Caroline Chénard

Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll.

Microorganisms act both as drivers and indicators of perturbations in the marine environment. In an effort to establish baselines to predict the response of marine habitats to environmental change, here we report a broad survey of microbial diversity across the Indian Ocean, including the first microbial samples collected in the pristine lagoon of Salomon Islands, Chagos Archipelago. This was the first large-scale ecogenomic survey aboard a private yacht employing a ‘citizen oceanography’ approach and tools and protocols easily adapted to ocean going sailboats. Our data highlighted biogeographic patterns in microbial community composition across the Indian Ocean. Samples from within the Salomon Islands lagoon contained a community which was different even from adjacent samples despite constant water exchange, driven by the dominance of the photosynthetic cyanobacterium Synechococcus. In the lagoon, Synechococcus was also responsible for driving shifts in the metatranscriptional profiles. Enrichment of transcripts related to photosynthesis and nutrient cycling indicated bottom-up controls of community structure. However a five-fold increase in viral transcripts within the lagoon during the day, suggested a concomitant top-down control by bacteriophages. Indeed, genome recruitment against Synechococcus reference genomes suggested a role of viruses in providing the ecological filter for determining the β-diversity patterns in this system.

Ecological succession of the microbial communities of an air-conditioning cooling coil in the tropics

Air-conditioning systems harbor microorganisms, potentially spreading them to indoor environments. While air and surfaces in air-conditioning systems are periodically sampled as potential sources of indoor microbes, little is known about the dynamics of cooling coil-associated communities and their effect on the downstream airflow. Here, we conducted a 4-week time series sampling to characterize the succession of an air-conditioning duct and cooling coil after cleaning. Using an universal primer pair targeting hypervariable regions of the 16S/18S ribosomal RNA, we observed a community succession for the condensed water, with the most abundant airborne taxon Agaricomycetes fungi dominating the initial phase and Sphingomonas bacteria becoming the most prevalent taxa toward the end of the experiment. Duplicate air samples collected upstream and downstream of the coil suggest that the system does not act as ecological filter or source/sink for specific microbial taxa during the duration of the experiment.

Supervised Classification of Metatranscriptomic Reads Reveals the Existence of Light-dark Oscillations During Infection of Phytoplankton by Viruses

In the era of next generation sequencing technologies microbial species identification is typically performed using sequence similarity and sequence phylogeny based approaches. Particularly challenging is the discrimination of closely related sequences such as auxiliary metabolic genes (AMGs) in cyanobacteria and their viruses (cyanophages). Here we developed a method which combines Support Vector Machine based classification of AMGs short fragments and Empirical Mode Decomposition of periodic features in time-series. We applied this method to investigate the transcriptional dynamics of viral infection in the ocean, using data extracted from a previously published metatranscriptome profile of a naturally occurring oceanic bacterial assemblage sampled Lagrangially over 3 days. We discovered the existence of light-dark oscillations in the expression patterns of AMGs in cyanophages which follow the harmonic diel transcription of both oxygenic photoautotrophic and heterotrophic members of the community. These findings suggest that viral infection might provide the link between light-dark oscillations of microbial populations in the North Pacific Subtropi-

Exploring the Viral Ecology of High Latitude Aquatic Systems

Viruses are abundant and ubiquitous in aquatic systems. While most of our knowledge in the field of aquatic viral ecology comes from the study of temperate environments, new insights are starting to emerge from polar systems. It is becoming increasingly evident that viruses play a pivotal role in structuring high latitude aquatic systems where microbes are important players and major drivers of biogeochemical cycles. In this chapter, we summarize the latest findings about the abundance, distribution and production of viruses from polar regions. We also review viral-mediated bacterial mortality and phage-host dynamics in freshwater and marine polar waters. For example, we summarize temporal studies performed in polar freshwater systems, showing a seasonal trend with a high percent of lysogenic bacteria in the winter and an undetectable rate in the summer. These findings suggest that lysogeny represents an important life strategy in polar regions. We conclude with the latest analysis of large scale meta-omics datasets, which suggest that polar viral assemblages might be a reservoir of new lineages of viruses and unknown viral diversity.

Complete genome sequence of bacillus altitudinis type strain SGAir0031 isolated from tropical air collected in Singapore

ABSTRACT Bacillus altitudinis strain SGAir0031 (Firmicutes) was isolated from tropical air samples collected in Singapore. Its genome was assembled using short reads and single-molecule real-time sequencing, comprising one chromosome with 3.81 Mb and one plasmid with 32 kb. The genome consists of 3,820 protein-coding genes, 81 tRNAs, and 24 rRNAs.