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. 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. 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.

中文翻译：

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发掘亚马逊河微生物群降解雨林有机质的基因组潜力

亚马逊河是世界上最大的河流之一，从周围的雨林中接收大量的陆地有机物（TeOM）。尽管TeOM通常是顽强的（即抗降解），但只有一小部分到达海洋，这表明河流微生物组会导致TeOM大量降解。但是，鲜有涉及亚马逊河中TeOM降解的微生物基因。在这里，我们通过分析沿河分布的30个采样点的106个元基因组，检查了亚马逊河微生物群。我们构建了亚马逊河流域微生物非冗余基因目录（AMnrGC），其中包括约370万个非冗余基因，主要与细菌相关。我们发现，与其他相关的已知环境（河流和雨林土壤）相比，亚马逊河微生物群包含大量的基因新颖性。编码可能参与木质素降解途径的蛋白质的基因与三方三羧酸盐转运蛋白和半纤维素降解机制相关，指出可能具有引发作用。在此基础上，我们提出了一个模型，说明如何通过亚马逊河水域中的不稳定化合物调节顽固性TeOM的降解。我们的研究结果还表明，沿河道微生物群落及其基因组潜力的变化。我们的工作极大地促进了我们对世界上最大的河流微生物组及其与TeOM降解相关的潜在代谢的理解。此外，