| Title | 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 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 x 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. |
| Source | Biological invasions 17 (3), pp. 923–940 |
| Keywords | MetagenomicsNext-generation sequencing platformsMarine microbial ecologyJellyfish biomass |
| Journal | Biological invasions |
| Editor | Kluwer Academic Publishers, London ;, Paesi Bassi |
| Year | 2015 |
| Type | Articolo in rivista |
| DOI | 10.1007/s10530-014-0810-2 |
| Authors | Manzari, Caterina; Fosso, Bruno; Marzano, Marinella; Annese, Anita; Caprioli, Rosa; D'Erchia, Anna Maria; Gissi, Carmela; Intranuovo, Marianna; Picardi, Ernesto; Santamaria, Monica; Scorrano, Simonetta; Sgaramella, Giuseppe; Stabili, Loredana; Piraino, Stefano; Pesole, Graziano |
| Text | 330818 2015 10.1007/s10530 014 0810 2 ISI Web of Science WOS 000350675900008 Metagenomics Next generation sequencing platforms Marine microbial ecology Jellyfish biomass 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 Manzari, Caterina; Fosso, Bruno; Marzano, Marinella; Annese, Anita; Caprioli, Rosa; D Erchia, Anna Maria; Gissi, Carmela; Intranuovo, Marianna; Picardi, Ernesto; Santamaria, Monica; Scorrano, Simonetta; Sgaramella, Giuseppe; Stabili, Loredana; Piraino, Stefano; Pesole, Graziano University of Bari; Consiglio Nazionale delle Ricerche CNR ; Universita di Modena e Reggio Emilia; Consorzio Nazl Interuniv Sci Mare Co NIS Ma; University of Salento; University of Milan; Tuscia University; Consiglio Nazionale delle Ricerche CNR 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 x 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. 17 Published version The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon Biological_Invasions_2014.pdf Articolo in rivista Kluwer Academic Publishers 1387 3547 Biological invasions Biological invasions loredana.stabili STABILI LOREDANA marinella.marzano MARZANO MARINELLA monica.santamaria SANTAMARIA MONICA bruno.fosso FOSSO BRUNO |
