Contribution of single-cell omics to microbial ecology.

Micro-organisms play key roles in various ecosystems, but many of their functions and interactions remain undefined. To investigate the ecological relevance of microbial communities, new molecular tools are being developed. Among them, single-cell omics assessing genetic diversity at the population and community levels and linking each individual cell to its functions is gaining interest in microbial ecology. By giving access to a wider range of ecological scales (from individual to community) than culture-based approaches and meta-omics, single-cell omics can contribute not only to micro-organisms' genomic and functional identification but also to the testing of concepts in ecology. Here, we discuss the contribution of single-cell omics to possible breakthroughs in concepts and knowledge on microbial ecosystems and ecoevolutionary processes.

The effect of pre-operative gastric ultrasound examination on the choice of general anaesthetic induction technique for non-elective paediatric surgery. A prospective cohort study.

Ultrasound examination of the gastric antrum is a non-invasive tool that allows reliable estimation of gastric contents. We performed this prospective cohort study in non-elective paediatric surgery to assess whether gastric ultrasound may help to determine the best anaesthetic induction technique, whether rapid sequence or routine. The primary outcome was the reduction of inappropriate induction technique. A pre-operative clinical assessment was performed by the attending anaesthetist who made a provisional plan for induction. Gastric ultrasound was performed in the semirecumbent and right lateral decubitus positions for a qualitative assessment of gastric contents, using a 0-2 grading scale. A final induction plan was made based on this assessment. Immediately after tracheal intubation, gastric contents were suctioned through a multi-orifice nasogastric tube; these were defined as above risk threshold for regurgitation and aspiration if there was clear fluid > 0.8 ml.kg-1 , and/or the presence of thick fluid and/or solid particles. Gastric ultrasound was feasible in 130 out of 143 (90%) of children, and led to a change in the planned induction technique in 67 patients: 30 from routine to rapid sequence, and 37 from rapid sequence to routine. An appropriate induction technique was therefore performed in 85% of children, vs. 49% planned after pre-operative clinical assessment alone (p < 0.00001). Our results suggest that gastric ultrasound is a useful guide to the general anaesthetic induction technique with respect to the risk of pulmonary aspiration, in comparison with pre-operative clinical assessment alone.

Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient.

Observations of distributions of microorganisms and their differences in community composition across habitats provide evidence of biogeographical patterns. However, little is known about the processes controlling transfers across habitat gradients. By analysing the overall microbial community composition (bacteria, fungi, archaea) across a terrestrial-freshwater gradient, the aim of this study was to understand the spatial distribution patterns of populations and identify taxa capable of crossing biome borders. Barcoded 454 pyrosequencing of taxonomic gene markers was used to describe the microbial communities in adjacent soil, freshwater and sediment samples and study the role of biotic and spatial factors in shaping their composition. Few habitat generalists but a high number of specialists were detected indicating that microbial community composition was mainly regulated by species sorting and niche partitioning. Biotic interactions within microbial groups based on an association network underlined the importance of Actinobacteria, Sordariomycetes, Agaricomycetes and Nitrososphaerales in connecting among biomes. Even if dispersion seemed limited, the shore of the lake represented a transition area, allowing populations to cross the biome boundaries. In finding few broadly distributed populations, our study points to biome specialization within microbial communities with limited potential for dispersal and colonization of new habitats along the terrestrial-freshwater continuum.

atz gene expressions during atrazine degradation in the soil drilosphere.

One of the various ecosystemic services sustained by soil is pollutant degradation mediated by adapted soil bacteria. The pathways of atrazine biodegradation have been elucidated but in situ expression of the genes involved in atrazine degradation has yet to be demonstrated in soil. Expression of the atzA and atzD genes involved in atrazine dechlorination and s-triazine ring cleavage, respectively, was investigated during in situ degradation of atrazine in the soil drilosphere and bulked samples from two agricultural soils that differed in their ability to mineralize atrazine. Interestingly, expression of the atzA gene, although present in both soils, was not detected. Atrazine mineralization was greatest in Epoisses soil, where a larger pool of atzD mRNA was consistently measured 7 days after atrazine treatment, compared with Vezin soil (146 vs. 49 mRNA per 10(6)16S rRNA, respectively). Expression of the atzD gene varied along the degradation time course and was profoundly modified in soil bioturbated by earthworms. The atzD mRNA pool was the highest in the soil drilosphere (casts and burrow-linings) and it was significantly different in burrow-linings compared with bulk soil (e.g. 363 vs. 146 mRNA per 10(6)16S rRNA, 7 days after atrazine treatment in Epoisses soil). Thus, consistent differences in atrazine mineralization were demonstrated between the soil drilosphere and bulk soil. However, the impact of bioturbation on atrazine mineralization depended on soil type. Mineralization was enhanced in casts, compared with bulk soil, from Epoisses soil but in burrow-linings from Vezin soil. This study is the first to report the effects of soil bioturbation by earthworms on s-triazine ring cleavage and its spatial variability in soil.

Short-term response of soil bacteria to carbon enrichment in different soil microsites.

The response of bacteria in bulk soil and earthworm casts to carbon enrichment was studied by an RNA stable-isotope probing/terminal restriction fragment length polymorphism strategy with (13)C-labeled glucose and acetate. Both the soil microsite status and the carbon enrichment selected rapidly for different active bacterial communities, which resulted in different degradation kinetics. Our study clearly illustrates the biases that are generated by adding C substrates to detect metabolically active bacteria in soil.