Microbial diversity and dynamics of a groundwater and a still bottled natural mineral water

Abstract

The microbial abundance and diversity at source, after bottling and through 6 months of storage of a commercial still natural mineral water were assessed by culture-dependent and culture-independent methods. The results revealed clear shifts of the dominant communities present in the three different stages. The borehole waters displayed low cell densities that increased 1.5-fold upon bottling and storage, reaching a maximum (6.2 × 10(8) cells l(-1) ) within 15 days after bottling, but experienced a significant decrease in diversity. In all cases, communities were largely dominated by Bacteria. The culturable heterotrophic community was characterized by recovering 3626 isolates, which were primarily affiliated with the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. This study indicates that bottling and storage induce quantitative and qualitative changes in the microbial assemblages that seem to be similar as revealed by the two sample batches collected on 2 consecutive years. To our knowledge, this is the first study combining culture-independent with culture-dependent methods, and repeated tests to reveal the microbial dynamics occurring from source to stored bottled water.

Moderate halophilic bacteria colonizing the phylloplane of halophytes of the subfamily Salicornioideae (Amaranthaceae)

“…Our results contrast with other culture-independent studies that showed a significant percentage of sequences remained unclassified [7,63]. The success of the current study may be related to the fact that most of the microbiota thriving in the phylloplane is readily cultivable [26,56], but also because the identification approach used relied on phylogenetic inference (by means of the OPU approach) [21] and not just on sequence identity clustering (classification by means of OTU clustering and blast matches of their representatives), as commonly used [7,17,26].…”

“…In previous studies [21,65], OTUs were defined by clustering the units according to an identity threshold. Here, the OTUs based on MALDI-TOF/MS measures corresponded to each independent cluster formed by profile identity limits, which were dependent on each dataset.…”

Diversity of extremely halophilic cultivable prokaryotes in Mediterranean, Atlantic and Pacific solar salterns: Evidence that unexplored sites constitute sources of cultivable novelty

“…This study may be regarded as one with the largest set of identified cultures obtained from environmental samples. Although this culture set may seem small compared to the one of 284,899 clinical isolates [45], it is comparable to the 3626 isolates from bottled natural mineral water identified by random amplified polymorphic DNA (RAPD) fingerprinting and 16S rRNA gene analyses [16]. MALDI-TOF/MS profiling has been shown to be very advantageous for analyzing the microbial diversity of the cultured fraction of environmental samples [34].…”

“…Complete sequences were used to reconstruct de novo trees using the neighbor-joining algorithm, while the partial sequences were added into a pre-existing tree using the ARB-Parsimony tool, both implemented in the ARB software package. Sequences were grouped in operational phylogenetic units (OPUs) as an alternative to using strict cut-off values of identity thresholds in order to identify isolated clades derived from the phylogenetic tree topology that produce biologically meaningful units [16,29]. An OPU was considered as the smallest clade containing one or more amplified sequences affiliating together with reference sequences available in the public repositories.…”

Seasonal and altitudinal changes of culturable bacterial and yeast diversity in Alpine forest soils

“…Random amplified polymorphic DNA (RAPD) analysis was used as primary fingerprinting method to recognize genomic diversity among the isolates following procedures described before (França et al 2015). Representative strains of each unique RAPD profile were selected.…”