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Over the past decade Amazonian rainforest has been converted to commodity production (pasture and soybean) at a rate of 6.54 M hectares per year (Kim et al., 2015). To circumvent the limitations presented by nutrient-poor soils, many farmers adopt slash-andburn practices, which use fire to quickly mineralize nutrients stored in the plant biomass and make them available for subsequent crops.

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Wastewater is considered a renewable resource water and energy. An advantage of decentralized sanitation systems is the separation of the blackwater (BW) stream, contaminated with human pathogens, from the remaining household water. However, the composition and functions of the microbial community in BW are not known. In this study, we used shotgun metagenomics to assess the dynamics of microbial community structure and function throughout a new BW anaerobic digestion system installed at The Netherlands Institute of Ecology. Samples from the influent (BW), primary effluent (anaerobic digested BW), sludge and final effluent of the pilot upflow anaerobic sludge blanket (UASB) reactor and microalgae pilot tubular photobioreactor (PBR) were analyzed. Our results showed a decrease in microbial richness and diversity followed by a decrease in functional complexity and co-occurrence along the different modules of the bioreactor. The microbial diversity and function decrease were reflected both changes in substrate composition and wash conditions. Our wastewater treatment system also decreased microbial functions related to pathogenesis. In summary, the new sanitation system studied here fosters microbial groups and functions that allow the system to efficiently and robustly recover carbon and nutrients while reducing pathogenic groups, ultimately generating a final effluent safe for discharge and reuse.