Degradation of terrestrial organic matter by aquatic microbial genomes in the Amazon River

Abstract

Rivers connect the carbon cycle in land with that in aquatic ecosystems by transporting and transforming terrestrial organic matter (TeOM). The Amazon River receives huge loads of TeOM from the surrounding rainforest, promoting a substantial microbial heterotrophic activity and consequently, CO2 outgassing. In the Amazon River, microbes degrade up to 55% of the lignin present in the TeOM. Yet, the main microbial genomes involved in TeOM degradation were unknown. Here, we characterize 51 Population Genomes (PGs) representing some of the most abundant microbes in the Amazon River deriving from 106 metagenomes. The 51 reconstructed PGs are among the most abundant microbes in the Amazon River, and 53% of them are not able to degrade TeOM. Among the PGs capable of degrading TeOM, 20% were exclusively cellulolytic, while the others could also oxidize lignin. The transport and consumption of lignin oxidation by-products seemed to be decoupled from the oxidation process, being apparently performed by different groups of microorganisms. By connecting the genomic features of abundant microbes in the Amazon River with the degradation machinery of TeOM, we suggest that a microbial consortium following a priming effect model could explain the quick turnover of TeOM previously observed in this ecosystem.

Genome-centric metagenomics reveals insights into the evolution and metabolism of a new free-living group in Rhizobiales

“…We reinforce that 2.17 represents genomes with lower percentages of contamination. To complete these analyses, we also add 18 genomes [11,12,16,[18][19][20][21][22][23] deposited in public sequence repositories (Table 1), which were not explored deeply in the context of this investigation. Also according to MIMAG standards [14], these genomes were assigned with high-quality or medium-quality drafts (Table 1).…”

“…In this case, Aestuariivirgaceae metabolism would reflect a basal metabolism of Rhizobiales. The presence of Embden-Meyerhof-Parnas (Glycolysis) pathway also suggest that Aestuariivirgaceae family is well adapted to survive in environments rich in organic matter, as such marine sediments, soils [10,12], estuarine ecosystems [16] and rivers [18], where the organic matter derived from biological biomass is abundant. Furthermore, Nordella sp005884715 (AP_21 genome) has potential to perform pyruvate fermentation to lactate generation, which would represent adaptation and alternative metabolism to survive in soils (Fig.…”