The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy

The rapid expansion of multicellular native and alien species outbreaks in aquatic and terrestrial ecosystems (bioinvasions) may produce significant impacts on bacterial community dynamics and nutrient pathways with major ecological implications. In aquatic ecosystems, bioinvasions may cause adverse effects on the water quality resulting from changes in biological, chemical and physical properties linked to significant transformations of the microbial taxonomic and functional diversity. Here we used an effective and highly sensitive experimental strategy, bypassing the efficiency bottleneck of the traditional bacterial isolation and culturing method, to identify changes of the planktonic microbial community inhabiting a marine coastal lagoon (Varano, Adriatic Sea) under the influence of an outbreak-forming alien jellyfish species. Water samples were collected from two areas that differed in their level of confinement inside in the lagoon and jellyfish densities (W, up to 12.4 medusae m−3; E, up to 0.03 medusae m−3) to conduct a snapshot microbiome analysis by a metagenomic approach. After extraction of the genetic material in the environmental water samples, we deep-sequenced metagenomic amplicons of the V5–V6 region of the 16S rRNA bacterial gene by an Illumina MiSeq platform. Experiments were carried out in triplicates, so six libraries of dual indexed amplicons of 420 bp were successfully sequenced on the MiSeq platform using a 2 × 250 bp paired-end sequencing strategy. Approximately 7.5 million paired-end reads (i.e. 15 million total reads) were generated, with an average of 2.5 million reads (1.25 M pairs) per sample replicate. The sequence data, analyzed through a novel bioinformatics pipeline (BioMaS), showed that the structure of the resident bacterial community was significantly affected by the occurrence of jellyfish outbreaks. Clear qualitative and quantitative differences were found between the western and eastern areas (characterized by many or few jellyfish), with 84 families, 153 genera and 324 species in the W samples, and 104 families, 199 genera and 331 species in the E samples. Significant differences between the two sampling areas were particularly detected in the occurrence of 16 families, 22 genera and 61 species of microbial taxa. This is the first time that a NGS platform has been used to screen the impact of jellyfish bioinvasions on the aquatic microbiome, providing a preliminary assessment of jellyfish-driven changes of the functional and structural microbial biodiversity

Complexity and dynamics of the winemaking bacterial communities in berries, musts, and wines from apulian grape cultivars through time and space

Currently, there is very little information available regarding the microbiome associated with the wine production chain. Here, we used an amplicon sequencing approach based on high-throughput sequencing (HTS) to obtain a comprehensive assessment of the bacterial community associated with the production of three Apulian red wines, from grape to final product. The relationships among grape variety, the microbial community, and fermentation was investigated. Moreover, the winery microbiota was evaluated compared to the autochthonous species in vineyards that persist until the end of the winemaking process. The analysis highlighted the remarkable dynamics within the microbial communities during fermentation. A common microbial core shared among the examined wine varieties was observed, and the unique taxonomic signature of each wine appellation was revealed. New species belonging to the genus Halomonas were also reported. This study demonstrates the potential of this metagenomic approach, supported by optimized protocols, for identifying the biodiversity of the wine supply chain. The developed experimental pipeline offers new prospects for other research fields in which a comprehensive view of microbial community complexity and dynamics is desirable.Peer ReviewedPostprint (published version

Complexity and dynamics of the winemaking bacterial communities in berries, musts, and wines from apulian grape cultivars through time and space

Currently, there is very little information available regarding the microbiome associated with the wine production chain. Here, we used an amplicon sequencing approach based on high-throughput sequencing (HTS) to obtain a comprehensive assessment of the bacterial community associated with the production of three Apulian red wines, from grape to final product. The relationships among grape variety, the microbial community, and fermentation was investigated. Moreover, the winery microbiota was evaluated compared to the autochthonous species in vineyards that persist until the end of the winemaking process. The analysis highlighted the remarkable dynamics within the microbial communities during fermentation. A common microbial core shared among the examined wine varieties was observed, and the unique taxonomic signature of each wine appellation was revealed. New species belonging to the genus Halomonas were also reported. This study demonstrates the potential of this metagenomic approach, supported by optimized protocols, for identifying the biodiversity of the wine supply chain. The developed experimental pipeline offers new prospects for other research fields in which a comprehensive view of microbial community complexity and dynamics is desirable.Peer Reviewe

Stacked box-plot of relative taxa abundances.

<p>Stacked box-plot displaying the relative abundances of the taxa (≥1%). In particular, a specific plot was produced for each wine variety (Cabernet, Negramaro, and Primitivo) to describe the changes in genera abundance at the five time points (<i>sAF</i>, <i>24hAF</i>, <i>sMLF</i>, <i>hMLF</i>, and <i>eMLF</i>). Taxa for which the relative abundance was less than 1% were grouped and named “others” in the graph.</p

Graphical summary of the results obtained by applying the BioMaS pipeline.

<p>Box plot showing the number of PE reads that were produced by the MiSeq platform for both sequencing runs (raw data), including low quality reads removed after denoising, host reads mapped to <i>Vitis vinifera</i>, and bacterial reads taxonomically classified by BioMaS.</p

Scatter plot of the calculated Shannon index values.

<p>Shannon index values calculated based on the OTU matrix, obtained from the Illumina MiSeq raw data, are shown for all the tested wine varieties. Only the OTUs that were taxonomically labelled as bacterial or not mapped to <i>Vitis Vinifera</i> plastids were considered. The values calculated for each sample are plotted for Cabernet (a), Negramaro (b), and Primitivo (c). Different colours and shapes were used to distinguish the five time points (<i>sAF</i>, <i>24hAF</i>, <i>sMLF</i>, <i>hMLF</i>, and <i>eMLF</i>) and the technical replicates (sequencing runs A and B), respectively.</p

Venn diagrams showing the number of common and unique species detected in the tested wine varieties.

<p>Venn diagrams showing the number of species detected in the three analysed wines (Cabernet, Negramaro, and Primitivo) at each time point: <i>sAF</i> (a), <i>24hAF</i> (b), <i>sMLF</i> (c), <i>hMLF</i> (d), and <i>eMLF</i> (e). (f) Venn diagram showing the number of species detected in samples from the three wines throughout fermentation (from <i>sAF</i> to <i>eMLF</i>).</p

Rarefaction curves for the tested samples.

<p>Rarefaction curves calculated using the OTU matrix obtained from the Illumina MiSeq raw data by using QIIME are shown for all the analysed samples and sequencing runs. The five time points are shown in different colours: <i>sAF</i> (yellow), <i>24hAF</i> (green), <i>sMLF</i> (red), <i>hMLF</i> (blue), and <i>eMLF</i> (black), and the wine varieties Cabernet, Negramaro, and Primitivo are shown as solid, dot-dash, and dashed lines, respectively.</p

Principal coordinate analysis plots generated at the genus level for the five fermentation time points.

<p>Principal coordinate analysis (PCoA) plots based on the taxonomical classification at the genus level are shown for the five tested time points: <i>sAF</i>, <i>24hAF</i>, <i>sMLF</i>, <i>hMLF</i>, and <i>eMLF</i>. Biological replicates (1 and 2) and sequencing runs (A and B) of the three analysed wines (Cabernet, Negramaro and Primitivo) are all shown in each plot as different shapes.</p