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

Microbiome

Fernando Pellon de Miranda¹  Ramiro Logares²  Hugo Sarmento³  Flávio Henrique-Silva⁴  Célio Dias Santos-Júnior⁵ 

[1] Centro de Pesquisas e Desenvolvimento Leopoldo Américo Miguez de Mello, Petróleo Brasileiro S.A. (Petrobras), Av. Horácio Macedo 950, 21941-915, Rio de Janeiro, RJ, Brazil;Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta 37-49, ES08003, Barcelona, Catalonia, Spain;Laboratory of Microbial Processes & Biodiversity, Department of Hydrobiology – DHB, Universidade Federal de São Carlos – UFSCar, Via Washington Luis KM 235 - Monjolinho, 13565-905, São Carlos, SP, Brazil;Molecular Biology Laboratory, Department of Genetics and Evolution – DGE, Universidade Federal de São Carlos – UFSCar, Rod. Washington Luis KM 235 - Monjolinho, 13565-905, São Carlos, SP, Brazil;Molecular Biology Laboratory, Department of Genetics and Evolution – DGE, Universidade Federal de São Carlos – UFSCar, Rod. Washington Luis KM 235 - Monjolinho, 13565-905, São Carlos, SP, Brazil;Institute of Science and Technology for Brain-Inspired Intelligence – ISTBI, Fudan University, Handan Rd 220, Wu Jiao Chang, Yangpu, 200433, Shanghai, China;

关键词: Amazon River;    Freshwater bacteria;    Biodiversity;    Metagenomics;    Lignin degradation;    Cellulose degradation;    Priming effect;    Gene catalogue;   

DOI  :  10.1186/s40168-020-00930-w

来源: Springer

【 摘 要 】

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.2Uu_3sWfgQecUdsXZ4EGSVideo abstract.

【 授权许可】

CC BY