A preliminary survey of marine cave habitats in the Maltese Islands

The Mediterranean Sea is a hotspot for marine biodiversity. Past studies of Mediterranean marine caves have revealed the unique biocoenotic and ecological characteristics of these habitats, which are protected by European Union legislation. The Maltese Islands have an abundance of partially and fully submerged marine caves with di fferent geomorphological characteristics, yet there have been no systematic studies on these habitats and their associated species. This study is a firrst synthesis of existing information on the biotic assemblages and physical characteristics of Maltese marine caves. The work combines a review of the available information with a preliminary survey of some marine caves in Gozo, during which several species were recorded for the first time for the Maltese Islands. Characteristic species recorded from local marine caves are highlighted, including several species of red and brown algae, sessile invertebrates including bryozoans, ascidians and sponges, and mobile forms including crustaceans and fi sh. A marked zonation from the cave entrance to the inside of the caves was identifi ed: photophilic algae at the mouth of the cave are progressively replaced by more sciaphilic species, followed by a middle section dominated by sessile invertebrates, and then a completely dark inner section that is mostly devoid of sessile organisms. Several species protected by national and international legislation were found to occur.peer-reviewe

Worldwide Analysis of Sedimentary DNA Reveals Major Gaps in Taxonomic Knowledge of Deep-Sea Benthos

International audienceDeep-sea sediments represent the largest but least known ecosystem on earth. With increasing anthropogenic pressure, it is now a matter of urgency to improve our understanding of deep-sea biodiversity. Traditional morpho-taxonomic studies suggest that the ocean floor hosts extraordinarily diverse benthic communities. However, due to both its remoteness and a lack of expert taxonomists, assessing deep-sea diversity is a very challenging task. Environmental DNA (eDNA) metabarcoding offers a powerful tool to complement morpho-taxonomic studies. Here we use eDNA to assess benthic metazoan diversity in 39 deep-sea sediment samples from bathyal and abyssal depths worldwide. The eDNA dataset was dominated by meiobenthic taxa and we identified all animal phyla commonly found in the deep-sea benthos; yet, the diversity within these phyla remains largely unknown. The large numbers of taxonomically unassigned molecular operational taxonomic units (OTUs) were not equally distributed among phyla, with nematodes and platyhelminthes being the most poorly characterized from a taxonomic perspective. While the data obtained here reveal pronounced heterogeneity and vast amounts of unknown biodiversity in the deep sea, they also expose the difficulties in exploiting metabarcoding datasets resulting from the lack of taxonomic knowledge and appropriate reference databases. Overall, our study demonstrates the promising potential of eDNA metabarcoding to accelerate the assessment of deep-sea biodiversity for pure and applied deep-sea environmental research but also emphasizes the necessity to integrate such new approaches with traditional morphology-based examination of deep-sea organisms

Action plan for the conservation of habitats and species associated with seamounts, underwater caves and canyons, aphotic hard beds and chemo-synthetic phenomena in the Mediterranean Sea (Dark Habitats action plan)

Dark habitats are environments where the luminosity is extremely weak, or even absent (aphotic area) leading to an absence of macroscopic autochthonous photosynthesis. The bathymetric extension of this lightless area depends to a great extent on the turbidity of the water and corresponds to benthic and pelagic habitats starting from the deep circa-littoral. Caves which show environmental conditions that favour the installation on of organisms characteristic of dark habitats, are also taken into account. Dark habitats are dependent on very diverse geomorphological structures (e.g. underwater caves, canyons, slopes, isolated rocks, abyssal plains, cold seeps, brine anoxic lakes, hydrothermal springs and seamounts). Dark habitats represent outstanding and potential ecosystems with regard to their: Frailty and vulnerability to any land-based pressure Play an important part in the way the Mediterranean ecosystem functions, insofar as they constitute the main route for transferring matter between the coast and the deep sea Considered as biodiversity hotspots and recruiting areas forming a veritable reservoirs of knowledge and biodiversity Natural habitats that come under Habitat Directive on the conservation of natural habitats and of wild fauna and flora and appear as such as priority habitats requiring protection (Directive 92/43). A certain number of underwater caves enjoy protection status because they fall within the geographical boundaries of Marine Protected Areas (MPAs) Understanding of these functions is necessary for a better understanding and management of the biodiversity of Mediterranean coastal zones and continental shelf.peer-reviewe

Feeding strategies and resource partitioning mitigate the effects of oligotrophy for marine cave mysids

We investigated how large populations of several mysid species can coexist in oligo trophic underwater marine caves and their relationships in the marine cave food web using carbon and nitrogen stable isotopes. Isotopic signatures indicate food partitioning among the 5 species of cave-dwelling mysids from the northwest Mediterranean Sea we studied. Hemimysis speluncola feeds mainly on phytoplankton and zooplankton from outside the caves, Siriella gracilipes on sedimentary organic matter and zooplankton from outside, Harmelinella mariannae on small cave-dwelling crustaceans, and Hemimysis margalefi and Hemimysis lamornae mediterranea on sedimentary particulate organic matter. These differences in diet could promote coexistence of such diverse and abundant mysid faunas in marine caves by reducing interspecific competition for scarce resources. The analysis of both seston and cave sediments revealed that the quantity and quality of organic matter are strongly reduced in marine caves, suggesting that cave-dwelling mysids find most of their food elsewhere. This inference agrees with documented distributions of some of these mysids outside of caves at night where they can feed in the rich littoral zone. These migrations of some species make cave-dwelling mysids important vectors of organic matter transfer from the outside euphotic littoral zone to various locations inside caves. Outside organic matter is then made available to other cave dwellers through mysid fecal pellet production and predation, as suggested by the isotopic compositions of predators like teleost fishes, decapod crustaceans, and carnivorous cladorhizid sponges

Description of <i>Heteromysis</i> (<i>Olivemysis</i>) <i>ekamako</i> sp nov (Mysida, Mysidae, Heteromysinae) from a marine cave at Nuku Hiva Island (Marquesas, French Polynesia, Pacific Ocean)

International audienceCombined faunistic and genetic studies in the marine Ekamako Cave at the southern coast of Nuku Hiva, Marquesas, in the central Pacific, yielded Heteromysis (Olivemysis) ekamako as a new species. This taxon differs from its congeners by a specific combination of morphological characters: flagellate, modified spines dorsally on each of the three segments of the antennular peduncle, a large smooth spine at the tip of only the second male pleopod, series of small flagellate spines along the oblique terminal margin of only the third and fourth male pleopods, and by 2-3 simple spines medially near the statocyst on the endopods of uropods. Although abundant at the entrance of Ekamako Cave, it has not been observed in nine additional submersed marine caves investigated at the Marquesas

Local scale connectivity in the cave-dwelling brooding fish Apogon imberbis

International audienceA lower degree of population connectivity is generally expected for species living in a naturally fragmented habitat than for species living in a continuum of suitable environment. Due to clear-cut environmental conditions with the surrounding littoral zone, underwater marine caves of the Mediterranean Sea constitute a good model to explore the effect of habitat discontinuity on the population structure of their inhabitants. With this goal, the genetic population structure of Apogon imberbis, a mouth-brooding teleost, was explored using the mitochondrial cytochrome b gene and 7 nuclear microsatellite loci from 164 fishes sampled at the micro-scale (ca. 40 km) of the Marseille area (Bay of Marseille and Calanques coast, in NW Mediterranean). Both marker types indicated a low level of genetic structure within the studied area. We propose that each suitable crack and cavity is used as a stepping-stone habitat between disconnected large cave-habitats. This, together with larval dispersal, ensures enough gene flow between caves to homogenize the genetic pattern at microscale while isolation by distance and by open waters could explain the small structure observed. The present study indicates that the effect of natural fragmentation in connectivity disruption can largely be counter-balanced by life history traits and overlooked details in habitat preferences. (C) 2014 Elsevier B.V. All rights reserved

Preliminary DNA-based diet assessment of a gutless carnivore, the sponge Asbestopluma hypogea

International audienceDeep-sea and underwater cave habitats are oligotrophic environments representing strong selective pressures for marine organisms. One family of sponges, Cladorhizidae, consists of very peculiar sponge species that have successfully colonised the deepest oceans as well as caves. They are not filter-feeders as every other Porifera but have evolved to become gutless carnivores. Assessing the diet of such organisms lacking a regular gut appears challenging using classic trophic ecological methods but is rather promising using molecular approaches. We here assessed the in situ diet of the carnivorous sponge Asbestopluma hypogea Vacelet & Boury-Esnault, 1995 by targeting the remaining prey DNA. Using 18S rDNA primers that do not amplify the sponge predator, we were able to amplify prey DNA over a large taxonomic range. DNA belonging to e.g. copepods, polychaetes, nematodes, brittle stars and mysids was detected. Some of these organisms were indeed visually identified as effective prey for the carnivorous sponge A. hypogea and these findings are in accordance with its opportunistic mode of feeding. When combined with stable isotope approach and morphological identification of captured prey, this method can be very useful to understand some of the diet of cladorhizid sponges. (C) 2015 Elsevier B.V. All rights reserved

Molecular and distribution data on the poorly known, elusive, cave mysid Harmelinella mariannae (Crustacea: Mysida)

International audienceMediterranean underwater marine caves harbour abundant populations of several species of mysids that are increasingly used as biological models in ecological and evolutionary studies. One exception is the species Harmelinella mariannae, described in 1989 and then hardly ever again reported in the literature. We here provide the first data on the distribution of this poorly known taxon that, contrary to expectations for a rare brooding cave dweller, we now report from Madeira Island in the nearby Atlantic, to the easternmost parts of the Mediterranean. Brief behavioural observations are added, particularly its atypical solitary habits and its feeding behaviour as a high trophic level carnivore. Molecular characterization of the different specimens captured provided three sorts of information. Mitochondrial COI and 16S haplotypes suggest different colonization waves in the Mediterranean, with one group in the Eastern Basin, two in the Marseille region in the NW part of this sea, and another group with a very wide extension from Madeira to Liguria and Malta. Mitochondrial data also support that one of the groups in Marseille might have diverged as a cryptic species of Harmelinella. 18S rRNA gene displays a single common sequence to all specimens from the four groups, and seems to confirm the original proposed placement of this taxon within the subfamily Heteromysinae, not Leptomysinae

Hydrothermal-vent alvinellid polychaete dispersal in the eastern Pacific .1. Influence of vent site distribution, bottom currents, and biological patterns

Deep-sea hydrothermal-vent habitats are typically linear, discontinuous, and short-lived. Some of the vent fauna such as the endemic polychaete family Alvinellidae are thought to lack a planktotrophic larval stage and therefore not to broadcast-release their offspring. The genetic evidence points to exchanges on a scale that seems to contradict this type of reproductive pattern. However, the rift valley may topographically rectify the bottom currents, thereby facilitating the dispersal of propagules between active vent sites separated in some cases by 10s of kilometers or more along the ridge axis. A propagule flux model based on a matrix of intersite distances, long-term current-meter data, and information on the biology and ecology of Alvinellidae was developed to test this hypothesis. Calculations of the number of migrants exchanged between two populations per generation (N-m) allowed comparisons with estimates obtained from genetic studies. N, displays a logarithmic decrease with increasing dispersal duration and reaches the critical value of 1 after 8 d when the propagule Aux model was run in standard conditions. At most, propagule traveling time cannot reasonably exceed 15-30 d, according to the model, whereas reported distances between sites would require longer lasting dispersal abilities. Two nonexclusive explanations are proposed. First, some aspects of the biology of Alvinellidae have been overlooked and long-distance dispersal does occur. Second, such dispersal never occurs in Alvinellidae, but the spatial-temporal dynamics of vent sites over geological timescales allows short-range dispersal processes to maintain gene flow

Extensive Mitochondrial mRNA Editing and Unusual Mitochondrial Genome Organization in Calcaronean Sponges

International audienceOne of the unusual features of DNA-containing organelles in general and mitochondria in particular is the frequent occurrence of RNA editing [1]. The term “RNA editing” refers to a variety of mechanistically unrelated biochemical processes that alter RNA sequence during or after transcription [2]. The editing can be insertional, deletional, or substitutional and has been found in all major types of RNAs [3, 4]. Although mitochondrial mRNA editing is widespread in some eukaryotic lineages [5-7], it is rare in animals, with reported cases limited both in their scope and in phylogenetic distribution [8-11] (see also [12]). While analyzing genomic data from calcaronean sponges Sycon ciliatum and Leucosolenia complicata, we were perplexed by the lack of recognizable mitochondrial coding sequences. Comparison of genomic and transcriptomic data from these species revealed the presence of mitochondrial cryptogenes whose transcripts undergo extensive editing. This editing consisted of single or double uridylate (U) insertions in pre-existing short poly(U) tracts. Subsequent analysis revealed the presence of similar editing in Sycon coactum and the loss of editing in Petrobiona massiliana, a hypercalcified calcaronean sponge. In addition, mitochondrial genomes of at least some calcaronean sponges were found to have a highly unusual architecture, with nearly all genes located on individual and likely linear chromosomes. Phylogenetic analysis of mitochondrial coding sequences revealed accelerated rates of sequence evolution in this group. The latter observation presents a challenge for the mutational-hazard hypothesis [13], which posits that mRNA editing should not occur in lineages with an elevated mutation rate