Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter

18 pages, 7 figures, 1 table, supplementary information https://doi.org/10.1186/s40168-020-00930-w

Background. The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analysing 106 metagenomes from 30 sampling points distributed along the river. Results. We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~ 3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course. Conclusions. Our work contributes to expand significantly our comprehension of the world’s largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers

CDSJ was supported by a PhD scholarship from Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil (CNPq #141112/2016-6). FHS and HS work was supported by Research Productivity grants from CNPq (Process # 311746/2017-9 and #309514/2017-7, respectively). RL was supported by a Ramón y Cajal fellowship (RYC-2013-12554, MINECO, Spain). This work was supported by Petróleo Brasileiro S.A. (Petrobras), as part of a research agreement (#0050.0081178.13.9) with the Federal University of São Carlos, SP, Brazil, within the context of the Geochemistry Thematic Network. Additionally, this work was supported by the projects INTERACTOMICS (CTM2015-69936-P, MINECO, Spain) and MicroEcoSystems (240904, RCN, Norway) to RL and Fundação de Amparo à Pesquisa do Estado de São Paulo – FAPESP (Process #2014/14139-3) to HS. This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001 (CAPES #88881.131637/2016-01)

With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)

Peer reviewed