Abstract
Rapid gravity sand filtration is a drinking water production technology widely used around the world. Microbially catalyzed processes dominate the oxidative transformation of ammonia, reduced manganese and iron, methane and hydrogen sulfide, which may all be present at millimolar concentrations when groundwater is the source water. In this study, six metagenomes from various locations within a groundwater-fed rapid sand filter (RSF) were analyzed. The community gene catalog contained most genes of the nitrogen cycle, with particular abundance in genes of the nitrification pathway. Genes involved in different carbon fixation pathways were also abundant, with the reverse tricarboxylic acid cycle pathway most abundant, consistent with an observed Nitrospira dominance. From the metagenomic data set, 14 near-complete genomes were reconstructed and functionally characterized. On the basis of their genetic content, a metabolic and geochemical model was proposed. The organisms represented by draft genomes had the capability to oxidize ammonium, nitrite, hydrogen sulfide, methane, potentially iron and manganese as well as to assimilate organic compounds. A composite Nitrospira genome was recovered, and amo-containing Nitrospira genome contigs were identified. This finding, together with the high Nitrospira abundance, and the abundance of atypical amo and hao genes, suggests the potential for complete ammonium oxidation by Nitrospira, and a major role of Nitrospira in the investigated RSFs and potentially other nitrifying environments.
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Acknowledgements
We thank K Amoako, MD Dalgaard, and BJR Cockx for supporting sample collection, library preparation and NG sequencing, and graphics. This research was financially supported by MERMAID (An initial training network funded by the People Programme - Marie Skłodowska-Curie Actions- of the European Union's Seventh Framework Programme FP7/2007-2013/ under REA grant agreement n°607492).
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The original study design was conceived by AG, AP, TSP and BFS. Sampling and DNA extraction were performed by AG. AP performed bioinformatic analyses, supported by SJF, TSP and SR. AP and SJF lead interpretation of the results. AP drafted the manuscript; all authors contributed to its revision and completion, and approved the final submission.
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Palomo, A., Jane Fowler, S., Gülay, A. et al. Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.. ISME J 10, 2569–2581 (2016). https://doi.org/10.1038/ismej.2016.63
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DOI: https://doi.org/10.1038/ismej.2016.63
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