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

Klebsiella pneumoniae is an opportunistic pathogen important in hospital-acquired infections, which are complicated by the rise of drug-resistant strains and the capacity of cells to adhere to surfaces and form biofilms. In this work, we carried out an analysis of the genes in the K. pneumoniae yfiRNB operon, previously implicated in biofilm formation. The results indicated that in addition to the previously reported effect on type 3 fimbriae expression, this operon also affected biofilm formation due to changes in cellulose as part of the extracellular matrix. Deletion of yfiR resulted in enhanced biofilm formation and an altered colony phenotype indicative of cellulose overproduction when grown on solid indicator media. Extraction of polysaccharides and treatment with cellulase were consistent with the presence of cellulose in biofilms. The enhanced cellulose production did not, however, correlate with virulence as assessed using a Caenorhabditis elegans assay. In addition, cells bearing mutations in genes of the yfiRNB operon varied with respect to the WT control in terms of susceptibility to the antibiotics amikacin, ciprofloxacin, imipenem and meropenem. These results indicated that the yfiRNB operon is implicated in the production of exopolysaccharides that alter cell surface characteristics and the capacity to form biofilms -a phenotype that does not necessarily correlate with properties related with survival, such as resistance to antibiotics.

Ultraviolet radiation (UVR) is widely known as deleterious for many organisms since it can cause damage to biomolecules either directly or indirectly via the formation of reactive oxygen species. The goal of this study was to analyze the capacity of high-mountain Espeletia hartwegiana plant phyllosphere microorganisms to survive UVR and to identify genes related to resistance strategies. A strain of Deinococcus swuensis showed a high survival rate of up to 60% after UVR treatment at 800J/m2 and was used for differential expression analysis using RNA-seq after exposing cells to 400J/m2 of UVR (with >95% survival rate). Differentially expressed genes were identified using the R-Bioconductor package NOISeq and compared with other reported resistance strategies reported for this genus. Genes identified as being overexpressed included transcriptional regulators and genes involved in protection against damage by UVR. Non-coding (nc)RNAs were also differentially expressed, some of which have not been previously implicated. This study characterized the immediate radiation response of D. swuensis and indicates the involvement of ncRNAs in the adaptation to extreme environmental conditions.

Antibiotic-resistant bacteria represent a global risk to public health. Horizontal gene transfer, a common mechanism for genetic exchange in bacteria, plays an essential role in the acquisition of resistance genes. In this work, we evaluated the effect of sub-lethal concentrations of antibiotics on plasmid transfer by conjugation and transformation in the opportunistic pathogen Klebsiella pneumoniae. Despite not being naturally competent, this bacterium could acquire extracellular DNA from various plasmids at a very low frequency, which increased upon incubating cells with the aminoglycoside antibiotics amikacin and gentamicin. Transfer by conjugation analyzed using a clinical isolate carrying plasmid pNDM-1 also increased in the presence of sub-lethal concentrations of antibiotics. An RNAseq analysis showed differential expression of several genes when cells were incubated in the presence of sub-lethal concentrations of amikacin suggesting metabolic and regulatory changes, as well as alteration of cell envelope components that could affect the uptake of foreign DNA. These results suggest that sub-lethal concentrations of some aminoglycosides, in particular amikacin, can promote the transfer of resistance-bearing genetic elements in K. pneumoniae, which is relevant for understanding the spread of resistance determinants in this human pathogen.

Klebsiella pneumoniae is an opportunistic pathogen associated with nosocomial infections. Persister cells are a fraction of a bacterial population that can escape antibiotic treatment and are associated with antibiotic therapy failure. In this work, we analyzed persistent cells in planktonic cultures and biofilms using10 K. pneumoniae clinical isolates and four different antibiotic types. The isolates had different antibiotic susceptibility profiles that did not correlate with their capacity to form biofilms. Persister cells were found under all conditions tested, although their population numbers varied depending on the antibiotic used. A larger number of persister cells were found in biofilms than in planktonic cultures. Antibiotic treatment with trimethoprim-sulfamethoxazole resulted in the largest persister cell sub-population compared with other antibiotics tested, while ciprofloxacin was the antibiotic that produced fewer persister cells. These results indicate that K. pneumoniae clinical isolates vary not only in their susceptibility to antibiotics but also in properties relevant to diseases, such as biofilm formation and persister cell populations.

Ultraviolet radiation (UVR) is widely known as deleterious for many organisms since it can cause damage to biomolecules either directly or indirectly via the formation of reactive oxygen species. The goal of this study was to analyze the capacity of high-mountain Espeletia hartwegiana plant phyllosphere microorganisms to survive UVR and to identify genes related to resistance strategies. A strain of Deinococcus swuensis showed a high survival rate of up to 60% after UVR treatment at 800J/m 2 and was used for differential expression analysis using RNA-seq after exposing cells to 400J/m 2 of UVR (with >95% survival rate). Differentially expressed genes were identified using the R-Bioconductor package NOISeq and compared with other reported resistance strategies reported for this genus. Genes identified as being overexpressed included transcriptional regulators and genes involved in protection against damage by UVR. Non-coding (nc)RNAs were also differentially expressed, some of which have not been previously implicated. This study characterized the early resistance strategy used by D. swuensis and indicates the involvement of ncRNAs in the adaptation to extreme environmental conditions. 2 and/or radiation conditions are attractive sources of microorganisms with exceptional 3 phenotypic and genotypic properties. The high-mountain Paramo biome, similar to the 4 tundra biome of high latitudes, consists of high-elevation areas subject to harsh 5 environmental conditions. The Paramo biome has a high solar incidence that can induce 6 damage by ultraviolet radiation (UVR) that represents a survival challenge for 7 organisms [50]. Ionizing radiation and UVR affect organisms by damaging cellular 8 components such as nucleic acids, proteins, and lipids [30]. The deleterious effect on 9 cells is caused by direct damage to DNA, such as chromosomal lesions that introduce 10 both double-strand breaks (DSBs) and single-strand breaks (SSBs), and damage due to 11 pyrimidine dimerization and photoproducts that inhibit DNA replication and 12 July 31, 2019 1/19 transcription [2]. Most of the damage, however, is caused indirectly by the production of 13 reactive oxygen species (ROS), such as the chemically reactive superoxide and hydroxyl 14 radicals that in turn affect various cellular constituents, including proteins [30]. 15 The electromagnetic spectrum of UVR is divided into ultraviolet A (UVA) with 16 wavelengths from 315-400 nm (6.31e-19 -4.97e-19 J/m 2 s), ultraviolet B (UVB, from 17 280-315 nm, 7.10e-19 -6.31e-19 J/m 2 s) and ultraviolet C (UVC, from 100-280 nm, 18 1.99e-18 -7.10e-19 J/m 2 s) [64]. The UV electromagnetic spectrum covering UVB and 19 UVC is considered ionizing radiation [51]. While UVC is absorbed by the ozone layer 20 and the atmosphere, about 8% of UVA and 1% of UVB reach the Earth's surface [51]. 21 The harmful effects of UVR on cellular components depend on the wavelength: UVA 22 can travel farther into tissues and contributes to ROS (damage to lipids, proteins, and 23 DNA) whereas UVB produces direct breaks...