Fowler, Jane

Gülay, Arda

Palomo, Alejandro

Rasmussen, Simon

Schramm, Andreas

Sicheritz-Pontén, Thomas

Smets, Barth F.

The recent discovery of complete ammonia oxidizing (comammox) Nitrospira has revealed that the metabolic division of labor in nitrification is not obligate as was assumed during the last century. Despite the detection and enrichment of commamox Nitrospira from different nitrifying environments, the ecological relevance of comammox remains unknown. In this study, we analyzed the microbial communities from various locations within a groundwater-fed rapid sand filter (RSF), where Nitrospira were at very high relative abundances. Through metagenomics, a highly abundant composite multi-genome of Nitrospira genus was recovered harboring metabolic capacity for complete ammonia oxidation. We developed a cell extraction strategy that enables the disruption of Nitrospira cell clusters attached to the mineral coating of the sand. Individual cells were identified via fluorescent in situ hybridization (FISH) with Nitrospira-specific 16S rRNA probes and sorted via fluorescence-activated cell sorting (FACS). Sorted cells were screened and selected Nitrospira spp. were subject to whole-genome sequencing. The single cell genomes confirmed the genomic presence of a complete ammonia oxidation pathway and revealed clear taxonomic differences with the recently described comammox Nitrospira genomes. The high abundance of comammox Nitrospira spp. together with the low abundance of canonical ammonia oxidizing prokaryotes in the investigated RSF system suggests the essential role of this novel comammox Nitrospira in the RSFs and potentially other nitrifying environments

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                       General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.  • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal   If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.     Downloaded from orbit.dtu.dk on: Dec 18, 2017Metagenomics and single-cell genomics reveal high abundance of comammoxNitrospira in a rapid gravity sand filter treating groundwaterPalomo, Alejandro; Fowler, Jane; Gülay, Arda; Rasmussen, Simon; Schramm, Andreas; Sicheritz-Pontén, Thomas; Smets, Barth F.Publication date:2016Document VersionPeer reviewed versionLink back to DTU OrbitCitation (APA):Palomo, A., Fowler, J., Gülay, A., Rasmussen, S., Schramm, A., Sicheritz-Pontén, T., & Smets, B. F. (2016).Metagenomics and single-cell genomics reveal high abundance of comammox Nitrospira in a rapid gravity sandfilter treating groundwater. Abstract from 16th International Symposium on Microbial Ecology, Montreal, Canada.Topic:	Applying	-omics	approaches	to	understand	microbial	functioning	Metagenomics	and	single-cell	genomics	reveal	high	abundance	of	comammox	Nitrospira	 in	a	rapid	gravity	sand	filter	treating	groundwater.	Alex Palomo1,2, S. Jane Fowler1, Arda Gülay1, Simon Rasmussen2, Andreas Schramm3, Thomas Sicheritz-Ponten2, Barth F. Smets1 1Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark. 2Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark 3Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark  The recent discovery of complete ammonia oxidizing (comammox) Nitrospira has revealed that the metabolic division of labor in nitrification is not obligate as was assumed during the last century. Despite the detection and enrichment of commamox Nitrospira from different nitrifying environments, the ecological relevance of comammox remains unknown. In this study, we analyzed the microbial communities from various locations within a groundwater-fed rapid sand filter (RSF), where Nitrospira were at very high relative abundances. Through metagenomics, a highly abundant composite multi-genome of Nitrospira genus was recovered harboring metabolic capacity for complete ammonia oxidation. We developed a cell extraction strategy that enables the disruption of Nitrospira cell clusters attached to the mineral coating of the sand. Individual cells were identified via fluorescent in situ hybridization (FISH) with Nitrospira-specific 16S rRNA probes and sorted via fluorescence-activated cell sorting (FACS). Sorted cells were screened and selected Nitrospira spp. were subject to whole-genome sequencing. The single cell genomes confirmed the genomic presence of a complete ammonia oxidation pathway and revealed clear taxonomic differences with the recently described comammox Nitrospira genomes. The high abundance of comammox Nitrospira spp. together with the low abundance of canonical ammonia oxidizing prokaryotes in the investigated RSF system suggests the essential role of this novel comammox Nitrospira in the RSFs and potentially other nitrifying environments.  

Metagenomics and single-cell genomics reveal high abundance of comammox Nitrospira in a rapid gravity sand filter treating groundwater

http://orbit.dtu.dk/ws/files/126602348/ISME_Abstract_Palomo2016.pdf

Metagenomics and single-cell genomics reveal high abundance of comammox Nitrospira in a rapid gravity sand filter treating groundwater

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