TY - JOUR

T1 - Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp

AU - Palomo, Alejandro

AU - Jane Fowler, S

AU - Gülay, Arda

AU - Rasmussen, Simon

AU - Sicheritz-Ponten, Thomas

AU - Smets, Barth F

PY - 2016/11

Y1 - 2016/11

N2 - 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.

AB - 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.

KW - Ammonia/metabolism

KW - Ammonium Compounds/metabolism

KW - Bacteria/classification

KW - Bacterial Proteins/genetics

KW - Filtration

KW - Gravitation

KW - Groundwater/chemistry

KW - Iron/metabolism

KW - Manganese/metabolism

KW - Metagenomics

KW - Methane/metabolism

KW - Nitrites/metabolism

KW - Oxidation-Reduction

KW - Silicon Dioxide/chemistry

U2 - 10.1038/ismej.2016.63

DO - 10.1038/ismej.2016.63

M3 - Journal article

C2 - 27128989

VL - 10

SP - 2569

EP - 2581

JO - I S M E Journal

JF - I S M E Journal

SN - 1751-7362

IS - 11

ER -