Epilithic Bacterial Assemblages on Subtidal Rocky Reefs: Variation Among Alternative Habitats at Ambient and Enhanced Nutrient Levels

Abstract

Temperate rocky reefs often support mosaics of alternative habitats such as macroalgal forests, algal turfs and sea urchin barrens. Although the composition of epilithic microbial biofilms (EMBs) is recognized as a major determinant of macroalgal recruitment, their role in regulating the stability of alternative habitats on temperate rocky reefs remains unexplored. On shallow rocky reefs of the Island of Capraia (NW Mediterranean), we compared EMB structure among canopy stands formed by the fucoid Ericaria brachycarpa, algal turfs, and urchin barrens under ambient versus experimentally enhanced nutrient levels. The three habitats shared a core microbial community consisting of 21.6 and 25.3% of total ASVs under ambient and enhanced nutrient conditions, respectively. Although Gammaproteobacteria, Alphaproteobacteria and Flavobacteriia were the most abundant classes across habitats, multivariate analyses at the ASV level showed marked differences in EMB composition among habitats. Enhancing nutrient level had no significant effect on EMBs, although it increased their similarity between macroalgal canopy and turf habitats. At both ambient and enriched nutrient levels, ASVs mostly belonging to Proteobacteria and Bacteroidetes were more abundant in EMBs from macroalgal canopies than barrens. In contrast, ASVs belonging to the phylum of Proteobacteria and, in particular, to the families of Rhodobacteraceae and Flavobacteriaceae at ambient nutrient levels and of Rhodobacteraceae and Bacteriovoracaceae at enhanced nutrient levels were more abundant in turf than canopy habitats. Our results show that primary surfaces from alternative habitats that form mosaics on shallow rocky reefs in oligotrophic areas host distinct microbial communities that are, to some extent, resistant to moderate nutrient enhancement. Understanding the role of EMBs in generating reinforcing feedback under different nutrient loading regimes appears crucial to advance our understanding of the mechanisms underpinning the stability of habitats alternative to macroalgal forests as well as their role in regulating reverse shifts.

Keywords: Algal turfs; Epilithic microbial biofilms; Marine forests; Temperate rocky reefs; Urchin barrens.

Fig. 1

Nitrite, nitrate, and phosphate concentrations in seawater collected from enriched versus control areas in June and November 2015 (means ± SE; n = 12)

Fig. 2

Taxonomic composition of epilithic microbial biofilms at the class level

Fig. 3

Two-dimensional nMDS on Euclidean distances calculated from untransformed data comparing the structure of epilithic microbial biofilms among habitats (macroalgal canopies versus urchin barrens versus algal turfs) at ambient and enriched nutrient levels

Fig. 4

The normalized pairwise distance (where 1.0 represents the maximum observed Euclidean distance) visualized for the urchin barren and algal turf communities with and without added nutrients compared to the macroalgal canopy communities

Fig. 5

Venn diagrams showing the percentage of total ASVs shared across the three habitats (i.e., the core microbiome) and between each pair of habitats, at A ambient versus B enhanced nutrient levels. Stacked barplots (C) illustrate the composition of the core microbiome, at the family level, separately for ambient and enhanced nutrient levels

Fig. 6

Mean CLR-transformed abundance of ASV differing significantly between macroalgal canopy and urchin barren habitats at A ambient and B enhanced nutrient levels

Fig. 7

Mean CLR-transformed abundance of ASV differing significantly between macroalgal canopy and algal turf habitats at A ambient and B enhanced nutrient levels