This is the repository for the metabolic marker gene databases compiled by lab members of Greening lab (http://www.greeninglab.com/) since 2016.
The original database was released in 2020 on Figshare (https://bridges.monash.edu/collections/Greening_lab_metabolic_marker_gene_databases/5230745).
The extended and modified database are migrated to this github page.
Carbon fixation
AclB ATP-citrate lyase (rTCA cycle)
AcsB Acetyl-CoA synthase (Wood−Ljungdahl pathway)
HbsC Crenarchaeota 4-hydroxybutyryl-CoA synthase (4-hydroxybutyrate cycle)
HbsT Thaumarchaeota 4-hydroxybutyryl-CoA synthase (4-hydroxybutyrate cycle)
Mcr Malonyl-CoA reductase (3-hydroxypropionate cycle)
RbcL RuBisCO (CBB cycle; also include form II & III RuBisCO)
Trace gas metabolism
CooS Anaerobic [NiFe]-carbon monoxide dehydrogenase (anaerobic CO oxidation)
CoxL Form I [MoCu]-carbon monoxide dehydrogenase (aerobic CO oxidation)
[Fe] [Fe]-hydrogenase (H2 metabolism)
[FeFe] [FeFe]-hydrogenase (H2 metabolism)
[NiFe] [NiFe]-hydrogenase (H2 metabolism)
McrA Methyl-CoM reductase (methanogenesis) [updated in 2024]
rMcrA Reverse methyl-CoM reductase (anaerobic CH4 oxidation) [updated in 2024]
PmoA Particulate methane monooxygenase (aerobic CH4 oxidation) [updated in 2024]
MmoA Soluble methane monooxygenase (aerobic CH4 oxidation) [updated in 2024]
IsoA Isoprene monooxygenase (isoprene oxidation) [updated in 2024]
Nitrogen metabolism
AmoA Ammonia monooxygenase (ammonia oxidation) [updated in 2024]
HzsA Hydrazine synthase (anammox)
NxrA Nitrite oxidoreductase (nitrite oxidation)
NifH Nitrogenase (nitrogen fixation)
NapA Periplasmic nitrate reductase (nitrate reduction)
NarG Dissimilatory nitrate reductase (nitrate reduction)
NrfA Ammonifying nitrite reductase (nitrite reduction to ammonium)
NirK Copper-containing nitrite reductase (nitrite reduction to nitric oxide)
NirS Cytochrome bd1 nitrite reductase (nitrite reduction to nitric oxide)
NorB Cytochrome c dependent nitric oxide reductase (nitric oxide reduction)
NosZ Nitrous oxide reductase (N2O reduction)
Nod Nitric oxide dismutase (oxygenation via nitric oxide disproportionation)
Sulfur metabolism
FCC Flavocytochrome c sulfide dehydrogenase (sulfide oxidation)
Sqr Sulfide quinone oxidoreductase (sulfide oxidation)
SoxB Thiosulfohydrolase (thiosulfate oxidation)
rDsrA Oxidative Dsr (sulfite oxidation)
AsrA Anaerobic sulfite reductase (sulfate reduction)
DsrA Dissimilatory sulfite reductase (sulfate reduction)
Sor Sulfur oxygenase reductase (sulfur disproportionation)
Alternative electron donor
ARO Arsenite oxidase (arsenite oxidation)
Cyc2 Iron oxidising cytochrome (iron oxidation)
FdhA Formate dehydrogenase (formate oxidation)
Alternative electron acceptor
FrdA Fumarate reductase (fumarate reduction)
MtrB Decaheme iron reductase (iron reduction)
OmcB Polyheme iron reductase (iron reduction)
RdhA Reductive dehalogenase (reductive dehalogenation)
YgfK Selenate reductase (selenate reduction)
Phototrophy
PsaA Photosystem 1 (photosystem 1 dependent phototrophy)
PsbA Photosystem 2 (photosystem 2 dependent phototrophy)
RHO Microbial rhodopsin (rhodopsin dependent phototrophy)
Aerobic respiration
AtpA ATP synthase (ATP synthesis)
SdhA Succinate dehydrogenase (succinate oxidation)
CoxA Cytochrome aa3 oxidase (aerobic respiration)
CyoA Cytochrome bo3 oxidase (aerobic respiration)
CcoN Cytochrome cbb3 oxidase (aerobic respiration)
CydA Cytochrome bd oxidase (aerobic respiration)
NuoF Complex I F subunit (NADH oxidation)
Other
ArsC Arsenate reductase (arsenic detoxification)
Trace gas metabolism
McrA Methyl-CoM reductase (methanogenesis) [updated in 2024]
rMcrA Reverse methyl-CoM reductase (anaerobic CH4 oxidation) [updated in 2024]
PmoA Particulate methane monooxygenase (aerobic CH4 oxidation) [updated in 2024]
MmoX Soluble methane monooxygenase (Group III SDIMO) (aerobic CH4 oxidation) [updated in 2024]
Volatile organic compound metabolism
AcrA Alkyl-CoM reductase (anaerobic alkane oxidation)
PxmA PmoA-like monooxygenase (putative aerobic alkane oxidation)
HmoA Particulate hydrocarbon monooxygenase (aerobic hydrocarbon oxidation)
TmoA Toluene monooxygenase (Group I SDIMO) (toluene oxidation)
IsoA Isoprene monooxygenase (Group I SDIMO) (isoprene oxidation) [updated in 2024]
DmpN Phenol monooxygenase (Group II SDIMO) (phenol oxidation)
BmoX Soluble short-chain alkane monooxygenase (Group III SDIMO) (aerobic short-chain alkane oxidation)
EtnC Soluble alkene monooxygenase (Group IV SDIMO) (aerobic alkene oxidation)
PrmA Soluble propane monooxygenase (Group V & VI SDIMO) (aerobic propane oxidation)
ZmoA Soluble alkene-active monooxygenase (Group VII SDIMO) (putative aerobic alkene oxidation)
SmoX Unclassified soluble diiron monooxygenase
Nitrogen metabolism
AmoA Ammonia monooxygenase (ammonia oxidation) [updated in 2024]
Original 2020 database
- Greening C†* & Geier R†, Wang C, Woods LC, Morales SE, McDonald MJ, Rushton-Green R, Morgan XC, Koike S, Leahy SC, Kelly WJ, Cann I, Attwood GT, Cook GM, Mackie RI* (2019). Diverse hydrogen production and consumption pathways influence methane production in ruminants. The ISME Journal 13, 2617-2632
- Ortiz M† & Leung PM†*, Shelley G, Jirapanjawat T, Nauer PA, Van Goethem MW, Bay SK, Islam ZF, Jordaan K, Vikram S, Chown SL, Hogg ID, Makhalanyane TP, Grinter R, Cowan DA*, Greening C* (2021). Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils. PNAS 118, e2025322118
Extended and modified 2024 database
- Leung PM†* & Jeffrey LC†*, Bay SK, Gomez-Alvarez P, Hall M, Johnston SG, Dittmann J, Jirapanjawat T, Hutchinson TF, Coleman NV, Dong X, Deschaseaux E, Maher DT & Greening C* (2025). Bark microbiota modulate climate-active gas fluxes in Australian forests. Science (in press), doi: 10.1101/2024.07.02.601631
[NiFe]-, [FeFe]-, and [Fe]-hydrogenases
- Søndergaard D*, Pedersen CNS, Greening C* (2016) HydDB: a web tool for hydrogenase classification and analysis. Scientific Reports 6, 34212
- Greening C*, Biswas A, Carere CR, Jackson CJ, Taylor MC, Stott MB, Cook GM, Morales SE* (2016). Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely-utilised energy source for microbial growth and survival. The ISME Journal 10, 761-777
Form I carbon monoxide dehydrogenase
- Cordero PRF† & Bayly K†, Leung PM, Huang C, Islam ZF, Schittenhelm R, King GM, Greening C* (2019). Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival. The ISME Journal 13, 2868-2881