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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
  1. Main prokaryotic genera, or genomes from the Genome Taxonomy Database (GTDB) without assigned genera, contributing genes to TeOM degradation in the Amazon River sections as well as in plume and ocean samples are indicated. Only taxa contributing functions in more than half of the samples of each studied zone are reported
  2. aGenera or GTDB reference-genome names are indicated. For reference genome names, the lowest taxonomic level indicated in GTDB is shown in brackets
  3. FP funneling pathways, TTT tripartite tricarboxylic transporter, N/A not applicable