- by Nitrobacter.
• Denitrification: NO3- is converted to N2 by Bacillus, Paracoccus, and Pseudomonas.
• N2 Fixation: N2 + 8H is fixed to 2NH3 + H2 by Azotobacter (aerobic), Cyanobacteria, Clostridium, purple/green phototrophic bacteria, and Methanobacterium (Archaea) which are free-living Bacteria, and Rhizobium, Bradyrhizobium, and Frankia performing symbiotic N2 fixation.
• Ammonification: Organic-N is converted to NH4+ by many organisms.
• Anammox: NO2- + NH3 are converted to 2 N2 by Brocadia.

ANAMMOX

• Anaerobic ammonia oxidation (ANAMMOX) involves NO2- being reduced and ammonia being oxidized to produce N2.
• Organisms that perform anammox usually contain an anammoxosome.
• Anammoxosomes are pseudo-organelles that generate PMF.

Microbial Symbioses

• Microbial symbioses are intimate and prolonged relationships between organisms.
• Symbioses can be characterized based on their effect on their host organism.
• Parasitic relationships benefit the microbe at the expense of the host.
• Pathogenic relationships cause disease in the host due to the microbe.
• Commensal relationships have no discernable impact on the host from the microbe.
• Mutualistic relationships are beneficial to the host.

Legume-Root Nodule Symbiosis

• Most organisms get N from fixed sources such as NH3 and NO3.
• Bacteria and some archaea fix N2 to replenish organic N, that is lost due to denitrification.
• The mutualistic association of nitrogen-fixing bacteria and plants is an important symbiosis.
• Leguminous plants and nitrogen-fixing rhizobia have a well-studied symbiotic relationship.
• Legumes include soybeans, clover, alfalfa, beans, peas, etc.
• Rhizobia infect legume roots and trigger forming root nodules, allowing for gains in soil nitrogen from N2 fixation.

Rhizosphere Symbiosis

• Symbiosis requires specific plant and rhizobia species - known as cross-inoculation groups.
• Plants secrete plant flavonoids to promote the growth of surrounding microbes.
• Rhizobia penetrate and multiply within an infection thread.
• Bacteria in the infection thread grow until they reach the root cell.
• A bacteroid state is formed within root plant cells, and plant-bacterial cell division continues to form nodules.

Symbiosome Details

• Rhizobia multiply in plant cells, swell, and are misshapen into branched cells called bacteroids, which are contained in plant membranes.
• Bacteria create oligosaccharide Nod (nodulation) factors that regulate nodule formation.
• Root hair curling, plant cell division, and nodule formation are all induced by the Nod factor.
• Bacteroid imports organic acids like succinate, malate, fumarate, and pyruvate from the host plant.
• Organic acids provides the reducing power for nitrogen fixation.
• Nitrogenase then fixes N₂ to NH3, which is then exported to the plant.

Oxygen's Role in Root Nodules

• Nitrogen-fixing bacteria need O2 to generate energy for N2 fixation.
• Enzymes that fix N2, i.e., nitrogenases, are inactivated by O2.
• O2 is bound by leghemoglobin (red color) within the nodule.

Microbe-Microbe Symbioses

• Chlorochromatium aggregatum is a freshwater mutualistic microbial consortia
• Green sulfur bacteria (epibionts) and an unnamed flagellated rod-shaped bacterium
• The green sulfur bacteria (Chlorobium) uses light energy to fix CO2 using electrons from H2S via anoxygenic photosynthesis
• 13-69 ebibionts surround a single flagellated bacterium
• The motile bacterium move in the water column in response to light, oxygen, and sulfide