Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsOur 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.5mC5z9F231eP-ddBjFuPssVideo abstract.
Highlights
The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest
Functional metagenomics was already performed in the Amazon River [12,13,14,15,16,17,18], so far, no comprehensive gene catalogue was generated, which hinders our understanding of the genomic machinery that degrades almost half of the 1.9 Pg C discharged into rivers every year as recalcitrant TeOM [1]
The Amazon River microbiome differed from other microbiomes We compared the metagenomic information contained in the Amazon River microbiome with that from the Amazon rainforest soil and other available temperate rivers (Canada watersheds and Mississippi River) using k-mers (Supplementary Table 3 in Additional file 1)
Summary
The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Even though the gene repertoire of river microbiomes can provide crucial insights to understand the links between terrestrial and marine ecosystems, as well as the fate of organic matter synthesized on land, very little is known about the genomic machinery of riverine microbes that degrade TeOM. Functional metagenomics was already performed in the Amazon River [12,13,14,15,16,17,18], so far, no comprehensive gene catalogue was generated, which hinders our understanding of the genomic machinery that degrades almost half of the 1.9 Pg C discharged into rivers every year as recalcitrant TeOM [1] This is relevant in tropical rainforests, like the Amazon forest, which accounts for ~ 10% of the global primary production, fixing 8.5 Pg C per year [19, 20]. Despite its relevance for global-scale processes, there is a limited understanding of the Amazon River microbiome
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