Table 1 Low-rank taxa contributing genes to TeOM degradation in the Amazon River system
From: Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter
Zone | Genera or closest reference genomes from GTDBa | TeOM degradation step |
|---|---|---|
Upstream, downstream, and estuary | Ramlibacter | Lignin oxidation |
Planktophila | Hemicellulose hydrolysis | |
Methylopumilus, Planktophila, Polynucleobacter | Cellulose hydrolysis | |
Acidovorax_D, Cupriavidus, Curvibacter_A, Fonsibacter, Hylemonella, Ideonella_A, Limnohabitans, PALSA-911 (Acetobacteraceae), Polaromonas, Polynucleobacter, Ramlibacter, Reyranella, SCGC-AAA027-K21 (Burkholderiaceae), UBA3064 (Burkholderiaceae), UBA6679 (Burkholderiaceae), Z2-YC6860 (Xanthobacteraceae) | TTT system | |
AAA044-D11 (Nanopelagicaceae), AcAMD-5 (Nanopelagicales), GCA-2737595 (Nanopelagicaceae), Limnohabitans, Nanopelagicus, Planktophila, Polynucleobacter, RS62 (Burkholderiaceae), UBA6679 (Burkholderiaceae), UBA7398 (Nanopelagicaceae) | ABC transporters | |
Planktophila, Polynucleobacter | FP-dimers | |
Limnohabitans | FP-monomers | |
GCA-2737595 (Nanopelagicaceae), Methylopumilus, Planktophila, Fonsibacter | O-demethylation/C1 metabolism | |
Acidovorax_D, Curvibacter_A, Limnohabitans, Pelomonas | Ring cleavage | |
Ocean and plume | HIMB11 (Rhodobacteraceae), Pelagibacter | Lignin oxidation |
HIMB11 (Rhodobacteraceae) | Hemicellulose hydrolysis | |
D2472 (Gammaproteobacteria), UBA4465 (Cyclobacteriaceae) | Cellulose hydrolysis | |
HIMB11 (Rhodobacteraceae), HIMB59 (Alphaproteobacteria), Pelagibacter | TTT system | |
Pelagibacter, Pelagibacter_A, TMED189 (Acidimicrobiia) | ABC transporters | |
HIMB11 (Rhodobacteraceae), Pelagibacter | FP-dimers | |
HIMB11 (Rhodobacteraceae), Pelagibacter | FP-monomers | |
HIMB11 (Rhodobacteraceae), Pelagibacter, SCGC-AAA076-P13 (Gammaproteobacteria) | O-demethylation | |
N/A | Ring cleavage |