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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

Background Microbial communities present in environmental waters constitute a reservoir for antibiotic-resistant pathogens that impact human health. For this reason, a diverse variety of water environments are being analyzed using metagenomics to uncover public health threats. However, the composition of these communities along the coastal environment of a whole city, where sewage and beach waters are mixed, is poorly understood. Results We shotgun-sequenced 20 coastal areas from the city of Montevideo (capital of Uruguay) including beach and sewage water samples to characterize bacterial communities and their virulence and antibiotic resistance repertories. As expected, we found that sewage and beach environments present significantly different bacterial communities. This baseline allowed us to detect a higher prevalence and a more diverse repertory of virulence and antibiotic-resistant genes in sewage samples. Many of these genes come from well-known enterobacteria and represent carbapenemases and extended-spectrum betalactamases reported in hospital infections in Montevideo. Additionally, we were able to genotype the presence of both globally disseminated pathogenic clones and emerging antibiotic-resistant bacteria in sewage waters. Conclusions Our study represents the first in using metagenomics to jointly analyze beaches and the sewage system from an entire city, allowing us to characterize antibiotic-resistant pathogens circulating in urban waters. The data generated in this initial study represent a baseline metagenomic exploration to guide future longitudinal (time-wise) studies, whose systematic implementation will provide useful epidemiological information to improve public health surveillance. Electronic supplementary material The online version of this article (10.1186/s40168-019-0648-z) contains supplementary material, which is available to authorized users.

BackgroundThe evolution of insecticide resistance in Spodoptera frugiperda (Lepidoptera: Noctuidae) has resulted in large economic losses and disturbances to the environment and agroecosystems. Resistance to lufenuron, a chitin biosynthesis inhibitor insecticide, was recently documented in Brazilian populations of S. frugiperda. Thus, we utilized large-scale cDNA sequencing (RNA-Seq analysis) to compare the pattern of gene expression between lufenuron-resistant (LUF-R) and susceptible (LUF-S) S. larvae in an attempt to identify the molecular basis behind the resistance mechanism(s) of S. frugiperda to this insecticide.ResultsA transcriptome was assembled using approximately 19.6 million 100 bp-long single-end reads, which generated 18,506 transcripts with a N50 of 996 bp. A search against the NCBI non-redundant database generated 51.1 % (9,457) functionally annotated transcripts. A large portion of the alignments were homologous to insects, with the majority (45 %) being similar to sequences of Bombyx mori (Lepidoptera: Bombycidae). Moreover, 10 % of the alignments were similar to sequences of various species of Spodoptera (Lepidoptera: Noctuidae), with 3 % of them being similar to sequences of S. frugiperda. A comparative analysis of the gene expression between LUF-R and LUF-S S. frugiperda larvae identified 940 differentially expressed transcripts (p ≤ 0.05, t-test; fold change ≥ 4). Six of them were associated with cuticle metabolism. Of those, four were overexpressed in LUF-R larvae. The machinery involved with the detoxification process was represented by 35 differentially expressed transcripts; 24 of them belonging to P450 monooxygenases, four to glutathione-S-transferases, six to carboxylases and one to sulfotransferases. RNA-Seq analysis was validated for a number of selected candidate transcripts by using quantitative real time PCR (qPCR).ConclusionsThe gene expression profile of LUF-R larvae of S. frugiperda differs from LUF-S larvae. In general, gene expression is much higher in resistant larvae when compared to the susceptible ones, particularly for those genes involved with pathways for xenobiotic detoxification, mainly represented by P450 monooxygenases transcripts. Our data indicate that enzymes involved with the detoxification process, and mostly the P450, are one of the resistance mechanisms employed by the LUF-R S. frugiperda larvae against lufenuron.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2183-z) contains supplementary material, which is available to authorized users.

A major goal of phylogeographic analysis using molecular markers is to understand the ecological and historical variables that influence genetic diversity within a species. Here, we used sequences of the mitochondrial Cox1 gene and nuclear internal transcribed spacer to reconstruct its phylogeography and demographic history of the intertidal red seaweed Chondrus ocellatus over most of its geographical range in the Northwest Pacific. We found three deeply separated lineages A, B and C, which diverged from one another in the early Pliocene-late Miocene (c. 4.5-7.7 Ma). The remarkably deep divergences, both within and between lineages, appear to have resulted from ancient isolations, accelerated by random drift and limited genetic exchange between regions. The disjunct distributions of lineages A and C along the coasts of Japan may reflect divergence during isolation in scattered refugia. The distribution of lineage B, from the South China Sea to the Korean Peninsula, appears to reflect postglacial recolonizations of coastal habitats. These three lineages do not coincide with the three documented morphological formae in C. ocellatus, suggesting that additional cryptic species may exist in this taxon. Our study illustrates the interaction of environmental variability and demographic processes in producing lineage diversification in an intertidal seaweed and highlights the importance of phylogeographic approaches for discovering cryptic marine biodiversity.