Inorganic and C1 Metabolism

Nitrogen Metabolism

Microbial processes transforming nitrogen forms

aerobic and anaerobic

Nitrogen metabolism occurs across both —conditions and are central to the nitrogen cycle.

Nitrogen fixation, Nitrogen assimilation, Nitrification, Ammonification, Denitrification

Components of Nitrogen Metabolism

Nitrogen fixation

refers to the process by which certain microorganisms convert atmospheric nitrogen gas (N₂) into ammonia (NH₃), a form that cells can use to build proteins, nucleic acids, and other essential biomolecules.

Bacteria Rhizobium, Aztobacter

Archaea Methanococcus

Nitrogen Fixation is done by

nitrogenase

what is the enzyme involved in Nitrogenase enzyme system in nitrogen fixation

• Dinitrogenase (contains iron and molybdenum; site of N₂ reduction) ●

• Dinitrogenase reductase (transfers electrons)

nitrogenase consists of two proteins:

FeMo-cofactor

Site of nitrogenase system

• Requires 6 electrons (but 8 are used, with some lost as H₂ gas)

• Requires 16 ATP to produce 2 NH₃

Nitrogen fixation is energy-intensive due to the strong triple bond in N₂:

donor → dinitrogenase reductase → dinitrogenase → N₂

Electron flow in nitrogen fixation

Ferredoxin / Flavodoxin

Electron carriers of Nitrogen fixation

O2

Nitrogenase inhibited by

Rapid consumption of O₂ through respiration, Production of protective slime layers, Formation of specialized cells called heterocysts (in some cyanobacteria), where oxygen is absent.

Nitrogenase is inhibited by oxygen (O₂), so organisms protect it in different ways:

Nitrogen Assimiliation

refers to the process by which organisms take up inorganic nitrogen (such as nitrate NO₃⁻ or ammonia NH₃) and convert it into organic forms like amino acids, nucleotides, and other nitrogen-containing biomolecules.

Nitrate reductase and Nitrite reductase

enzymes involved in nitrogen assimilation

NADH / NADPH

Nitrogen assimilation requires

GS-GOGAT PATHWAY and GDH PATHWAY

what are the two Ammonia Incorporation Pathways

Glutamine Synthetase (GS)/Glutamate Synthase (GOGAT) pathway

• primary route for nitrogen assimilation

• highly efficient and is especially important under low ammonia conditions

• glutamine synthetase (GS) catalyzes the ATP-dependent conversion of ammonia and glutamate into glutamine. Then, glutamate synthase (GOGAT) transfers the amide group from glutamine to α-ketoglutarate, producing two molecules of glutamate.

(GDH) pathway

• ammonia is directly combined with α-ketoglutarate to form glutamate.

• his pathway requires less energy, it has a lower affinity for ammonia

• typically used only when ammonia is abundant.

glutamate and glutamine

The products of these pathways (GS/GOGAT and GDH)

Nitrification

• refers to the biological oxidation of ammonia (NH₃) into nitrate (NO₃⁻) through a two-step aerobic process carried out by specialized microorganisms.

• is an aerobic process that requires oxygen

• Occurs in soil & water

• This process converts reduced nitrogen into a more oxidized form that plants can absorb and use

1. Ammonia Oxidation

2. Nitrite Oxidation

steps in Nitrification

Ammonia oxidation

first stage of nitrification involves the oxidation of ammonia (NH₃) into nitrite

AMO (Ammonia Monooxygenase) and HAO (Hydroxylamine Oxidoreductase)

enzymes involved in ammonia oxidation

Nitrite Oxidation

nitrite (NO₂⁻) is oxidized into nitrate (NO₃⁻) by nitrite-oxidizing bacteria (NOB).

nitrite oxidoreductase (NXR)

enzymes involved in nitrite oxidation

neutral pH and moderate temperatures

what pH is nitrifiation efficient

Ammonification

• also known as mineralization, refers to the process by which organic nitrogen from dead organisms, waste products, and other biological materials is converted into ammonia (NH₃) or ammonium (NH₄⁺) by microorganisms.

• Recycles nitrogen

• Maintains soil fertility

Proteases and Nucleases

enzymes involved in ammonification

Deamination

Process in ammonification that releases NH3

Aerobic & anaerobic

ammonification occurs in — environments

Denitrification

• refers to the biological reduction of nitrate (NO₃⁻) or nitrite (NO₂⁻) into gaseous forms of nitrogen, such as nitric oxide (NO), nitrous oxide (N₂O), and nitrogen gas (N₂

• Prevents nitrate buildup

• Reduces eutrophication

low oxygen or anaerobic

denitrification occurs in — environments

C1 metabolism

refers to the group of microbial processes that involve compounds containing only one carbon atom, such as carbon dioxide (CO₂), methane (CH₄), methanol (CH₃OH), and formaldehyde (CH₂O).

• Production of C1 compounds.

• Utilization of C1 compounds.

C1 metabolism can be divided into two major sides:

methanogenesis (formation of methane) and acetogenesis (formation of acetate from CO₂

Production of C1 compounds.

methylotrophy (use of various C1 compounds) and methanotrophy (use of methane specifically)

Utilization of C1 compounds.

Methylotrophy

refers to the metabolic capability of microorganisms to use reduced one-carbon compounds as sources of energy.

NON-Methane utilizing methylotroph:

only include methanol (CH₃OH), formaldehyde (CH₂O), methylamine, and other methylated compounds

Methylobacterium, Methylomonas, and Methylococcus.

An example of bacteria that exhibit methylotrophy

Formaldehyde (CH₂O)

in methylotrophy, this serves as a central intermediate.

1. Oxidize it completely to CO₂ for energy, or

2. 2. Assimilate it into biomass through specialized pathways.

Because formaldehyde is toxic, methylotrophs must rapidly either:

Serine Pathway and Ribulose Monophosphate (RuMP) Pathway

To grow, methylotrophs must incorporate C1 units into cellular biomass. Two major pathways are used:

Serine Pathway

• C1 assimilation route in methylotrophs using formaldehyde (CH₂O)

• Key step: formaldehyde + glycine → serine

• Energy-demanding (requires ATP and NADH)

serine hydroxymethyltransferase (SHMT)

Major enzyme in Serine Pathway

Ribulose Monophosphate (RuMP) Pathway

• energy-efficient C1 assimilation using formaldehyde

• Produces intermediates that enter glycolysis; requires ATP, but no NADH

• Favored by fast-growing methylotrophs

• Key step: formaldehyde + ribulose-5- phosphate → hexulose-6-phosphate

HPS and HPI

Major enzyme in Ribulose Monophosphate (RuMP) Pathway

Type I Methylotrophs

Uses RuMP Pathway, Methylomonas, Methylobacter

Type I Methylotrophs

Uses SerinePathway, Methylosinus, Methylocytis

Type X Methylotrophs

Uses both pathway RuMP and Serine, Methylococcus capsulatus, Bath, Methylocaldum szegidiense

Methanotrophy

is the process in which certain microorganisms oxidize methane (CH₄) into methanol and further metabolites for energy and carbon.

Methanotrophs

• are specialized methylotrophic microorganisms that use methane as their main carbon and energy source by oxidizing it with the enzyme methane monooxygenase (MMO).

• are important in the carbon cycle because they act as a biological filter, preventing methane (a potent greenhouse gas) from entering the atmosphere

methane monooxygenase (MMO).

what enzyme do methanotrophs use

• Aerobic Methane Oxidation Pathway

• Anaerobic Methane Oxidation

• Intra-aerobic Methanotrophy

Types of Methanotrophy

Aerobic Methane Oxidation Pathway

• Methane is first oxidized to methanol by methane monooxygenase (MMO) using O₂

• Methanol is then converted to formaldehyde (CH₂O) by methanol dehydrogenase.

• Formaldehyde is either oxidized to CO₂ for energy or used to form biomass via the serine or RuMP pathways

Methylococcus

what species is Aerobic Methane Oxidation Pathway common

Anaerobic Methane Oxidation

• occurs in oxygen-free environments like marine sediments.

• Methane is oxidized without O₂ through archaeal–bacterial partnerships.

• Electrons are transferred to sulfate-reducing bacteria, which reduce sulfate (SO₄ ²⁻) to hydrogen sulfide (HS⁻). Electron transfer occurs through direct contact or conductive structures like cytochromes and nanowires.

Intra-aerobic Methanotrophy

• occurs in anoxic environments like sediments.

• The internally generated O₂ is immediately used to oxidize methane.

• This allows aerobic methane oxidation to happen without external oxygen

Methylomirabilis oxyfera

species that undergo Intra-aerobic methanotrophy