title: From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists.
abstract: The microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. However, studies addressing the dynamic nature of these systems are very scarce. Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to >40%), by means of CARD-FISH and DGGE. Microbial community structure was statistically correlated with several environmental parameters, including ionic composition and meteorological factors, indicating that the microbial community was dynamic as specific phylotypes appeared only at certain times of the year. In addition to total salinity, microbial composition was strongly influenced by temperature and specific ionic composition. Remarkably, DGGE analyses unveiled the presence of most phylotypes previously detected in hypersaline systems using metagenomics and other molecular techniques, such as the very abundant Haloquadratum and Salinibacter representatives or the recently described low GC Actinobacteria and Nanohaloarchaeota. In addition, an uncultured group of Bacteroidetes was present along the whole range of salinity. Database searches indicated a previously unrecognized widespread distribution of this phylotype. Single-cell genome analysis of five members of this group suggested a set of metabolic characteristics that could provide competitive advantages in hypersaline environments, such as polymer degradation capabilities, the presence of retinal-binding light-activated proton pumps and arsenate reduction potential. In addition, the fairly high metagenomic fragment recruitment obtained for these single cells in both the intermediate and hypersaline ponds further confirm the DGGE data and point to the generalist lifestyle of this new Bacteroidetes group.
authors.affiliation: 1] Department of Materials, Optics and Electronics, University Miguel Hernández of Elche, Alicante, Spain [2] Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain.
authors.forename: María
authors.initials: M
authors.lastname: Gomariz
authors.affiliation: Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Martínez-García
authors.affiliation: Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain.
authors.forename: Fernando
authors.initials: F
authors.lastname: Santos
authors.affiliation: Departament of Applied Mathematics, University of Alicante, Alicante, Spain.
authors.forename: Francisco
authors.initials: F
authors.lastname: Rodriguez
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain.
authors.forename: Salvador
authors.initials: S
authors.lastname: Capella-Gutiérrez
authors.affiliation: 1] Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain [2] Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.affiliation: Marine Microbiology Group, Department of Ecology and Marine Resources, Institut Mediterrani d'Estudis Avançats IMEDEA (CSIC-UIB), Esporles, Spain.
authors.forename: Ramon
authors.initials: R
authors.lastname: Rosselló-Móra
authors.affiliation: Department of Materials, Optics and Electronics, University Miguel Hernández of Elche, Alicante, Spain.
authors.forename: Inmaculada
authors.initials: I
authors.lastname: Meseguer
authors.affiliation: Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain.
authors.forename: Josefa
authors.initials: J
authors.lastname: Antón
mesh_terms: D039903:Actinobacteria / Q000302:isolation & purification; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D041963:Bacteroidetes / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D044822:Biodiversity; D016680:Genome, Bacterial; D006216:Halobacteriaceae / Q000302:isolation & purification; D056186:Metagenomics; D064307:Microbiota; D061005:Ponds / Q000382:microbiology*; D054712:Salinity