The ability to fight bacterial infections with antibiotics has been a longstanding cornerstone of modern medicine. However, wide-spread overuse and misuse of antibiotics has led to unintended consequences, which in turn require large-scale changes of policy for mitigation. In this review, we address two broad classes of corollaries of antibiotics overuse and misuse. Firstly, we discuss the spread of antibiotic resistance from hotspots of resistance evolution to the environment, with special concerns given to potential vectors of resistance transmission. Secondly, we outline the effects of antibiotic pollution independent of resistance evolution on natural microbial populations, as well as invertebrates and vertebrates. We close with an overview of current regional policies tasked with curbing the effects of antibiotics pollution and outline areas in which such policies are still under development.

Northern lakes are ice-covered for a large part of the year, yet our understanding of microbial diversity and activity during winter lags behind that of the ice-free period. In this study, we investigated under-ice diversity and metabolism of Verrucomicrobia in seasonally ice-covered lakes in temperate and boreal regions of Quebec, Canada using 16S rRNA sequencing, metagenomics and metatranscriptomics. Verrucomicrobia, particularly the V1, V3 and V4 subdivisions, were abundant during ice-covered periods. A diversity of Verrucomicrobia genomes were reconstructed from Quebec lake metagenomes. Several genomes were associated with the ice-covered period and were represented in winter metatranscriptomes, supporting the notion that Verrucomicrobia are metabolically active under ice. Verrucomicrobia transcriptome analysis revealed a range of metabolisms potentially occurring under ice, including carbohydrate degradation, glycolate utilization, scavenging of chlorophyll degradation products, and urea use. Genes for aerobic sulfur and hydrogen oxidation were expressed, suggesting chemolithotrophy may be an adaptation to conditions where labile carbon may be limited. The expression of genes for flagella biosynthesis and chemotaxis was detected, suggesting Verrucomicrobia may be actively sensing and responding to winter nutrient pulses, such as phytoplankton blooms. These results increase our understanding on the diversity and metabolic processes occurring under ice in northern lakes ecosystems.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

The Arctic Ocean is relatively isolated from other oceans and consists of strongly stratified water masses with distinct histories, nutrient, temperature, and salinity characteristics, therefore providing an optimal environment to investigate local adaptation. The globally distributed SAR11 bacterial group consists of multiple ecotypes that are associated with particular marine environments, yet relatively little is known about Arctic SAR11 diversity. Here, we examined SAR11 diversity using ITS analysis and metagenome-assembled genomes (MAGs). Arctic SAR11 assemblages were comprised of the S1a, S1b, S2, and S3 clades, and structured by water mass and depth. The fresher surface layer was dominated by an ecotype (S3-derived P3.2) previously associated with Arctic and brackish water. In contrast, deeper waters of Pacific origin were dominated by the P2.3 ecotype of the S2 clade, within which we identified a novel subdivision (P2.3s1) that was rare outside the Arctic Ocean. Arctic S2-derived SAR11 MAGs were restricted to high latitudes and included MAGs related to the recently defined S2b subclade, a finding consistent with bi-polar ecotypes and Arctic endemism. These results place the stratified Arctic Ocean into the SAR11 global biogeography and have identified SAR11 lineages for future investigation of adaptive evolution in the Arctic Ocean.

The diversity and distribution of methylotrophic bacteria have been investigated in the oceans and lakes using the methanol dehydrogenase mxaF gene as a functional marker. However, pelagic marine (OM43) and freshwater (LD28 and PRD01a001B) methylotrophs within the Betaproteobacteria lack mxaF, instead possessing a related xoxF4-encoded methanol dehydrogenase. Here, we developed and employed xoxF4 as a complementary functional gene marker to mxaF for studying methylotrophs in aquatic environment. Using xoxF4, we detected OM43-related and LD28-related methylotrophs in the ocean and freshwaters of North America, respectively, and showed the coexistence of these two lineages in a large estuarine system (St Lawrence Estuary). Gene expression patterns of xoxF4 supported a positive relationship between xoxF4-containing methylotroph activity and spring time productivity, suggesting phytoplankton blooms are a source of methylotrophic substrates. Further investigation of methanol dehydrogenase diversity in pelagic ecosystems using comparative metagenomics provided strong support for a widespread distribution of xoxF4 (as well as several distinct xoxF5) containing methylotrophs in marine and freshwater surface waters. In total, these results demonstrate a geographical distribution of OM43/LD28-related methylotrophs that includes marine and freshwaters and suggest that methylotrophy occurring in the water column is an important component of lake and estuary carbon cycling and biogeochemistry.

Here we harnessed the power of metaproteomics to assess the metabolic diversity and function of stratified aquatic microbial communities in the deep and expansive Lower St. Lawrence Estuary, located in eastern Canada. Vertical profiling of the microbial communities through the stratified water column revealed differences in metabolic lifestyles and in carbon and nitrogen processing pathways. In productive surface waters, we identified heterotrophic populations involved in the processing of high and low molecular weight organic matter from both terrestrial (e.g. cellulose and xylose) and marine (e.g. organic compatible osmolytes) sources. In the less productive deep waters, chemosynthetic production coupled to nitrification by MG-I Thaumarchaeota and Nitrospina appeared to be a dominant metabolic strategy. Similar to other studies of the coastal ocean, we identified methanol oxidation proteins originating from the common OM43 marine clade. However, we also identified a novel lineage of methanol-oxidizers specifically in the particle-rich bottom (i.e. nepheloid) layer. Membrane transport proteins assigned to the uncultivated MG-II Euryarchaeota were also specifically detected in the nepheloid layer. In total, these results revealed strong vertical structure of microbial taxa and metabolic activities, as well as the presence of specific "nepheloid" taxa that may contribute significantly to coastal ocean nutrient cycling.

1Northern lakes are ice-covered for a large part of the year, yet our understanding 2 of microbial diversity and activity during winter lags behind that of the ice-free period. In 3 this study, we investigated under-ice diversity and metabolism of Verrucomicrobia in 4 seasonally ice-covered lakes in temperate and boreal regions of Quebec, Canada using 5 16S rRNA sequencing, metagenomics and metatranscriptomics. Verrucomicrobia, 6 particularly the V1, V3 and V4 subdivisions, were abundant during ice-covered periods. 7A diversity of Verrucomicrobia genomes were reconstructed from Quebec lake 8 metagenomes. Several genomes were associated with the ice-covered period and were 9represented in winter metatranscriptomes, supporting the notion that Verrucomicrobia are 10 metabolically active under ice. Verrucomicrobia transcriptome analysis revealed a range 11 of metabolisms potentially occurring under ice, including carbohydrate degradation, 12 glycolate utilization, scavenging of chlorophyll degradation products, and urea use. 13Genes for aerobic sulfur and hydrogen oxidation were expressed, suggesting 14 chemolithotrophy may be an adaptation to conditions where labile carbon may be limited. 15The expression of genes for flagella biosynthesis and chemotaxis was detected, 16suggesting Verrucomicrobia may be actively sensing and responding to winter nutrient 17 pulses, such as phytoplankton blooms. These results increase our understanding on the 18 diversity and metabolic processes occurring under ice in northern lakes ecosystems. 19This study demonstrates the importance of studying the ice-covered period in the face of 33 climate change and should spur future year-round investigations on microbial community 34 structure and function in ice-covered freshwater ecosystems. 35 36 37 4 Hampton, 2016;Hampton et al., 2017). To better understand the contribution of winter 60 communities to lake metabolism and nutrient cycling, year-round investigation of the 61 metabolic traits and activities of freshwater microorganisms is warranted. 62

Global warming is profoundly influencing the Arctic Ocean. Rapid ice melt and increased freshwater input is increasing ocean stratification, driving shifts in nutrient availability and the primary production that supports marine food webs.

Many studies of community assembly focus on a single ontogenetic stage (typically adults) when trying to infer assembly processes from patterns of biodiversity. This focus ignores the finding that assembly mechanisms may strongly differ between life‐stages, and the role of ontogenetic dependency: the mechanisms by which one life stage directly affects the composition of another life stage. Within a 4‐ha forest dynamics plot in California USA, we explored how the relative importance of multiple assembly processes shifts across life stages and assessed ontogenetic dependency of seedlings on adults in woody plant communities. To assess variation in assembly processes across life stages, we examined how β‐diversity of adult and seedling communities were each influenced by space and 13 environmental variables (soils, topography) using distance‐based redundancy analysis and variation partitioning. We then assessed the ontogenetic dependency of seedlings on adults by including adult composition as a predictor in the seedling community variation partitioning. We found differences between adult and seedling composition. For the adults, we found 18 species including pines, oaks and manzanitas characteristic of this mid‐elevation forest. For seedlings, we found 11 species, and that oaks made up 75% of all seedlings while only making up 45% of all adults. Adult β‐diversity was primarily explained by space (44.0%) with environment only explaining 18.6% and 37.4% unexplained. In contrast, most of the explained variation in seedling β‐diversity was due to ontogenetic dependency alone (13.6% explained by adult composition) with 1.6% explained by space and the environment jointly, and 62.8% unexplained. Synthesis: Here, we describe a conceptual framework for integrating ontogeny more explicitly into community assembly research and demonstrate how different assembly processes structured adult and seedling β‐diversity in a temperate dry forest. While adult β‐diversity was largely driven by spatial processes, seedling β‐diversity was largely unexplained, with ontogenetic dependency comprising most of the explained variation. These patterns suggest that future assembly research should consider how assembly processes and their underlying mechanisms may shift with ontogeny, and that interactions between ontogenetic stages (ontogenetic dependency) are critical to consider when assessing variation in assembly processes.