Soil and Rhizosphere Associated Fungi in Gray Mangroves (Avicennia marina) from the Red Sea — A Metagenomic Approach

Covering a quarter of the world’s tropical coastlines and being one of the most threatened ecosystems, mangroves are among the major sources of terrestrial organic matter to oceans and harbor a wide microbial diversity. In order to protect, restore, and better understand these ecosystems, researchers have extensively studied their microbiology, yet few surveys have focused on their fungal communities. Our lack of knowledge is even more pronounced for specific fungal populations, such as the ones associated with the rhizosphere. Likewise, the Red Sea gray mangroves (Avicennia marina) remain poorly characterized, and understanding of their fungal communities still relies on cultivation-dependent methods. In this study, we analyzed metagenomic datasets from gray mangrove rhizosphere and bulk soil samples collected in the Red Sea coast, to obtain a snapshot of their fungal communities. Our data indicated that Ascomycota was the dominant phylum (76%–85%), while Basidiomycota was less abundant (14%–24%), yet present in higher numbers than usually reported for such environments. Fungal communities were more stable within the rhizosphere than within the bulk soil, both at class and genus level. This finding is consistent with the intrinsic patchiness in soil sediments and with the selection of specific microbial communities by plant roots. Our study indicates the presence of several species on this mycobiome that were not previously reported as mangrove-associated. In particular, we detected representatives of several commercially-used fungi, e.g., producers of secreted cellulases and anaerobic producers of cellulosomes. These results represent additional insights into the fungal community of the gray mangroves of the Red Sea, and show that they are significantly richer than previously reported

A review of contemporary patterns of endemism for shallow water reef fauna in the Red Sea

Aim: The Red Sea is characterised by a unique fauna and historical periods of desiccation, hypersalinity and intermittent isolation. The origin and contemporary composition of reef-associated taxa in this region can illuminate biogeographical principles about vicariance and the establishment (or local extirpation) of existing species. Here we aim to: (1) outline the distribution of shallow water fauna between the Red Sea and adjacent regions, (2) explore mechanisms for maintaining these distributions and (3) propose hypotheses to test these mechanisms. Location: Red Sea, Gulf of Aden, Arabian Sea, Arabian Gulf and Indian Ocean. Methods: Updated checklists for scleractinian corals, fishes and non-coral invertebrates were used to determine species richness in the Red Sea and the rest of the Arabian Peninsula and assess levels of endemism. Fine-scale diversity and abundance of reef fishes within the Red Sea were explored using ecological survey data. Results: Within the Red Sea, we recorded 346 zooxanthellate and azooxanthellate scleractinian coral species of which 19 are endemic (5.5%). Currently 635 species of polychaetes, 211 echinoderms and 79 ascidians have been documented, with endemism rates of 12.6%, 8.1% and 16.5% respectively. A preliminary compilation of 231 species of crustaceans and 137 species of molluscs include 10.0% and 6.6% endemism respectively. We documented 1071 shallow fish species, with 12.9% endemic in the entire Red Sea and 14.1% endemic in the Red Sea and Gulf of Aden. Based on ecological survey data of endemic fishes, there were no major changes in species richness or abundance across 1100 km of Saudi Arabian coastline. Main conclusions: The Red Sea biota appears resilient to major environmental fluctuations and is characterized by high rates of endemism with variable degrees of incursion into the Gulf of Aden. The nearby Omani and Arabian Gulfs also have variable environments and high levels of endemism, but these are not consistently distinct across taxa. The presence of physical barriers does not appear to explain species distributions, which are more likely determined by ecological plasticity and genetic diversity

Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

Background The capacity of reef-building corals to tolerate (or adapt to) heat stress is a key factor determining their resilience to future climate change. Changes in coral microbiome composition (particularly for microalgal endosymbionts and bacteria) is a potential mechanism that may assist corals to thrive in warm waters. The northern Red Sea experiences extreme temperatures anomalies, yet corals in this area rarely bleach suggesting possible refugia to climate change. However, the coral microbiome composition, and how it relates to the capacity to thrive in warm waters in this region, is entirely unknown. Results We investigated microbiomes for six coral species (Porites nodifera, Favia favus, Pocillopora damicornis, Seriatopora hystrix, Xenia umbellata, and Sarcophyton trocheliophorum) from five sites in the northern Red Sea spanning 4° of latitude and summer mean temperature ranges from 26.6 °C to 29.3 °C. A total of 19 distinct dinoflagellate endosymbionts were identified as belonging to three genera in the family Symbiodiniaceae (Symbiodinium, Cladocopium, and Durusdinium). Of these, 86% belonged to the genus Cladocopium, with notably five novel types (19%). The endosymbiont community showed a high degree of host-specificity despite the latitudinal gradient. In contrast, the diversity and composition of bacterial communities of the surface mucus layer (SML)—a compartment particularly sensitive to environmental change—varied significantly between sites, however for any given coral was species-specific. Conclusion The conserved endosymbiotic community suggests high physiological plasticity to support holobiont productivity across the different latitudinal regimes. Further, the presence of five novel algal endosymbionts suggests selection of certain genotypes (or genetic adaptation) within the semi-isolated Red Sea. In contrast, the dynamic composition of bacteria associated with the SML across sites may contribute to holobiont function and broaden the ecological niche. In doing so, SML bacterial communities may aid holobiont local acclimatization (or adaptation) by readily responding to changes in the host environment. Our study provides novel insight about the selective and endemic nature of coral microbiomes along the northern Red Sea refugia

Same same but different: The distribution of the benthic shrimp Notocrangon antarcticus

The population genetic of the Antarctic benthic shrimp Notocrangon antarcticus was analyzed with 3 polymorphic microsatellite markers and with the 16S rDNA gene. Therefore, samples from 7 different locations: Antarctic Peninsula (Larsen A, Larsen B and Larsen C), South Orkney Island, South Georgia Island, East Weddell Sea and Terre Adélie were collected during the CEAMARC (2007) and CAMBIO (2011) expedition. The results of the mitochondrial 16S gene marker showed two clades within the haplotype network, one for South Georgian samples and the other one for the rest of the samples tested herein (Antarctic Peninsula, South Orkney Island, East Weddell Sea and Terre Adélie). The microsatellite data reinforced the results from the 16S haplotype network showing as well genetically differentiated population clusters – one for SGI and one for the rest of specimen of the continental shelf and the South Orkney Island (SOI). In addition, the microsatellite data gave some hints on a further genetically partially differentiated population for the samples of the Larsen C shelf of the Antarctic Peninsula. Last mentioned however, still needs to be further analyzed. All in all, the population of SGI shows a clear genetic isolation from all other tested populations and can be considered as an independent evolutionary significant unit (ESU). Furthermore N. antarcticus seems to have a circumpolar distribution with more or less constant gene flow around the Antarctic continental shelf including the island of South Orkney. Nevertheless, further microsatellite primers should be isolated in order to give higher evidence to the data. Usually, six to eight polymorphic markers are recommended for such tests. In addition, the number of individuals tested per location should also be increased

Genetic Connectivity of the Reef Building Coral Pocillopora sp. in the Red Sea

The Red Sea is a challenging environment for many marine organisms. It has one of the highest salinity concentrations (up to 40.2 ppt) and is the northernmost tropical sea worldwide. Due to almost complete isolation from the world’s oceanic system it is additionally a very unique region in terms of biodiversity and a potential species incubator. The 2,000 km long (N/S) but narrow (W/E) basin, pushes strong latitudinal environmental changes especially regarding salinity (40.2–37.5 ppt) and temperature (28–33.8°C), which are the main stressors for most marine invertebrates and drivers of adaptive strategies. Nevertheless, its waters harbor a species rich and diverse environment, which is still widely unexplored. To assess the impact of the temperature and salinity gradient on the connectivity of reef organisms, the abundant reef-building coral Pocillopora sp. was sampled from North, Central and South offshore reefs. Ten out of fourteen microsatellite markers available for Pocillopora spp. were employed on individuals to detect the presence or absence of an underlying population genetic structure. To assure the exclusion of putative cryptic species, specimen used in this study were chosen from a single mitochondrial lineage. Samples were taken off the coast of Saudi Arabia and the sampled area covered over 850 km from North to South. Despite the long distances between collection sites, no significant genetic population structure was found, rejecting possible subdivision of the species driven by environmental factors and suggesting rather panmixia and sufficient gene flow (FST = 0.0005, p = 0.340; Variance among sites = 0.0%, based on 9 loci). This result is striking considering additional seasonal temperature fluxes from over 6°C and suggests high tolerance levels of Pocillopora sp. to diverse environmental conditions. Moreover, maintaining genetic diversity and frequent larval dispersal over wide distances and among contrasting habitats further supports the adaptive potential and reproductive success of Pocillopora species worldwide

A new species of Schindleria (Teleostei: Gobiiformes: Gobiidae) from the Red Sea (Saudi Arabia) with a specialized caudal-fin complex

Species of the gobiid genus Schindleria are among the smallest and fastest reproducing vertebrates of the oceans. We describe a new species, Schindleria qizma, from the Red Sea, Saudi Arabia. It is an extreme example of progenesis, within the already paedomorphic genus, with morphological traits clearly differentiating it from its congeners. Schindleria qizma has a unique, unflexed notochord with a straight urostyle of which the tip is inserted into the hypural cartilage, rather than the typical flexed notochord with an upturned urostyle of the other species of Schindleria. Schindleria qizma belongs to the short dorsal-fin type of Schindleria. It is further characterized by an elongated but relatively deep body; a short dorsal fin originating just slightly anterior to the anal fin (predorsal-fin length 59.4% of SL vs. preanal-fin length 60.2% of SL); a head continuously increasing in depth posteriorly with a straight dorsal profile; a short snout (18.6% of head length); large eyes (34.4% of head length); a short pectoral-radial plate (6.3% of SL); 13 dorsal-fin rays; 11 anal-fin rays; 0–2 procurrent rays (where the last procurrent ray is short, if present); an anal fin with the first anal-fin ray situated opposite the second dorsal-fin ray; toothless oral jaws; females with few (10–11, total) but very large (4.6% of SL) eggs and with a conspicuous urogenital papilla characterized by a wide urogenital opening flanked by two long, bilobed projections; a dorsally pigmented swim-bladder; blackish, iridescent eyes, capped by a silvery layer with irregular rows of black dots or blotches; and no additional external pigmentation on its body, at least in preserved specimens

A new species of toothless, short dorsal-fin Schindleria (Gobiiformes: Gobiidae) from the Red Sea (Egypt)

Abstract We describe a new, tiny species of Schindleria from a reef lagoon in the Red Sea off the coast of Hurghada, Egypt. Schindleria edentata, new species, belongs to the short dorsal-fin type of Schindleria, with the dorsal and anal fins of about equal length. Schindleria edentata is characterized by an elongated but relatively deep body (body depth at anal-fin origin 10.8% of SL and at 4th anal-fin ray 10.9 % of SL); a short dorsal fin originating just slightly anterior to the anal fin (predorsal-fin length 60.9% of SL, pre-anal fin length 64.8% of SL); a stubby head with a steep frontal profile, a short snout (i.e., 23.1% of head length), and large eye (i.e., 27.7% of the head’s length); a long pectoral radial plate (length 7.6% of SL); four dorsal and four ventral procurrent caudal-fin rays increasing in length posteriorly; last procurrent ray simple without additional spine and, although the longest, not distinctly elongate; 15 dorsal-fin rays; 13 anal-fin rays; the base of the first anal-fin ray positioned below the base of the third dorsal-fin ray; upper and lower jaws toothless; in vivo with translucent body; eye black; swim bladder capped by a melanophore blotch; no pigmentation externally on body after preservation

Absence of genetic differentiation in the coral Pocillopora verrucosa along environmental gradients of the Saudi Arabian Red Sea

The Red Sea is the world's northernmost tropical sea. The 2000 km long, but narrow basin creates distinct environmental conditions along its latitudinal spread. The Red Sea displays a pronounced salinity gradient from 41 to 37 PSU (north to south) with an opposing temperature gradient from 21 to 27°C in the north to 27–33.8°C in the south. The Red Sea further displays a decreasing nutrient gradient from south to north that can also influence underwater light fields due to higher phytoplankton content and turbidity. Despite this strong variation in temperature, salinity, nutrients, and light conditions, the Red Sea supports large and diverse coral reef ecosystems along its nearly entire coastline. Only few studies have targeted whether these prevailing gradients affect genetic connectivity of reef organisms in the Red Sea. In this study, we sampled the abundant reef-building coral Pocillopora verrucosa from 10 reefs along a latitudinal gradient in the Red Sea covering an area of more than 850 km. We used nine Pocillopora microsatellite markers to assess the underlying population genetic structure and effective population size. To assure the exclusion of cryptic species, all analyzed specimens were chosen from a single mitochondrial lineage. Despite large distances between sampled regions covering pronounced, but smooth temperature and salinity gradients, no significant genetic population structure was found. Rather, our data indicate panmixia and considerable gene flow among regions. The absence of population subdivision driven by environmental factors and over large geographic distances suggests efficient larval dispersal and successful settlement of recruits from a wide range of reef sites. It also advocates, broadcast spawning as the main reproductive strategy of Pocillopora verrucosa in the Red Sea as reflected by the absence of clones in sampled colonies. These factors might explain the success of Pocillopora species throughout the Indo-Pacific and Arabian Seas.publishe

Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies

peer reviewedAim: Several marine biogeographical provinces meet at the Arabian Peninsula. Where and how these junctions affect species is poorly understood. We herein aimed to identify the barriers to dispersal and how these shape fish populations, leading to differing biogeographies despite shared habitat and co-ancestry. Taxon: Dascyllus marginatus (endemic) and Dascyllus abudafur (widespread). Location: Coral reefs from the Red Sea (RS), Djibouti, Yemen, Oman, and Madagascar. Methods: We tested potential barriers to gene flow using RADseq-derived SNPs and identified whether population genetic differences on each side of these barriers were neutral or selective to relate this to the biogeography of the species. Seven locations (ranging over 5100 km) were sampled for the endemic and six (ranging over 7400 km) for the widespread species, taking 20 individuals per location, with two exceptions. Results: Dascyllus marginatus populations (comprising 5648 SNPs) had an order of magnitude higher genetic differentiation compared to D. abudafur (comprising 10,667 SNPs), as well as several outlier loci that were absent in D. abudafur despite equal sampling locations. In both species, the RS and Djibouti specimens formed one genetic cluster separated from all other locations. Although ranging from the RS to Madagascar, D. abudafur was absent in Yemen and Oman. Main Conclusions: Stronger genetic structure at smaller geographical scales and outlier loci in the endemic species seem associated with faster adaptation to environmental differences and selective pressure. Genetic differentiation in the widespread species is neutral and only occurs at large geographical distances. Restrictive transitions (between the Gulf of Aqaba and the RS or the RS and the Gulf of Aden) do not hinder gene flow in either species, and the environmental shift within the RS (at 22°N/20°N) only affected the endemic species. The genetic break in the Gulf of Aden likely reflects historical colonization processes and not contemporary environmental regimes

Stranded alone: The first reported Peruvian population of Agarophyton chilensis is a single-male's clone

International audienceGracilariales, a red macroalgal order, is considered one of the top ten most invasive algal taxa. While Agarophyton vermiculophyllum is a well known example of an algal invader worldwide, its congeneric species A. chilensis has mainly remained within its original distribution range for thousands of years, and was only engaged in a few dispersal journeys to arrive from New Zealand to Chile over 19,000 years ago. Nowadays, A. chilensis is intensively farmed along the Chilean coast and the establishment of new populations has mostly been due to intentional/planned cultivation practices. No other source of range expansion has ever been reported, since its first description. However, in 2014 it was sighted for the first time at the docking of a small artisanal port in Peru, which nowadays represents its northernmost population. We genetically assessed 60 specimens taken from Peru in 2015 and 2017, using two different types of molecular markers (the ribosomal Internal Transcribed Spacer 2, ITS2 and six nuclear microsatellites). Altogether, our results suggest the population in Perú to be an unattached, vegetative, single male's clonal population. This population has sustained itself successfully, reproducing asexually through fragmentation, for at least four consecutive years and seems to have expanded in the area. The ITS2 sequences from these individuals corresponds all to one haplotype, the one ubiquitous among populations from Chile, the eastern coast of New Zealand and the Chatham Islands, not allowing to narrow down the potential area of origin of the Peruvian population. Based on first the allelic frequencies of six microsatellite loci estimated for 28 Chilean and five loci for seven New Zealander populations and second the analyses of Bayesian clustering, we propose the natural or unintentional anthropogenic introduction of a single male's thallus from Chile to be the source of the Peruvian population