Evaluating biodiversity for coral reef reformation and monitoring on complex 3D structures using environmental DNA (eDNA) metabarcoding

Quantifying coral reef biodiversity is challenging for cryptofauna and organisms in early life stages. We demonstrate the utility of eDNA metabarcoding as a tool for comprehensively evaluating invertebrate communities on complex 3D structures for reef reformation, and the role these structures play in provisioning habitat for organisms. 3D design and printing were used to create 18 complex tiles, which were used to form artificial reef structures. eDNA was collected from scraping tile surfaces for organismal biomass and from seawater samples around the artificial reefs in the Gulf of Eilat/Aqaba, Red Sea. Metabarcoding targeted the mitochondrial COI gene with specific primers for marine biodiversity. We provide the first eDNA biodiversity baseline for the Gulf of Eilat/Aqaba, capturing extensive information on species abundance, richness, and diversity. Tile tops had higher phylogenetic diversity and richness, despite a higher abundance of organisms on tile bottoms, highlighting the detection of cryptic organisms with eDNA. We recommend eDNA metabarcoding for reef restoration initiatives, especially for complex marine structures, to improve success and evaluation of biodiversity.

Untangling the molecular basis of coral response to sedimentation

Urbanized coral reefs are often chronically affected by sedimentation and reduced light levels, yet many species of corals appear to be able to thrive under these highly disturbed conditions. Recently, these marginal ecosystems have gained attention as potential climate change refugia due to the shading effect of suspended sediment, as well as potential reservoirs for stress-tolerant species. However, little research exists on the impact of sedimentation on coral physiology, particularly at the molecular level. Here, we investigated the transcriptomic response to sediment stress in corals of the family Merulinidae from a chronically turbid reef (one genet each of Goniastrea pectinata and Mycedium elephantotus from Singapore) and a clear-water reef (multiple genets of G. pectinata from the Gulf of Aqaba/Eilat). In two ex-situ experiments, we exposed corals to either natural sediment or artificial sediment enriched with organic matter and used whole-transcriptome sequencing (RNA sequencing) to quantify gene expression. Analysis revealed a shared basis for the coral transcriptomic response to sediment stress, which involves the expression of genes broadly related to energy metabolism and immune response. In particular, sediment exposure induced upregulation of anaerobic glycolysis and glyoxylate bypass enzymes, as well as genes involved in hydrogen sulphide metabolism and in pathogen pattern recognition. Our results point towards hypoxia as a probable driver of this transcriptomic response, providing a molecular basis to previous work that identified hypoxia as a primary cause of tissue necrosis in sediment-stressed corals. Potential metabolic and immunity trade-offs of corals living under chronic sedimentation should be considered in future studies on the ecology and conservation of turbid reefs.

A star is torn-molecular analysis divides the Mediterranean population of Poli's stellate barnacle, Chthamalus stellatus (Cirripedia, Chtamalidae)

Poli's stellate barnacle, Chthamalus stellatus Poli, populates the Mediterranean Sea, the North-Eastern Atlantic coasts, and the offshore Eastern Atlantic islands. Previous studies have found apparent genetic differences between the Atlantic and the Mediterranean populations of C. stellatus, suggesting possible geological and oceanographic explanations for these differences. We have studied the genetic diversity of 14 populations spanning from the Eastern Atlantic to the Eastern Mediterranean, using two nuclear genes sequences revealing a total of 63 polymorphic sites. Both genotype-based, haplotype-based and the novel SNP distribution population-based methods have found that these populations represent a geographic cline along the west to east localities. The differences in SNP distribution among populations further separates a major western cluster into two smaller clusters, the Eastern Atlantic and the Western Mediterranean. It also separates the major eastern cluster into two smaller clusters, the Mid-Mediterranean and Eastern Mediterranean. We suggested here environmental conditions like surface currents, water salinity and temperature as probable factors that have formed the population structure. We demonstrate that C. stellatus is a suitable model organism for studying how geological events and hydrographic conditions shape the fauna in the Mediterranean Sea.

Flatfoot in Africa, the cirripede Chthamalus in the west Indian Ocean

Barnacles of the genus Chthamalus are commonly encountered rocky intertidal shores. The phylogeography of the different species in the Western Indian Ocean is unclear. Using morphological characteristics as well as the molecular markers mitochondrial cytochrome oxygenase subunit I (COI) and the nuclear sodium-potassium ATPase (NaKA), we identified four clades representing four species in the Western Indian Ocean and its adjacent seas. Among these species, a newly identified species, Chthamalus barilani, which was found in Madagascar, Zanzibar and Tanzania. Chthamalus from the coasts of Tanzania and Zanzibar is identified morphologically as C. malayensis, and clusters with C. malayensis from the Western Pacific and the Indo Malayan regions. C. malayensis is regarded as a group of four genetically differentiated clades representing four cryptic species. The newly identified African clade is genetically different from these clades and the pairwise distances between them justify the conclusion that it is an additional cryptic species of C. malayensis. This type of genetic analyses offers an advantage over morphological characterization and allowed us to reveal that another species, C. barnesi, which is known from the Red Sea, is also distributed in the Arabian Sea and the Persian Gulf. We could also confirm the presence of the South African species C. dentatus in the Mozambique channel. This represents the Northeastern limit of C. dentatus, which is usually distributed along the coast of southern Africa up to the Islands of Cape Verde in West Africa. Altogether, based on a combination of morphology and genetics, we distinct between four clusters of Chthamalus, and designate their distribution in the West Indian Ocean. These distinctions do not agree with the traditional four groups reported previously based merely on morphological data. Furthermore, these findings underline the importance of a combining morphological and genetics tools for constructing barnacle taxonomy.

Molecular analysis reveals a cryptic species of Chthamalus (Crustacea: Cirripedia) in the Cape Verde Islands

The intertidal barnacle Chthamalus stellatus has a broad distribution, occurring in the Mediterranean, the east Atlantic shores and east Atlantic Macaronesian Islands (Madeira, the Canaries and the Azores). Traditionally, based on morphological characters, Chthamalus of the Cape Verde Islands were also regarded as C. stellatus. However, using a mitochondrial gene and two nuclear genes, we found that although Chthamalus from Cape Verde is morphologically similar to C. stellatus, there are genetic differences between the two that are larger than those found between different species of Chthamalus. We thus claim that these genetic differences justify the assignment of the Cape Verde populations as an evolutionarily significant unit and a sister clade to C. stellatus. We also show that the connection between taxonomic units that are close to each other lies not only in the resemblance between DNA sequences. We have found that numerous point mutations characterizing the Cape Verde Chthamalus are present as infrequent alleles in C. stellatus, indicating that two close taxonomic units can also share polymorphisms present in their common ancestor.

A stranger among us: the occurrence of Cantellius (Balnoidea: Pyrgomatidae) an epibiont of scleractinias in stylasterids (Hydrozoa)

Barnacles that fit morphologically into the description of the pyrgomatid genus Cantellius were retrieved from hydrozoan Stylasteridae. The use of molecular markers also confirmed the assignment of these barnacles to the genus Cantellius. Hitherto, stylasterids have not been recorded as hosts of pyrgomatids. This finding conflicts with and refutes the statement that scleractinans (Hexacorallia) are obligatory hosts of pyrgomatids. These are the first unequivocal records of living pyrgomatids in stylasterids, thus documenting a new type of habitat for this group of barnacles. Further inspections of stylasterids will probably reveal more new host records and, possibly, new pyrgomatids.

Multiple transgressions and slow evolution shape the phylogeographic pattern of the blind cave-dwelling shrimp Typhlocaris

Background

Aquatic subterranean species often exhibit disjunct distributions, with high level of endemism and small range, shaped by vicariance, limited dispersal, and evolutionary rates. We studied the disjunct biogeographic patterns of an endangered blind cave shrimp, Typhlocaris, and identified the geological and evolutionary processes that have shaped its divergence pattern.

Methods

We collected Typlocaris specimens of three species (T. galilea, T. ayyaloni, and T. salentina), originating from subterranean groundwater caves by the Mediterranean Sea, and used three mitochondrial genes (12S, 16S, cytochrome oxygnese subunit 1 (COI)) and four nuclear genes (18S, 28S, internal transcribed spacer, Histon 3) to infer their phylogenetic relationships. Using the radiometric dating of a geological formation (Bira) as a calibration node, we estimated the divergence times of the Typhlocaris species and the molecular evolution rates.

Results

The multi-locus ML/Bayesian trees of the concatenated seven gene sequences showed that T. salentina (Italy) and T. ayyaloni (Israel) are sister species, both sister to T. galilea (Israel). The divergence time of T. ayyaloni and T. salentina from T. galilea was 7.0 Ma based on Bira calibration. The divergence time of T. ayyaloni from T. salentina was 5.7 (4.4-6.9) Ma according to COI, and 5.8 (3.5-7.2) Ma according to 16S. The computed interspecific evolutionary rates were 0.0077 substitutions/Myr for COI, and 0.0046 substitutions/Myr for 16S.

Discussion

Two consecutive vicariant events have shaped the phylogeographic patterns of Typhlocaris species. First, T. galilea was tectonically isolated from its siblings in the Mediterranean Sea by the arching uplift of the central mountain range of Israel ca. seven Ma. Secondly, T. ayyaloni and T. salentina were stranded and separated by a marine transgression ca. six Ma, occurring just before the Messinian Salinity Crisis. Our estimated molecular evolution rates were in one order of magnitude lower than the rates of closely related crustaceans, as well as of other stygobiont species. We suggest that this slow evolution reflects the ecological conditions prevailing in the highly isolated subterranean water bodies inhabited by Typhlocaris.

Tidal and diel orchestration of behaviour and gene expression in an intertidal mollusc

Intertidal inhabitants are exposed to the 24-hour solar day, and the 12.4 hour rising and falling of the tides. One or both of these cycles govern intertidal organisms' behaviour and physiology, yet little is known about the molecular clockworks of tidal rhythmicity. Here, we show that the limpet Cellana rota exhibits robust tidally rhythmic behaviour and gene expression. We assembled a de-novo transcriptome, identifying novel tidal, along with known circadian clock genes. Surprisingly, most of the putative circadian clock genes, lack a typical rhythmicity. We identified numerous tidally rhythmic genes and pathways commonly associated with the circadian clock. We show that not only is the behaviour of an intertidal organism in tune with the tides, but so too are many of its genes and pathways. These findings highlight the plasticity of biological timekeeping in nature, strengthening the growing notion that the role of 'canonical' circadian clock genes may be more fluid than previously thought, as exhibited in an organism which has evolved in an environment where tidal oscillations are the dominant driving force.

On the genus Spirobranchus (Annelida, Serpulidae) from the northern Red Sea, and a description of a new species

Species of the genus Spirobranchus, commonly known as Christmas tree worms, are abundant throughout tropical Indo-Pacific and Atlantic Oceans. Information on the species inhabiting the Red Sea in general and the Gulf of Eilat (Gulf of Aqaba) in particular, has so far been very limited. Here we present a multigene phylogenetic analysis, examining both mitochondrial (Cyt-b) and nuclear (ITS2 and 18S) markers, to support the presence of four distinct Spirobranchus species in the Gulf of Eilat: S. corniculatus (including three taxa previously regarded as full species: S. gaymardi, S. cruciger, and S. corniculatus), S. cf. tetraceros, S. gardineri and a new species Spirobranchus aloni, likely endemic to the Red Sea (including two morphotypes with slightly different opercular morphology). The results presented here emphasise that the combination of molecular and in-depth morphological evaluation holds great prospects for a better understanding of species divergence and relationships.

Phylogeny of coral-inhabiting barnacles (Cirripedia; Thoracica; Pyrgomatidae) based on 12S, 16S and 18S rDNA analysis

The traditional phylogeny of the coral-inhabiting barnacles, the Pyrgomatidae, is based on morphological characteristics, mainly of the hard parts. It has been difficult to establish the phylogenetic relationships among Pyrgomatidae because of the apparent convergence of morphological characteristics, and due to the use of non-cladistic systematics, which emphasize ancestor-descendant relationships rather than sister-clade relationships. We used partial sequences of two mithochondrial genes, 12S rDNA and 16S rDNA, and a nuclear gene, 18S rDNA, to infer the molecular phylogeny of the pyrgomatids. Our phylogenetic results allowed us to reject previous classifications of Pyrgomatidae based on morphological characteristics. Our results also suggested the possibility of paraphyly of the Pyrgomatidae. The hydrocoral barnacle Wanella is not found on the same clade as the other pyrgomatids, but rather, with the free-living balanids. The basal position of Megatrema and Ceratoconcha is supported. The archeaobalanid Armatobalanus is grouped with Cantellius at the base of the Indo-Pacific pyrgomatines. Fusion of the shell plate and modification of the opercular valves are homoplasious features that occurred more than three times on different clades. The monophyly of the "Savignium" group, comprising four nominal genera, is also not supported, and the different taxa are placed on different clades.

Striving for normality: whole body regeneration through a series of abnormal generations

Embryogenesis and asexual reproduction are commonly considered to be coordinated developmental processes, which depend on accurate progression through a defined sequence of developmental stages. Here we report a peculiar developmental scenario in a simple chordate, Botryllus schlosseri, wherein a normal colony of individuals (zooids and buds) is regenerated from the vasculature (vascular budding) through a sequence of morphologically abnormal developmental stages. Vascular budding was induced by surgically removing buds and zooids from B. schlosseri colonies, leaving only the vasculature and the tunic that connects them. In vivo imaging and histological sections showed that the timing and morphology of developing structures during vascular budding deviated significantly from other asexual reproduction modes (the regular asexual reproduction mode in this organism and vascular budding in other botryllid species). Subsequent asexual reproduction cycles exhibited gradual regaining of normal developmental patterns, eventually leading to regeneration of a normal colony. The conversion into a normal body form suggests the activation of an alternative pathway of asexual reproduction, which involves gradual regaining of normal positional information. It presents a powerful model for studying the specification of the same body plan by different developmental programs.

Differential gene expression in Symbiodinium microadriaticum clade B following stress

Coral bleaching is caused by the loss of symbiont zooxanthellae and/or decrease in their pigments. Since the algal symbionts provide the energy basis for corals and whole reefs, their loss or impairment of function leads to widespread mortality. This phenomenon has been documented numerous times in recent years, and has extensively damaged coral reefs all over the world. Temperature has been found to be the major cause of bleaching, and rising sea temperatures have increased the frequency of these catastrophic episodes. To characterize the response of zooxanthellae to temperature stress at the molecular level, we used the mRNA differential display technique to monitor changes in the abundance of specific mRNA species in the cell under different temperature conditions. Axenically grown zooxanthellae were exposed to a range of temperatures (21.7, 17, 26 degrees C) before extraction of their mRNA. Of numerous differentially expressed sequences, seven mRNA species were amplified by the polymerase chain reaction (PCR) and sequenced. One of those sequences was positively identified as encoding a multifunction cell surface aminopeptidase, dipeptidyl peptidase IV, which is active in cell matrix adhesion. Our work illustrates the power of the differential display technique as a useful tool to study the response of zooxanthellae to stressors.

Protochordate concordant xenotransplantation settings reveal outbreaks of donor cells and divergent life span traits

If fulminate rejection in allogeneic and xenogeneic engraftments is not an evolutionary relict feature, then any treatment that ablates the host surveillance's effector arms capabilities and eliminates graft vs. host reactivity should induce donor chimerism in transplant settings. We demonstrate here marked proliferative response of Botryllus (Urochordata) blood cells months following their infusions (2x10(4)-10(5) blood cells per host) into the concordant xenogeneic environment of irradiated Botrylloides soma. The state of infused cells was followed by Botryllus specific microsatellite alleles on DNA samples from host zooids and vascular system. Increased growth rates and life spans of engrafted hosts in some cases, and sudden chimerical death following the outbreak of donor cells in others, indicate a 'double-edged sword' expression of concurrent evolutionary selected mechanisms. This DES phenomenon in immunity underlies divergent stem cell competition phenomena in multicellular organisms, leading in mammals, to cases of autoimmune diseases vis-à-vis long-lasting microchimerism events following an iatrogenic transplantation.