Diversity and dynamics of bacteria from iron-rich microbial mats and colonizers in the Mediterranean Sea (EMSO-Western Ligurian Sea Observatory): Focus on Zetaproteobacteria

Abstract

Autotrophic microaerophilic iron-oxidizing Zetaproteobacteria seem to play an important role in mineral weathering and metal corrosion in different environments. Here, we compare the bacterial and zetaproteobacterial communities of a mature iron-rich mat together with in situ incubations of different Fe-bearing materials at the EMSO-Ligure West seafloor observatory, which is located on the abyssal plain in the NW Mediterranean Sea. Our results on bacterial communities enable us to make a clear distinction between those growing on mild steel anthropic substrata and those developing on basaltic substrata. Moreover, on anthropic substrata we highlight an influence of mat age on the bacterial communities. Regarding zetaproteobacterial communities, our results point to an increase in ZetaOTUs abundance and diversification with the age of the mat. We corroborate the key role of the ZetaOTU 2 in mat construction, whatever the environment, the substrata on which they develop or the age of the mat. We also show that ZetaOTU 28 is specific to anthropogenic substrata. Finally, we demonstrate the advantage of using dPCR to precisely quantify very low abundant targets, as Zetaproteobacteria on our colonizers. Our study, also, allows to enrich our knowledge on the biogeography of Zetaproteobacteria, by adding new information on this class and their role in the Mediterranean Sea.

Fig 1. Iron-rich microbial mat image.

General view of the SJB structure at the ANTARES site (top left) and image of the iron-rich microbial mat sampled with the Nautile hydraulic arm from the SJB structure (bottom). Images taken by the HD camera of Nautile during the EMSO-LO 18 cruise.

Fig 2. Image and schema of colonizers.

A) Images of the colonizers deployed on the interphase between sediments and seawater at ANTARES site (left) containing Bnat EMLIG 20 and BH2 EMLIG 20 samples, and the one deployed on the sediments at MEUST site (right) containing BH2 EMLIG 22 and Gr EMLIG 22 samples. Images taken by the HD camera of Nautile, during the EMSO-LO 18 and ESSNaut 22 cruises, respectively. B) Schematic representation of microbial colonizers, showing the different substrata and the circulation of environmental seawater inside colonizers. Dark grey bars correspond to the colonizer support, blue arrows indicate the flow circulation, tubes containing substrata are in dashed lines.

Fig 3. Alpha and beta diversity of bacteria.

A) Box plot representing the Shannon and Inverse Simpson diversity indexes calculated for each bacterial community. B) NMDS plot representing the differences between the bacterial communities of all samples (stress = 0.08).

Fig 4. Bacterial bar plot.

A) Bar plot depicting the relative abundance (%) of bacterial phyla for each triplicate of each sample. Only the phyla having an incidence higher than 1% are represented in the plot. B) Bar plot representing the relative abundance (%) of classes belonging to the Proteobacteria phylum.

Fig 5. Zetaproteobacterial quantification by dPCR.

A) Bar plot representing the absolute quantification of Zetaproteobacteria as the number of zetaproteobacterial 16S rRNA gene copies per μl of DNA sample. B) Bar plot representing the proportion of Zetaproteobacteria vs the total number of Bacteria.

Fig 6. Zetaprotobacteria heatmap.

Heatmap representing the presence/absence and abundance of each ZetaOTU in each sample. To construct the heatmap, ZetaOTUs were organized using an NMDS ordination and the Bray-Curtis dissimilarity index.