Adélaïde Roguet

Neutral community model explains the bacterial community assembly in freshwater lakes.

Over the past decade, neutral theory has gained attention and recognition for its capacity to explain bacterial community structure (BCS) in addition to deterministic processes. However, no clear consensus has been drawn so far on their relative importance. In a metacommunity analysis, we explored at the regional and local scale the effects of these processes on the bacterial community assembly within the water column of 49 freshwater lakes. The BCS was assessed using terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA genes. At the regional scales, results indicated that the neutral community model well predicted the spatial community structure (R(2) mean = 76%) compared with the deterministic factors - which explained only a small fraction of the BCS total variance (less than 14%). This suggests that the bacterial compartment was notably driven by stochastic processes, through loss and gain of taxa. At the local scale, the bacterial community appeared to be spatially structured by stochastic processes (R(2) mean = 65%) and temporally governed by the water temperature, a deterministic factor, even if some bacterial taxa were driven by neutral dynamics. Therefore, at both regional and local scales the neutral community model appeared to be relevant in explaining the bacterial assemblage structure.

atpE gene as a new useful specific molecular target to quantify Mycobacterium in environmental samples

BackgroundThe environment is the likely source of many pathogenic mycobacterial species but detection of mycobacteria by bacteriological tools is generally difficult and time-consuming. Consequently, several molecular targets based on the sequences of housekeeping genes, non-functional RNA and structural ribosomal RNAs have been proposed for the detection and identification of mycobacteria in clinical or environmental samples. While certain of these targets were proposed as specific for this genus, most are prone to false positive results in complex environmental samples that include related, but distinct, bacterial genera. Nowadays the increased number of sequenced genomes and the availability of software for genomic comparison provide tools to develop novel, mycobacteria-specific targets, and the associated molecular probes and primers. Consequently, we conducted an in silico search for proteins exclusive to Mycobacterium spp. genomes in order to design sensitive and specific molecular targets.ResultsAmong the 3989 predicted proteins from M. tuberculosis H37Rv, only 11 proteins showed 80% to 100% of similarity with Mycobacterium spp. genomes, and less than 50% of similarity with genomes of closely related Corynebacterium, Nocardia and Rhodococcus genera. Based on DNA sequence alignments, we designed primer pairs and a probe that specifically detect the atpE gene of mycobacteria, as verified by quantitative real-time PCR on a collection of mycobacteria and non-mycobacterial species. The real-time PCR method we developed was successfully used to detect mycobacteria in tap water and lake samples.ConclusionsThe results indicate that this real-time PCR method targeting the atpE gene can serve for highly specific detection and precise quantification of Mycobacterium spp. in environmental samples.

High mycobacterial diversity in recreational lakes

Although nontuberculous mycobacteria (NTM) are natural inhabitants of freshwater ecosystems, few studies have focused on their distribution in these habitats. Thus, the knowledge about the abundance as well as the composition of NTM remains limited and patchy in these environments. In this context, a prospective study was performed to identify favourable habitats for mycobacteria in two recreational lakes. Mycobacterial density and diversity were measured using quantitative real-time PCR and the MiSeq Illumina platform. For both lakes, five compartments were investigated, i.e. water column, air–water interface, sediment, epilithon and epiphyton biofilms. Nontuberculous mycobacteria were detected in all compartments in large densities and displayed a remarkable diversity. NTM were dominated by fast-growing species. Lakes and compartments appeared to shape mycobacteria assemblage composition as well as their densities. In both lakes, some OTUs assigned to the species level were identified as related to known opportunistic pathogens.

An Integrated Approach for Assessing the Impact of Urban Stormwater Discharge on the Fecal Contamination in a Recreational Lake Near Paris

Urban stormwater discharges contribute to the fecal contamination of recreational lakes. It is essential to assess the spatial and temporal distribution of fecal bacterial indicators in the receiving waterbodies, to prevent public health risks. This study develops for the first time in continental waters an integrated monitoring and modelling approach, linking the SWMM and Delft-3D models and including a detailed monitoring of the stormwater discharge and at different points of the lake, for assessing Escherichia coli (E.coli) dynamics in stormwater discharges and the receiving urban lake. This integrated approach is applied to a recreational shallow lake and its adjacent urban catchment, with a single stormwater outlet which discharges into the lake. The SWMM model parameters are calibrated and validated with continuous measurements of the flow rate and mean concentration of E. coli in the stormwater discharge measured during each rainfall event. Using the simulated flow rate and E. coli concentration at the sewer outlet, the Delft3D-FLOW-WAQ model simulates E. coli transport in the urban lake with previously calibrated hydrodynamic parameters and default values of E. coli parameters. Comparing simulations with E. coli concentrations measured at different points in the lake, this integrated modelling approach yields promising results. Further studies will focus on the development of automatic model coupling and parameter optimisation, as well as on the evaluation of long-term impacts and management scenarios.