Uncovering the gene machinery of the Amazon River microbiome to degrade rainforest organic matter

Abstract 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 analyzing 106 metagenomes from 30 stations 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 sampled environments (rivers and rainforest soil). Analyses of TeOM-degradation genes revealed that lignin degradation pathways correlated to tricarboxylates and hemicellulose processing, pointing to a higher lignin degradation coupled to the consumption of labile compounds. We propose a model on how the degradation of recalcitrant TeOM modulated by labile compounds (i.e. priming effect) may operate in the Amazon River waters. Conclusions: Our work contributes to expand significantly our comprehension of the world’s largest river microbiome and its role in TeOM degradation. Furthermore, the AMnrGC represents an important resource for future works exploring the links between TeOM and its degradation by aquatic microbiotas in tropical ecosystems.