title: Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria.
abstract: Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua. Phylogenetic analysis of the 16S rRNA gene indicated that this Scalindua sp. belongs to a distinct group, separate from the anammox bacteria in the seawater column, that contains mostly sequences retrieved from high-salt environments. Using coverage- and composition-based binning, we extracted and assembled the draft genome of the dominant anammox bacterium. Comparative genomic analysis indicated that this Scalindua species uses compatible solutes for osmoadaptation, in contrast to other marine anammox bacteria that likely use a salt-in strategy. We propose the name Candidatus Scalindua rubra for this novel species, alluding to its discovery in the Red Sea.
authors.affiliation: Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands. dspeth@caltech.edu.|Division for Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA. dspeth@caltech.edu.
authors.forename: Daan R
authors.initials: DR
authors.lastname: Speth
authors.affiliation: ZIEL Institute for Food and Health, Technische Universität München, Freising, Germany.
authors.forename: Ilias
authors.initials: I
authors.lastname: Lagkouvardos
authors.affiliation: Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
authors.forename: Pei-Yuan
authors.initials: PY
authors.lastname: Qian
authors.affiliation: Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.|Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands.|Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Bas E
authors.initials: BE
authors.lastname: Dutilh
authors.affiliation: Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands.|Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
authors.forename: Mike S M
authors.initials: MSM
authors.lastname: Jetten
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics; D016680:Genome, Bacterial; D019156:Indian Ocean; D010084:Oxidation-Reduction; D010802:Phylogeny; D000644:Quaternary Ammonium Compounds; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012492:Salts; D012623:Seawater / Q000382:microbiology*
chemical_list: D000644:Quaternary Ammonium Compounds; D012336:RNA, Ribosomal, 16S; D012492:Salts; C017082:brine
keywords: Anammox; Genome binning; Metagenomics; Red Sea; Salt adaptation; Scalindua