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. 2023 Nov 25;27(1):108588.
doi: 10.1016/j.isci.2023.108588. eCollection 2024 Jan 19.

A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species

Jesús Zarcero  1   2 , Adrià Antich  1 , Marc Rius  1   3 , Owen S Wangensteen  2 , Xavier Turon  1
Affiliations

A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species

Jesús Zarcero et al. iScience. .

Abstract

Metabarcoding techniques are revolutionizing studies of marine biodiversity. They can be used for monitoring non-indigenous species (NIS) in ports and harbors. However, they are often biased by inconsistent sampling methods and incomplete reference databases. Logistic constraints in ports prompt the development of simple, easy-to-deploy samplers. We tested a new device called polyamide mesh for ports organismal monitoring (POMPOM) with a high surface-to-volume ratio. POMPOMS were deployed inside a fishing and recreational port in the Mediterranean alongside conventional settlement plates. We also compiled a curated database with cytochrome oxidase (COI) sequences of Mediterranean NIS. COI metabarcoding of the communities settled in the POMPOMs captured a similar biodiversity than settlement plates, with shared molecular operational units (MOTUs) representing ca. 99% of reads. 38 NIS were detected in the port accounting for ca. 26% of reads. POMPOMs were easy to deploy and handle and provide an efficient method for NIS surveillance.

Keywords: Biological sciences; Ecology; Evolutionary biology.

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Conflict of interest statement

The authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
Shannon diversity and molecular operational taxonomic unit (MOTU) richness Box-plots of the values of Shannon diversity (A) and MOTU richness (B) of the different types of samples. PM: polyamide mesh for port organismal monitoring (POMPOMs), PL: settlement plates. Horizontal lines are medians, boxes encompass the first and third quartiles, whiskers indicate 10th and 90th percentiles, and outliers are indicated as dot symbols.
Figure 2
Figure 2
Taxonomic composition in super-groups Barplots of the relative proportion of molecular operational taxonomic units (MOTUs) (A and C) and reads (B and D) of the different super-groups considered at each sampling time. Category “Others” pools the groups representing less than 5% of the MOTUs. Category “Unidentified” refers to eukaryote MOTUs that could not be assigned to any super-group.
Figure 3
Figure 3
Taxonomic composition in metazoan phyla Barplots of the relative proportion of molecular operational taxonomic units (MOTUs) (A and C) and reads (B and D) of the different metazoan phyla at each sampling time. Category “Others” pools the phyla representing less than 5% of the MOTUs. Category “Unidentified” refer to metazoan MOTUs that could not be assigned to any phylum.
Figure 4
Figure 4
Molecular operational taxonomic unit (MOTU) overlap Venn diagrams showing the overlap in MOTU composition between POMPOMs (polyamide mesh for port organismal monitoring) and plates. We also provide the percent of the total reads that the different compartments represent.
Figure 5
Figure 5
Non-metric multidimensional scaling (nmMDS) ordinations nmMDS configuration of POMPOM (polyamide mesh for port organismal monitoring) and plate samples inside the port. Lines join samples from the same date and collector type. Stress of the final configuration is indicated.
Figure 6
Figure 6
Heatmap of non-indigenous species (NIS) abundance Heatmaps showing read abundances (log-transformed) of the identified NIS in the two types of collector at each date: POMPOMs (A) and plates (B). Blue cells indicate 0 reads. Note that we have pooled molecular operational taxonomic units (MOTUs) assigned to the same nominal species, so the heatmaps show results for 33 species-level taxa.
See this image and copyright information in PMC

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