Revision of Corallinaceae (Corallinales, Rhodophyta): recognizing Dawsoniolithon gen. nov., Parvicellularium gen. nov. and Chamberlainoideae subfam. nov. containing Chamberlainium gen. nov. and Pneophyllum

New branched Porolithon species (Corallinales, Rhodophyta) from the Great Barrier Reef, Coral Sea, and Lord Howe Island

Porolithon is one of the most ecologically important genera of tropical and subtropical crustose (non-geniculate) coralline algae growing abundantly along the shallow margins of coral reefs and functioning to cement reef frameworks. Thalli of branched, fruticose Porolithon specimens from the Indo-Pacific Ocean traditionally have been called P. gardineri, while massive, columnar forms have been called P. craspedium. Sequence comparisons of the rbcL gene both from type specimens of P. gardineri and P. craspedium and from field-collected specimens demonstrate that neither species is present in east Australia and instead resolve into four unique genetic lineages. Porolithon howensis sp. nov. forms columnar protuberances and loosely attached margins and occurs predominantly at Lord Howe Island; P. lobulatum sp. nov. has fruticose to clavate forms and free margins that are lobed and occurs in the Coral Sea and on the Great Barrier Reef (GBR); P. parvulum sp. nov. has short (<2 cm), unbranched protuberances and attached margins and is restricted to the central and southern GBR; and P. pinnaculum sp. nov. has a mountain-like, columnar morphology and occurs on oceanic Coral Sea reefs. A rbcL gene sequence of the isotype of P. castellum demonstrates it is a different species from other columnar species. In addition to the diagnostic rbcL and psbA marker sequences, the four new species may be distinguished by a combination of features including thallus growth form, margin shape (attached or unattached), and medullary system (coaxial or plumose). Porolithon species, because of their ecological importance and sensitivity to ocean acidification, need urgent documentation of their taxonomic diversity.

Marine Flora of French Polynesia: An Updated List Using DNA Barcoding and Traditional Approaches

Located in the heart of the South Pacific Ocean, the French Polynesian islands represent a remarkable setting for biological colonization and diversification, because of their isolation. Our knowledge of this region's biodiversity is nevertheless still incomplete for many groups of organisms. In the late 1990s and 2000s, a series of publications provided the first checklists of French Polynesian marine algae, including the Chlorophyta, Rhodophyta, Ochrophyta, and Cyanobacteria, established mostly on traditional morphology-based taxonomy. We initiated a project to systematically DNA barcode the marine flora of French Polynesia. Based on a large collection of ~2452 specimens, made between 2014 and 2023, across the five French Polynesian archipelagos, we re-assessed the marine floral species diversity (Alismatales, Cyanobacteria, Rhodophyta, Ochrophyta, Chlorophyta) using DNA barcoding in concert with morphology-based classification. We provide here a major revision of French Polynesian marine flora, with an updated listing of 702 species including 119 Chlorophyta, 169 Cyanobacteria, 92 Ochrophyta, 320 Rhodophyta, and 2 seagrass species-nearly a two-fold increase from previous estimates. This study significantly improves our knowledge of French Polynesian marine diversity and provides a valuable DNA barcode reference library for identification purposes and future taxonomic and conservation studies. A significant part of the diversity uncovered from French Polynesia corresponds to unidentified lineages, which will require careful future taxonomic investigation.

Calcification traits for cryptic species identification: Insights into coralline biomineralization

Calcareous red algae are foundation species and ecosystem engineers with a global distribution. The principles governing their calcification pathways are still debated and the morphological characters are frequently unreliable for species segregation, as shown by molecular genetics. The recent description of the new species Lithophyllum pseudoracemus, previously undetected and morphologically confused with Lithophyllum racemus, offered a challenging opportunity to test the effectiveness of microanatomy and ultrastructural calcification traits as tools for the identification of these two species, for integrative taxonomy. High resolution SEM images of molecularly identified samples showed that the different size of the perithallial cells and the features of the asexual conceptacle chambers may contribute to the separation of the two species. The two species share the same crystallite morphology in the primary and secondary cell-wall calcification, as previously described in other species belonging to the same clade. However, the perithallial secondary calcification was significantly thicker in L. racemus than in L. pseudoracemus. We described a granular calcified layer in the innermost part of the cell wall, as a putative precursor phase in the biomineralization and formation of the secondary calcification. The hypothesis of different pathways for the formation of the primary and secondary calcification is supported by the observed cell elongation associated with thicker and higher Mg/Ca primary calcification, the inverse correlation of primary and secondary calcification thickness, and the absence of primary calcification in the newly formed wall cutting off an epithallial cell from the meristem.

Community assessment of crustose calcifying red algae as coral recruitment substrates

Successful recruitment of invertebrate larvae to reef substrates is essential to the health of tropical coral reef ecosystems and to their capacity to recover from disturbances. Crustose calcifying red algae (CCRA) are a species rich group of seaweeds that have been identified as important recruitment substrates for scleractinian corals. Most studies on the settlement preference of coral larvae on CCRA use morphological species identifications that can lead to unreliable species identification and do not allow for examining species-specific interactions between coral larvae and CCRA. Accurate identifications of CCRA species is important for coral reef restoration and management to assess CCRA community composition and to detect CCRA species that are favored as coral recruitment substrates. In this study, DNA sequence analysis, was used to identify CCRA species to (1) investigate the species richness and community composition of CCRA on experimental coral recruitment tiles and (2) assess if the coral Acropora surculosa preferred any of these CCRA species as recruitment substrates. The CCRA community assemblages on the coral recruitment tiles was species-rich, comprising 27 distinct CCRA species of the orders Corallinales and Peyssonneliales which constitute new species records for Guam. Lithophylloideae sp. 1 (Corallinales) was the CCRA species that was significantly favored by coral larvae as a recruitment substrate. Lithophylloideae sp. 1 showed to hold a valuable ecological role for coral larval recruitment preference. Lithophylloideae sp. 1 had the highest benthic cover on the recruitment tiles and contained most A. surculosa recruits. DNA barcoding revealed a high taxonomic diversity of CCRA species on a microhabitat scale and provided detailed insight into the species-specific ecological interactions between CCRA and corals. With a steady decline in coral cover, detailed information on species interactions that drive reef recovery is valuable for the planning of marine management actions and restoration efforts.

Geographic distance, sedimentation, and substrate shape cryptic crustose coralline algal assemblages in the world's largest subtropical intertidal algal reef

Algal reefs, concreted by crustose coralline algae (CCA), are the main biotic reefs in temperate waters but rare in the subtropics and tropics. The world's largest known intertidal algal reef in the subtropics is the Taoyuan Algal Reef (TAR) located in the northwestern coast of Taiwan. The biodiversity and ecology of the TAR are scarcely explored, and now the reef is imperiled by industrialization. Here, we document cryptic species of CCA in Taiwan, particularly the TAR, by sequencing the psbA genes of over 1,800 specimens collected across Taiwan. We also examine the ecological background of the TAR by surveying its benthic composition and measuring its environmental parameters. Our data reveal that the TAR harbors a high diversity of cryptic CCA species (27 molecular operational taxonomic units, or mOTUs), many of which are potentially new to science (18 mOTUs) and/or endemic to the TAR (9 mOTUs). Comparing the CCA species inventory of the TAR with the rest of Taiwan shows that the TAR represents a unique hotspot of CCA taxa in the waters of Taiwan. Our analyses show that variation in the CCA assemblages in the TAR is associated with geographic distance, sedimentation, and substrate type (for example, reef versus hermit crab shell), suggesting that dispersal limitation and contemporary environmental selection shape the CCA assemblages in the TAR. The data from this study can inform the monitoring of human impacts on the health of the TAR and contribute to our understanding of the ecological processes underlying algal reef development.

Phymatolithopsis gen. nov. (Hapalidiales, Corallinophycidae, Rhodophyta) based on molecular and morpho-anatomical evidence

A multigene (psbA, rbcL, 18S rDNA) molecular phylogeny of the genus Phymatolithon showed a polyphyletic grouping of two monophyletic clades within the Hapalidiales. DNA sequence data integrated with morpho-anatomical comparisons of type material and of recently collected specimens were used to establish Phymatolithopsis gen. nov. with three species, P. prolixa comb. nov., the generitype, P. repanda comb. nov. and P. donghaensis sp. nov. Phymatolithopsis is sister to Mesophyllum and occurs in a clade distinct from Phymatolithon and boreal species currently assigned to Lithothamnion. Morpho-anatomically, Phymatolithopsis is comprised of species that are non-geniculate and encrusting, bear epithallial cells with rounded walls (not flared), subepithallial initials that are usually as short as or shorter than their immediate inward derivatives, conceptacle primordia from all stages forming superficially directly from subepithallial initials, mature carposporangial conceptacles with a discontinuous fusion cell, gonimoblast filaments that develop at the margins of the fusion cell around the periphery of the carposporangial conceptacle chambers, and multiporate tetra/bisporangial conceptacles. Phymatolithopsis can be distinguished from Phymatolithon by the origin of its conceptacle primordia, which are initiated superficially, directly from the layer of subepithallial initials below the epithallial cells and the distribution of gonimoblast filaments in carposporangial conceptacles, that are at the margins of the fusion cells.

Diversity and taxonomic revision of tribes Rhipileae and Rhipiliopsideae (Halimedaceae, Chlorophyta) based on molecular and morphological data

Genera and species of the tribes Rhipileae and Rhipiliopsideae are abundant in most coral reef ecosystems worldwide. However, the group has been largely overlooked, and very little genetic data is available to accurately assess its diversity, phylogenetic relationships, and geographic distribution. Our study provided an in-depth reassessment of tribes Rhipileae and Rhipiliopsideae based on a species-rich dataset and the combination of molecular species delimitation, multilocus phylogenetic analyses (tufA, rbcL, and 18S rDNA), and morpho-anatomic observations. Our results revealed an unexpected diversity of 38 morphologically validated species hypotheses, including 20 new species, two of which are described in this paper and one resurrected species (Rhipilia diaphana). Based on our phylogenetic results we proposed to redefine the genera Rhipilia and Rhipiliopsis and described two new genera, Kraftalia gen. nov. (Rhipileae) and Rhipiliospina gen. nov. (Rhipiliopsideae). Finally, we validated Rhipiliella Kraft and included it in the tribe Rhipileae. Although Rhipilia and Rhipiliopsis have a pantropical distribution, none of the species studied here appeared cosmopolitan; instead, they have restricted distributions.

Type specimen sequencing, multilocus analyses, and species delimitation methods recognize the cosmopolitan Corallina berteroi and establish the northern Japanese C. yendoi sp. nov. (Corallinaceae, Rhodophyta)

A partial rbcL sequence of the lectotype specimen of Corallina berteroi shows that it is the earliest available name for C. ferreyrae. Multilocus species delimitation analyses (ABGD, SPN, GMYC, bPTP, and BPP) using independent or concatenated COI, psbA, and rbcL sequences recognized one, two, or three species in this complex, but only with weak support for each species hypothesis. Conservatively, we recognize a single worldwide species in this complex of what appears to be multiple, evolving populations. Included in this species, besides C. ferreyrae, are C. caespitosa, the morphologically distinct C. melobesioides, and, based on a partial rbcL sequence of the holotype specimen, C. pinnatifolia. Corallina berteroi, not C. officinalis, is the cosmopolitan temperate species found thus far in the NE Atlantic, Mediterranean Sea, warm temperate NW Atlantic and NE Pacific, cold temperate SW Atlantic (Falkland Islands), cold and warm temperate SE Pacific, NW Pacific and southern Australia. Also proposed is C. yendoi sp. nov. from Hokkaido, Japan, which was recognized as distinct by 10 of the 13 species discrimination analyses, including the multilocus BPP.

Corallinapetrales and Corallinapetraceae: A new order and family of coralline red algae including Corallinapetra gabrielii comb. nov

The coralline algal genus Corallinapetra is currently monospecific and was established on the species Corallinapetra novaezelandiae, known from a single collection from north-eastern New Zealand. On the basis of multi-gene phylogenetic analyses, Corallinapetra has been resolved apart from all currently recognized families and orders within the Corallinophycidae. We analyzed DNA sequence data from the holotype of Lithothamnion gabrielii, which has been considered a heterotypic synonym of L. muelleri, and an unidentified sample collected from Stewart Island in New Zealand, using psbA, rbcL, and COI-5P genes. We also observed detailed morpho-anatomical characters with light and scanning electron microscopy. Our phylogenetic analyses showed that L. gabrielii and the sample from New Zealand belonged to the same clade as Corallinapetra, distinct from other families and orders in the Corallinophycidae. Members of this clade are distinguishable from other families and orders in the Corallinophycidae by possessing sporangia that are surrounded by remnant sterile filaments that are weakly calcified in mature multiporate sporangial conceptacles that produce zonately divided tetrasporangia. Therefore, we propose that Corallinapetra be placed in its own family, Corallinapetraceae and order, Corallinapetrales, and that L. gabrielii should be assigned to Corallinapetra, as C. gabrielii, to reflect their phylogenetic relationships. We also obtained a partial rbcL sequence data from the lectotype of L. muelleri, the generitype of Lithothamnion. Comparison of the L. muelleri type sequence with L. gabrielii unambiguously demonstrated that these two species are not conspecific, and confirm the placement of L. muelleri within the Hapalidiales.

DNA Sequencing of Type Material Reveals Pneophyllum marlothii comb. nov. from South Africa and P. discoideum comb. nov. (Chamberlainoideae, Corallinales, Rhodophyta) from Argentina

A partial rbcL sequence from the type material of Spongites discoideus from southern Argentina showed that it was distinct from rbcL sequences of South African specimens to which that name had been applied based on morpho-anatomy. A partial rbcL sequence from an original syntype specimen, herein designated the lectotype, of Lithophyllum marlothii, type locality Camps Bay, Western Cape Province, South Africa, was identical to rbcL sequences of South African field-collected specimens assigned to S. discoideus. Based on phylogenetic analyses of rbcL and/or psbA sequences, both of these species belong in Pneophyllum and are transferred there as P. discoideum comb. nov. and P. marlothii comb. nov. The two species exhibit a distinct type of development where thick, secondary, monomerous disks are produced from thin, primary, dimerous crusts. Whether this type of development represents an example of convergent evolution or is characteristic of a clade of species within Pneophyllum remains to be resolved.

Sporolithon franciscanum sp. nov. (Sporolithales, Rhodophyta), a New Rhodolith-Forming Species from Northeast Brazil

This paper describes Sporolithon franciscanum, a new rhodolith-forming species of non-geniculate coralline algae found at depths between 47–52 m near the São Francisco river mouth, the second largest and the most extensive drainage basin in Brazil, and also at the Abrolhos Bank, in the world´s largest rhodolith beds. DNA sequences from plastidial psbA and rbcL markers indicate that the species is unique compared to all other Sporolithon species that have thus far been sequenced. Since morpho-anatomical features of the new species are shared with some other Sporolithon species, its identification was only confirmed by DNA sequences.

Nanocrystals as phenotypic expression of genotypes-An example in coralline red algae

Coralline red algae (CRA) are important ecosystem engineers in the world's oceans. They play key roles as primary food source and carbonate producers in marine habitats. CRA are also vital for modern reef systems where they act as substrate for coral growth and stabilizers of reef frameworks. However, morphotaxonomic identification of these important marine organisms is hampered by the fact that morphological concepts used for their classification do not correspond to molecular data. We present the first analysis of nanoscale features in calcified cell walls of CRA in a globally distributed sample set. We use new morphological traits based on these cell wall ultrastructures to construct an independent morphological phyletic tree that shows a promising congruency with existing CRA molecular phylogenies. Our results highlight cellular ultrastructures as a tool to define the phenotypic expression of genotypic information showing their potential to unify morphology with molecular phylogeny.

High diversity of coralline algae in New Zealand revealed: Knowledge gaps and implications for future research

Coralline algae (Corallinophycideae) are calcifying red algae that are foundation species in euphotic marine habitats globally. In recent years, corallines have received increasing attention due to their vulnerability to global climate change, in particular ocean acidification and warming, and because of the range of ecological functions that coralline algae provide, including provisioning habitat, influencing settlement of invertebrate and other algal species, and stabilising reef structures. Many of the ecological roles corallines perform, as well as their responses to stressors, have been demonstrated to be species-specific. In order to understand the roles and responses of coralline algae, it is essential to be able to reliably distinguish individual species, which are frequently morphologically cryptic. The aim of this study was to document the diversity and distribution of coralline algae in the New Zealand region using DNA based phylogenetic methods, and examine this diversity in a broader global context, discussing the implications and direction for future coralline algal research. Using three independent species delimitation methods, a total of 122 species of coralline algae were identified across the New Zealand region with high diversity found both regionally and also when sampling at small local spatial scales. While high diversity identified using molecular methods mirrors recent global discoveries, what distinguishes the results reported here is the large number of taxa (115) that do not resolve with type material from any genus and/or species. The ability to consistently and accurately distinguish species, and the application of authoritative names, are essential to ensure reproducible science in all areas of research into ecologically important yet vulnerable coralline algae taxa.

Reef-building coralline algae from the Southwest Atlantic: filling gaps with the recognition of Harveylithon (Corallinaceae, Rhodophyta) on the Brazilian coast

The Southwest Atlantic is notable for having extensive reef areas cemented by nongeniculate coralline red algae. Based on an analysis of four genetic markers and morpho-anatomical features, we clarify the species of Harveylithon in the tropical and warm temperate Southwest Atlantic. Species delimitation methods (mBGD, ABGD, SPN, and PTP), using three markers (psbA, rbcL, and COI), support the recognition of three new species: H. catarinense sp. nov., H. maris-bahiensis sp. nov., and H. riosmenum sp. nov., previously incorrectly called Hydrolithon samoënse. Our findings highlight the importance of using an approach with several lines of evidence to solve the taxonomic status of the cryptic species.

Disease Specific Bacterial Communities in a Coralline Algae of the Northwestern Mediterranean Sea: A Combined Culture Dependent and -Independent Approach

Crustose coralline red algae (CCA) are important components of marine ecosystems thriving from tropical waters and up to the poles. They fulfill important ecological services including framework building and induction of larval settlement. Like other marine organisms, CCAs have not been spared by the increase in marine disease outbreaks. The white-band syndrome has been recently observed in corallines from the Mediterranean Sea indicating that the disease threat has extended from tropical to temperate waters. Here, we examined the microbiome and the pathobiome of healthy and diseased Neogoniolithon brassica-florida coralline algae in the Mediterranean Sea by combining culture-dependent and -independent approaches. The coralline white-band syndrome was associated with a distinct pathobiome compared to healthy tissues and showed similarities with the white-band syndrome described in the Caribbean Sea. A sequence related to the genus Hoeflea, order Rhizobiales, characterized the white-band disease pathobiome described by amplicon sequencing. No representative of this genus was isolated by culture. We, however, successfully isolated an abundant member of the healthy CCA microbiome, an Alphaproteobateria of the family Rhodobacteraceae. In conclusion, we did not identify a potential causative agent of the disease, but through the complementarity of culture dependent and independent approaches we characterized the healthy microbiome of the coralline and the possible opportunistic bacteria colonizing diseased tissues.

Mediterranean Lithophyllum stictiforme (Corallinales, Rhodophyta) is a genetically diverse species complex: implications for species circumscription, biogeography and conservation of coralligenous habitats

Lithophyllum species in the Mediterranean Sea function as algal bioconstructors, contributing to the formation of biogenic habitats such as coralligenous concretions. In such habitats, thalli of Lithophyllum, consisting of crusts or lamellae with entire or lobed margins, have been variously referred to as either one species, L. stictiforme, or two species, L. stictiforme and L. cabiochiae, in the recent literature. We investigated species diversity and phylogenetic relationships in these algae by sequencing three markers (psbA and rbcL genes, cox2,3 spacer), in conjunction with methods for algorithmic delimitation of species (ABGD and GMYC). Mediterranean subtidal Lithophyllum belong to a well-supported lineage, hereby called the L. stictiforme complex, which also includes two species described from the Atlantic, L. lobatum and L. searlesii. Our results indicate that the L. stictiforme complex consists of at least 13 species. Among the Mediterranean species, some are widely distributed and span most of the western and central Mediterranean, whereas others appear to be restricted to specific localities. These patterns are interpreted as possibly resulting from allopatric speciation events that took place during the Messinian Salinity Crisis and subsequent glacial periods. A partial rbcL sequence from the lectotype of L. stictiforme unambiguously indicates that this name applies to the most common subtidal Lithophyllum in the central Mediterranean. We agree with recent treatments that considered L. cabiochiae and L. stictiforme conspecific. The diversity of Lithophyllum in Mediterranean coralligenous habitats has been substantially underestimated, and future work on these and other Mediterranean corallines should use identifications based on DNA sequences.

Adeylithon bosencei gen. et sp. nov. (Corallinales, Rhodophyta): a new reef-building genus with anatomical affinities with the fossil Aethesolithon

Adeylithon gen. nov. with one species, A. bosencei sp. nov., belonging to the subfamily Hydrolithoideae is described from Pacific coral reefs based on psbA sequences and morpho-anatomy. In contrast with Hydrolithon, A. bosencei showed layers of large polygonal "cells," which resulted from extensive lateral fusions of perithallial cells, interspersed among layers of vegetative cells. This anatomical feature is shared with the fossil Aethesolithon, but lacking DNA sequences from the fossils and the fragmentary nature of Aethesolithon type material, we cannot ascertain if Adeylithon and Aethesolithon are congeneric. Morpho-anatomical features of A. bosencei were generally congruent with diagnostic features of the subfamily Hydrolithoideae: (i) outline of cell filaments entirely lost in large portions due to pervasive and extensive cell fusions, (ii) trichocytes not arranged in tightly packed horizontal fields, (iii) basal layer without palisade cells, and (iv) cells lining the canal pore oriented more or less perpendicular to roof surface and not protruding into the canal. However, it showed a predominant monomerous thallus organization and trichocytes were disposed in large pustulate, horizontal fields, although they were not tightly packed and did not become distinctly buried in the thallus. Only mature tetrasporangial conceptacles were observed, therefore the type of conceptacle roof formation remained undetermined. Adeylithon bosencei occurs on shallow coral reefs, in Australia, Papua New Guinea, and South Pacific islands (Fiji, Vanuatu). Fossil Aethesolithon is considered an important component of shallow coral reefs since the Miocene; fossil records showed a broad Indo-Pacific distribution, but a long-term process of range contraction in the last 2.6 million years, resulting in an overlap with the distribution of the extant Adeylithon. While the congeneric nature of extant and fossil taxa remained uncertain, similarities in morpho-anatomy, habitat, and distribution may indicate that both taxa likely shared a common ancestor.