The microbiome of invasive species is increasingly seen as a potential key factor of their ecological success, and this appears particularly true in herbivorous invaders whose digestive abilities rely on the microbes hosted in their gut. We characterized the gut microbiome of two invasive herbivorous fishes (Siganus rivulatus and Siganus luridus) in their native (Red Sea) and invaded (Levantine Sea and Northern Crete) ranges. We found that gut bacterial communities contain a higher taxonomic and phylogenetic diversity while becoming increasingly different from the native microbiome as the fishes move away from the native zone. This shift resulted in the homogenization of the microbiomes between individuals from the same species as well as between the two species. Firmicutes and Tenericutes reduced drastically in abundance while Proteobacteria and Bacteroidetes became more dominant in both species. This led to a modification of the functional potential of the gut microbiome associated with the metabolism of short-chanin fatty acids that also became more homogeneous in the invaded range. Altogether, our results suggest that the plasticity of the gut microbiome in Siganidae could be a key factor underlying their ecological success in Mediterranean ecosystems.

Samples collection

Samples were collected in three regions. Both S. rivulatus and S. luridus were sampled in their native range in the Northern Red Sea (Eilat, Israel), as well as their non-native range in the Levantine Sea and the Northern Crete. Two sampling campaigns were led per region, one in late Spring (June 2018 and 2019 in Israel and Crete, respectively) and one in early Autumn (October 2018 and 2019 in Israel and Crete, respectively). In each region, two to four distrinct sites were selected to cover the various types of habitat structure and macrophytes communities observed locally.

Fish were collected in shallow habitats (2-10 m) by scuba divers using handnets and gillnets (fishing permit n° B13663). Only adult individuals with a standard length > 100 mm were collected. Fish were immediately euthanized, stored on ice and processed less than two hours after their capture. Fish were sized (mm), weighted (g) and dissected using tools cleaned with 70° ethanol. The last third of the gut (i.e. hindgut) was squeezed out on a piece of parafilm paper using a sterile pipette. Gut content was homogenized and collected in a 3 mL cryotube before storage at -80°C until DNA extraction.

Microbial communities from the surrounding environment (i.e. water, sediment, and potential food sources: macrophytes, seagrasses and turf) were collected at the same time and in the same locations. Water samples were collected at 1 m below the surface using 500 mL plastic bottles. Planktonic microbes were collected on 0.2 µm GTTP filters (Whattman) that were stored on ice immediately after filtration. Surface sediment samples were collected in 3 mL cryotubes and immediately stored on ice. Macroalgae, seagrasses and turf growing on rocks and hard substrates were collected in individual plastic bags. These samples were rinsed with deionized water to remove interstitial seawater and rubbed using buccal swabs (Cliniscience). The swabs were immediately stored on ice. Filters, cryotubes and swabs were stored at -80°C until DNA extraction.

A total of 380 microbiomes were analyzed, including 181 fishes (145 S. rivulatus and 36 S. luridus), 56 macroalgae, 29 seagrass, 31 sediment, 43 turf and 40 water samples.

DNA extraction

DNA extractions were performed in the molecular biology platforms of the MARBEC laboratory (UMR 9190, www.umr-marbec.fr/) and at the Genseq platform (genseq.umontpellier.fr/), using the Qiagen MagAttract PowerSoil DNA KF Kit, selected for its compliance with the Earth Microbiome Project (Marotz et al. 2017)⁠. Extractions were performed in 96 well plates in which 3 wells were left empty to serve as negative controls and 3 wells were loaded using standard mock communities (ZymoBIOMICS Microbial Community DNA Standards II, Zymo Research). These standards of known composition were used to evaluate the quality of our sample processing pipeline. Extraction wells were loaded using half of a GTTP filter for water samples, half of a swab for turf samples, and ~ 0.25 g of gut content and sediment samples. DNA extraction protocol included a bead beating step and a chemical lysis. DNA recovery was based on magnetic beads and automated with a Kingfisher Flex robot. DNA was eluted in 100µL of elution buffer before quantification of DNA quantity and quality using a Nanodrop 8000 spectrometer. Extracted DNA was stored at 4°C until PCR amplification, which was done the next day.

PCR amplification

PCR amplification was done using universal bacterial primers selected for their compliance with the Earth Microbiome Project (Parada et al. 2016)⁠: 515F-Y (5′-GTGYCAGCMGCCGCGGTAA) and 926R (5′-CCGYCAATTYMTTTRAGTTT). The targeted sequence was 411 bp and corresponded to the V3-V4 regions of the prokaryotic bacterial 16S rRNA gene. PCR amplification was carried out in 96 well plates in triplicate for each DNA extract and was done in a 25 µL reaction volume. The PCR mix consisted of 9.75µL of water, 0.75µL of DMSO, 0.5 µL of each primer (concentration), 12.5 µL of Phusion ready-to-use Taq mix (Phusion High-Fidelity PCR Master Mix with GC Buffer) and 1µL of DNA. After an initial denaturation of 30 sec at 98°C, the PCR cycle consisted of 30 cycles of 10 sec denaturation at 98°C, 1 min annealing at 58°C and 1 min 30 sec of extension at 72°C. Final extension was held for 10 min at 72°C before keeping the reaction at 4°C. The success of PCR amplification was checked using GelRed^TM on 2% agarose gel in TAE buffer and using a 100bp DNA ladder. The wells left empty during DNA extraction served as negative controls for contamination of the PCR reactions. PCR triplicates were pooled and stored at -20°C before sequencing. An amplicon library was constructed by the Genotoul platform (www.get.genotoul.fr) and sequencing was carried out using an Illumina MiSeq (2 × 250 bp) sequencer.