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

Abstract

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 outbreakforming 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 deepsequenced metagenomic amplicons of the V5-V6 region of the 16S rRNA bacterial gene by an Illumina MiSeq platform. Experiments were carried out in Caterina Manzari, Bruno Fosso and Marinella Marzano have contributed equally to this work.Stefano Piraino and Graziano Pesole are senior authors.Electronic supplementary material The online version of this article (doi:10.1007/s10530-014-0810-2) contains supplementary material, which is available to authorized users. triplicates, so six libraries of dual indexed amplicons of 420 bp were successfully sequenced on the MiSeq platform using a 2 9 250 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.

Isolation of Marine Paracoccus sp. Ss63 from the Sponge Sarcotragus sp. and Characterization of its Quorum‐Sensing Chemical‐Signaling Molecules by LC‐MS/MS Analysis

“…PaH2.06a (GQ391948). The latter was previously isolated from seawater during an invasive jellyfish bloom in the coastal lagoon of Varano (Italy) 26. Phylogenetic analysis also supported the taxonomic affiliation of Ss63 strain to the Paracoccus genus (Figure 1), hence the isolated strain was designated as Paracoccus sp.…”

Human access impacts biodiversity of microscopic animals in sandy beaches

“…The DNA extracted from each sample was used as a template for amplicon library preparation, adopting a modified version of the Illumina Nextera protocol 64 . In particular, the library preparation was based on two amplification steps.…”

Human Endometrial Microbiota at Term of Normal Pregnancies

“…The 16S rRNA gene corresponding part of each primer is underlined. The strategy used to prepare the 16S rRNA amplicon-based library was described in detail in [27]. From each sample, 100 ng of DNA was extracted and used for a two-step amplification reaction to yield amplicons having at their termini an Illumina adapter (P7 or P5) and an Illumina Nextera index sequence, as required by the dual index sequencing approach.…”