Rhodoliths are the main hard substrata for the attachment of benthic macroalgae in the NW Gulf of Mexico rubble habitats that are associated with salt domes, unique deep bank habitats at ∼50-90 m depth on the continental shelf offshore Louisiana and Texas. With the advent of additional sequencing technologies, methodologies for biodiversity assessments are now rapidly shifting to DNA metabarcoding, i.e., High Throughput Sequencing (HTS) of environmental DNA mixtures with standardized molecular markers, such as 16S V4, for rapid, cost-effective biodiversity measurement. We newly tested 16S V4 metabarcoding on endolithic portions of mesophtic rhodoliths exhibiting low phototroph colonization that revealed a hidden, cryptic algal diversity targeting spores, propagules, and unsuspected life history stages. We explored cryo-SEM as a potentially more informative method than regular SEM to minimize artifacts of sample preparation in the study of endolithic cell inclusions which brought to light a suite of microalgal stages. We were able to differentiate floridean starch from cellular inclusions. We associated the effect of anatomical growth pattern on presence or absence of cellular inclusions in biogenic rhodoliths. Analyses of combined 16S V4 metabarcodes and 16S Sanger sequences of two red algal orders, the Halymeniales and Bonnemaisoniales, increased the established record of diversity in the region. We view rhodoliths as marine biodiversity hotspots that may function as seedbanks, temporary reservoirs for life history stages of ecologically important eukaryotic microalgae, and macroalgae or as refugia for ecosystem resilience following environmental stress.

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The terete taxa Gracilariopsis (hereafter Gp.) lemaneiformis (Bory) Dawson, Acleto & Foldvik and Gracilaria (hereafter G.) chilensis Bird, McLachlan & Oliveira resemble each other in branching pattern. This study aims to analyze samples attributed to G. chilensis from a southern locality in Peru using molecular tools, in order to differentiate it from Gp. lemaneiformis samples collected along the Peruvian coast. Species identification of the Gracilariaceae, especially of the terete forms, is notoriously difficult due to morphological plasticity and convergence of their thalli, and the correct taxonomic identification of non-reproductive, cylindrical specimens remains a difficult task (Gurgel & Fredericq 2004). Utilizing traditional morphometric techniques, Edding et al. (2006) concluded that G. chilensis, comprising a single morphotype, is the main species of Gracilaria present along the Chilean coast, in which natural populations are distributed between 30°S and 45°S, from Coquimbo to Southern Chiloe (Bird et al. 1986), with farms extending further north to Antofagasta (24°S) (Santelices & Ugarte 1990). Hoffmann & Santelices (1997) found the establishment of G. chilensis on the coast of Coihaique (45°S) mainly due to aquaculture introduction. This species also occurs in the western Pacific Ocean, ranging from southeastern Australia to New Zealand (Nelson 1987). Gracilariopsis Dawson was long merged into Gracilaria until Fredericq & Hommersand (1989) resurrected Gracilariopsis on the basis of lack of nutritive cells in the cystocarp, and with chorda-type surface spermatangia. Gp. lemaneiformis has a geographical range from Paita, Peru to Antofagasta in northern Chile (Ramírez & Tapia 1991). DNA sequence analysis has been the most reliable and widely used molecular technique to infer phylogenic relationships at the species level within the Gracilariaceae (Gurgel & Fredericq 2004), and recognition of Gracilariopsis as a genus distinct from Gracilaria received strong support from the molecular studies of Bird et al. (1994), and Gurgel et al. (2003), among others. According to Gurgel et al. (2003), Gp. lemaneiformis is shown not to have a worldwide distribution but to be restricted to the vicinity of Peru, whereas the species going under the name Gp. “lemaneiformis” from North and South Carolina is now referred to as Gp. carolinensis Liao et Hommersand, and Gp. “lemaneiformis” from China and Japan constitutes an undescribed species that is related to Gp. heteroclada Zhang et Xia.