We describe an inexpensive, reliable, and easily executed improvement for the extraction of DNA from SterivexTM filter units, that involves the separation of the SterivexTM filter from its casing. Our study demonstrates that our modification of the original extraction protocol significantly increased DNA yields, with an average increase of 4.1‐fold more DNA than with the standard approach. A comparison of the diversity after Illumina MiSeq sequencing of bacterial communities extracted with both the standard approach and the proposed one indicated that our modified protocol has no or little impact on the results. This protocol provides a relatively straight forward means to achieve higher yields of DNA from the extraction of SterivexTM cartridges without altering the community composition and will likely be of interest to a wide range of scientists that use techniques based on the recovery of DNA from filters.
Bacteria are key players in biogeochemical cycles and control water quality in freshwater ecosystems. Nevertheless, little is known about the identity and ecology of riverine bacteria, especially during ice‐covered periods that are often mistakenly perceived as periods with negligible biological activities. Here, we analyzed in detail the effects of environmental and climatic conditions on freshwater bacterial community structure and diversity over a 2‐yr sampling campaign, targeting a seasonally ice‐covered river of the Quebec City (Canada) area, the Saint‐Charles River. Quantitative polymerase chain reaction and 16S ribosomal RNA gene high‐throughput sequencing demonstrated a strong seasonal cycle of the bacterial community composition with rapid successions of bacterial lineages, reflecting the harsh climatic condition of the region. During the summer, the bacterial community was dominated by typical freshwater microorganisms such as Limnohabitans, Sporichthyaceae hgcI/acI clade, and Pseudarcicella. In contrast, the results suggest that during the cold season, the low water temperatures, combined with other prevailing conditions such as reduced light availability and minimal particulate inputs from the catchment, created various environmental niches for potential methanotrophic Gammaproteobacteria, such as Crenothrix and Methylobacter, other Betaproteobacteria, such as Candidatus Methylopumilus, Candidatus Nitrotoga, and Rhodoferax, as well as Verrucomicrobia and Parcubacteria. The presence of these taxa in the winter suggests active carbon, iron, and nitrogen cycling under ice, whereas summer lineages are dormant or in a phase of reduced activity. These results increase our understanding of bacterial dynamic and potential metabolic processes occurring in seasonally ice‐covered inland waters, providing evidence that winter can be an especially important period for freshwater ecological processes.
Two full-scale slow sand filters (SSFs) were sampled periodically from April until November 2011 to study the spatial and temporal structures of the bacterial communities found in the filters. To monitor global changes in the microbial communities, DNA from sand samples taken at different depths and locations within the SSFs and at different filters ages was used for Illumina 16S rRNA gene sequencing. Additionally, 15 water quality parameters were monitored to assess filter performance, with functionally relevant microbial members being identified by using multivariate statistics. The bacterial diversity in the SSFs was found to be much larger than previously documented, with community composition being shaped by the characteristics of the SSFs (filter age and depth) and sampling characteristics (month, side, and distance from the influent and effluent pipes). We found that several key genera (Acidovorax, Halomonas, Sphingobium, and Sphingomonas) were associated with filter performance. In addition, at the whole-community level, a strong positive correlation was found between species evenness and filter performance. This study is the first to comprehensively characterize the microbial community of SSFs and link specific microbes to water quality parameters. In doing so, we reveal key patterns in microbial community structure that relate to overall community function.
For over 200 years, slow sand filtration (SSF) has been an effective means of treating water for the control of microbiological contaminants in both small and large community water supplies. However, such systems lost popularity to rapid sand filters mainly due to smaller land requirements and less sensitivity to water quality variations. SSF is still a particularly attractive process because its operation does not require chemicals or electricity. It can achieve a high level of treatment, which is mainly attributed to naturally-occurring, biochemical processes in the filter. Several microbiologically-mediated purification mechanisms (e.g. predation, scavenging, adsorption and bio-oxidation) have been hypothesised or assumed to occur in the biofilm that forms in the filter but these have not yet been comprehensively verified. Thus, SSFs are operated as ‘black boxes’ and knowledge gaps pertaining to the underlying ecology and ecophysiology limit the design and optimisation of the technology. The objective of this review is to outline the biological aspects of SSF in to the context of recent developments in molecular microbial ecology.
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