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

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• 作者：Caterina Manzari ; Bruno Fosso ; Marinella Marzano ; Anita Annese…
• 关键词：Metagenomics ; Next ; generation sequencing platforms ; Marine microbial ecology ; Jellyfish biomass
• 刊名：Biological Invasions
• 出版年：2015
• 出版时间：March 2015
• 年：2015
• 卷：17
• 期：3
• 页码：923-940
• 全文大小：541 KB
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• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Plant Sciences
  Ecology
  Hydrobiology
  Zoology
  Forestry
  
• 出版者：Springer Netherlands
• ISSN：1573-1464

文摘

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?; E, up to 0.03 medusae m?) 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.