Biology subjects

Callieri, C.

Publications and source records attributed to Callieri, C..

3 recordsLinked to original sources

bioRxiv2024

Zooplankton impacts on the persistence of the anthropogenic pollution marker intI1 in lake water

Wastewater treatment plants (WWTP) effluents can release microbiological pollutants, including the intI1 gene (integrases of class 1 integrons), which has been proposed as a target for monitoring anthropogenic pollution in surface waters. This gene has also a strong correlation with antibiotic resistance, making of it an important proxy to evaluate the level of genetic contamination in aquatic environments. he ecological factors that influence the abundance and dynamics of intI1 within natural water bodies are largely unknown. To better understand the fate of class 1 integrons in aquatic systems, we resorted to classical limnological monitoring of intI1 over multiple years. We also conducted experiments to elucidate the impact of Daphnia grazing on its abundance. The monitoring of different size fractions of the Lake Maggiore microbial community has shown a particle-bound life-style for intI1-harbouring bacteria. Most of the bacteria hosting intI1, originating from both a wastewater effluent that discharges intro Lake Maggiore and lake water itself, grow on particulate substrates in open waters, making them particularly vulnerable to grazing by large filter feeders such as Daphnia. Daphnia grazing is independent from the origin (lake water or wastewater) of the bacterial genera; it selectively removes bacteria that are present in aggregates or even filamentous forms from both origins. To understand if intI1 is related to viable bacteria or just DNA residues, it is important to study the persistence of class 1 integrons with their gene cassettes, which often contain antibiotic resistance genes in freshwater ecosystems. Significance StatementWhile faecal pollution of freshwaters is commonly monitored, genetic pollution through wastewater treatment plant outflows, such as antibiotic resistance genes, is difficult to monitor due to the diverse nature of genes present. The intI1 gene is proposed as a proxy for anthropogenic pollution; however, there is a major lack of understanding regarding the persistence of this gene in freshwaters. In this study, we demonstrate that intI1 in freshwaters is associated with both the natural microbial community and allochthonous microbes arriving from wastewater. Furthermore, we show that intI1 harbouring bacteria preferentially reside in the aggregated microbial fraction and are easily removed by zooplankton grazing. This study is the first limnological investigation of this gene and highlights a significant gap in our knowledge regarding the ecology of class 1 integrons. Genetic pollution of surface waters is however a global problem and of very broad interest on the one hand, on the other hand, the question of the establishment of an allochthonous gene into a natural microbial community is also an interesting fundamental question in ecology, thus this study has both more applied and more fundamental aspects. Therefore, we consider it perfect for the readership of L&O.

ecology↗

bioRxiv2020

Microbiome of the Black Sea water column analyzed by genome centric metagenomics

BackgroundThe Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former albeit with lower salinity and (mostly) temperature. In spite of its well-known hydrology and physico chemistry, this enormous water mass remains poorly studied at the microbial genomics level. ResultsWe have sampled its different water masses and analyzed the microbiome by classic and genome-resolved metagenomics generating a large number of metagenome-assembled genomes (MAGs) from them. The oxic zone presents many similarities to the global ocean while the euxinic water mass has similarities to other similar aquatic environments of marine or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environments and includes Cyanobacteria (Synechococcus), photoheterotrophs (largely with marine relatives), facultative/microaerophilic microbes again largely marine, chemolithotrophs (N and S oxidizers) and a large number of anaerobes, mostly sulfate reducers but also a few methanogens and a large number of "dark matter" streamlined genomes of largely unpredictable ecology. ConclusionsThe Black Sea presents a mixture of similarities to other water bodies. The photic zone has many microbes in common with that of the Mediterranean with the relevant exception of the absence of Prochlorococcus. The chemocline already presents very different characteristics with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. Finally the euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy generating metabolism and a small but detectable methanogenesis.We are adding critical information about this unique and important ecosystem and its microbiome.

microbiology↗

bioRxiv2020

Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on >97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe. Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7-101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion. Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages.

microbiology↗