Highlights d Cities possess a consistent ''core'' set of non-human microbes d Urban microbiomes echo important features of cities and city-life d Antimicrobial resistance genes are widespread in cities d Cities contain many novel bacterial and viral species

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections.

A mesophilic, aerobic, facultatively chemolithoautotrophic bacterium, designated strain EPR70 T , was isolated from hydrothermal fluids from diffuse-flow vents on the East Pacific Rise at 96 509 N 1046 179 W. Cells were Gram-negative rods, approximately 0.8-1.0 mm long and 0.3-0.5 mm wide. Strain EPR70 T grew at 20-40 6C (optimum 30-35 6C), 1-25 % NaCl (optimum 2.5 %) and pH 5.0-7.5 (optimum pH 5.5). The shortest generation time observed for strain EPR70 T was 42 min. Growth occurred under aerobic chemolithoautotrophic conditions in the presence of thiosulfate and CO 2 . Strain EPR70 T grew heterotrophically with acetate or n-alkanes as sole carbon and energy sources, and in complex artificial seawater medium. Nitrate was not used as an electron acceptor. The G+C content of the genomic DNA was 64 mol%. Phylogenetic analysis of the 16S rRNA gene indicated that this organism is a member of the class Gammaproteobacteria, with Salinisphaera shabanensis E1L3A T as its closest relative (94 % sequence similarity). On the basis of phylogenetic analyses based on 16S rRNA, rbcL and alkB genes and physiological analysis, it is proposed that the organism represents a novel species within the genus Salinisphaera, for which the name Salinisphaera hydrothermalis sp. nov. is proposed. The type strain is EPR70 T (5DSM 21483 T 5JCM 15514 T ).Deep-sea hydrothermal vents are located in tectonically active areas of the sea floor and release either hightemperature fluids (focused-flow vents) or moderatetemperature fluids (diffuse-flow vents). At deep-sea vents, seawater interacts with volcanic rocks at high temperature and becomes enriched in a variety of reduced chemical species, which represent a constant flux of electron donors for microbial oxidations. In the absence of light, chemosynthetic micro-organisms oxidize these reduced chemical species (predominantly sulfur compounds) and mediate the primary production of organic carbon (Jannasch, 1995;McCollom & Shock, 1997).Typically, representatives of the genera Thiomicrospira and Thiobacillus have been isolated when diffuse-flow hydrothermal fluids were inoculated in culture media for the enrichment of chemosynthetic, aerobic, sulfide-, sulfur-and thiosulfate-oxidizing bacteria (Ruby et al., 1981;Ruby & Jannasch, 1982;Jannasch et al., 1985;Durand et al., 1993;Teske et al., 2000; Takai et al., 2004). Heterotrophic bacteria of the genera Marinobacter, Vibrio, Pseudoalteromonas and Halomonas, among others, have also been isolated routinely The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains EPR70 T , EPR72 and EPR71 are EU740416-EU740418. The accession numbers for the partial rbcL gene sequences from strains EPR70 T , EPR71 and EPR72 and S. shabanensis DSM 14853 T are EU740422-EU740425 and those for the partial alkB gene sequences of strain EPR70 T , S. shabanensis DSM 14853 T and strain EPR71 are EU740419-EU740421.Graphs showing the effects of temperature, pH and NaCl concentration on growth of strain EPR70 T and neighbour-joining trees based on amino a...

In April 1991, submarine volcanic eruptions initiated the formation of numerous hydrothermal vents between 9°45# and 9°52#N along the crest of the East Pacific Rise (EPR). Dramatic changes in biological community structure and vent fluid chemistry have been documented throughout this region since the eruptive event. By April 2004, mussels (Bathymodiolus thermophilus) dominated the faunal assemblages at several of the vent sites formed during of after the 1991 eruptions, whereas other habitats within the region were dominated by the vestimentiferan Riftia pachyptila. In the present paper, we build upon the extensive data sets obtained at these sites over the past decade and describe a manipulative experiment (conducted at 9°49.94#N; 104°14.43#W on the EPR) designed to assess interrelationships between vent fluid chemistry, temperature, biological community structure, and seismic activity. To this end, in situ voltammetric systems and thermal probes were used to measure H 2 S/HSand temperature over time in a denuded region of an extensive mussel bed in which an exclusion cage was placed to inhibit the subsequent migration of mussels into the denuded area. Fluid samples were taken from the same locations to characterize the associated microbial constituents. Basalt blocks, which were placed in the cage in April 2004 and subsequently recovered in April 2005, were colonized by more than 25 different species of invertebrates, including numerous vestimentiferans and remarkably few mussels. Recorded temporal changes in vent fluid chemistry and temperature regimes, when coupled with microbiological characterization of the vent fluids and seismic activity data obtained from ocean bottom seismometers, shed considerable light on factors controlling biological community structure in these hydrothermal ecosystems.

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