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Coral recruitment is a vital process for the maintenance and recovery of coral reefs, particularly due to their decline from global change. While it is well established that larval settlement cues significantly influence coral recruitment, the investigation of recruitment success associated with the surrounding community mainly focuses on algae. To investigate other factors controlling this process, we examined the impact of benthic invertebrate assemblages on coral recruitment using artificial reefs. Three types of artificial reefs (mono‐, bi‐, and tri‐species) with different assemblages of three common species, Pocillopora acuta, Acropora cytherea, and Tridacna maxima, were studied over 8 months. This study revealed that benthic assemblages play a significant role in coral recruitment and survival. High biodiversity was found to enhance coral recruitment and inhibit potential negative cues from A. cytherea. Our findings underscore the importance of preserving high biodiversity using not only hard coral but a wide range of phyla, including bivalves, in coral restoration efforts. Maintaining sustainable populations is an important goal to reach in the face of the multiple threats that impact coral reefs. [ABSTRACT FROM AUTHOR]

The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.

Abstract Background The development of new microarray technologies makes custom long oligonucleotide arrays affordable for many experimental applications, notably gene expression analyses. Reliable results depend on probe design quality and selection. Probe design strategy should cope with the limited accuracy of de novo gene prediction programs, and annotation up-dating. We present a novel in silico procedure which addresses these issues and includes experimental screening, as an empirical approach is the best strategy to identify optimal probes in the in silico outcome. Findings We used four criteria for in silico probe selection: cross-hybridization, hairpin stability, probe location relative to coding sequence end and intron position. This latter criterion is critical when exon-intron gene structure predictions for intron-rich genes are inaccurate. For each coding sequence (CDS), we selected a sub-set of four probes. These probes were included in a test microarray, which was used to evaluate the hybridization behavior of each probe. The best probe for each CDS was selected according to three experimental criteria: signal-to-noise ratio, signal reproducibility, and representative signal intensities. This procedure was applied for the development of a gene expression Agilent platform for the filamentous fungus Podospora anserina and the selection of a single 60-mer probe for each of the 10,556 P. anserina CDS. Conclusions A reliable gene expression microarray version based on the Agilent 44K platform was developed with four spot replicates of each probe to increase statistical significance of analysis.

The ragged sea hare (Bursatella leachii) and the long-tailed sea hare (Stylocheilus striatus) are two widely distributed species of benthic heterobranch sea slugs. In this paper, integrative taxonomic analyses have been conducted to detect possible cryptic diversity. Our results revealed that both nominal species are actually species complexes, consisting of five genetically distinct taxa. Two of them belong to the genus Bursatella and three to the genus Stylocheilus. The name B. leachii is retained for a widely distributed species, present in the Atlantic, the Mediterranean, and parts of the Indo-Pacific region. The name B. ocelligera is resurrected for the other species, restricted to the Indo-Pacific and co-occurring with B. leachii in that area. With the present data, it is not possible to test whether B. leachii and B. ocelligera have evolved allopatrically in the Atlantic and Indo-Pacific or sympatrically in the latter. Bursatella leachii has been able to maintain gene flow between the Atlantic and the Indo-Pacific Oceans, possibly because of a combined effect of the Agulhas Leakage process and the ability to survive the colder waters of South Africa. On the contrary, the three species of Stylocheilus are allopatric; the name S. striatus is retained for an Indo-Pacific species, while the names S. polyomma and S. rickettsi are resurrected for species inhabiting the Western Atlantic and the Eastern Pacific respectively. Finally, the discovery of a museum specimen mistakenly identified as B. leachii , but bearing a shell in its adult form, led to the resurrection of the genus Phycophila , previously synonymised with Aplysia. Phycophila euchlora , the only species described to date, is distributed in the Central and Western Pacific Ocean. In this study, we analysed specimens of two species of pantropical sea slugs, Bursatella leachii and Stylocheilus striatus , comparing morphology and DNA sequences of individuals across all the distributional range. Our results reveal that there are two distinct Bursatella species and three distinct species of Stylocheilus , which we formally redescribed in this paper. An additional genus, Phycophilla , discovered from a previously misidentified specimen, was resurrected from synonymy in this study. [ABSTRACT FROM AUTHOR]

Lack of wastewater treatment efficiency causes receiving seawaters and bivalve molluscan shellfish to become contaminated, which can lead to public health issues. Six wastewater samples, five seawater samples and three batches of giant clams from Tahiti (French Polynesia) were investigated for the presence of enteric viruses, but also if present, for the diversity, infectivity and integrity of human adenoviruses (HAdV). Enteroviruses (EV), sapoviruses (SaV) and human polyomaviruses (HPyV) were detected in all wastewater samples. In decreasing frequency, noroviruses (NoV) GII and HAdV, rotaviruses (RoV), astroviruses (AsV), NoV GI and finally hepatitis E viruses (HEV) were also observed. Nine types of infectious HAdV were identified. HPyV and EV were found in 80% of seawater samples, NoV GII in 60%, HAdV and SaV in 40% and AsV and RoV in 20%. NoV GI and HEV were not detected in seawater. Intact and infectious HAdV-41 were detected in one of the two seawater samples that gave a positive qPCR result. Hepatitis A viruses were never detected in any water types. Analysis of transcriptomic data from giant clams revealed homologues of fucosyltransferases (FUT genes) involved in ligand biosynthesis that strongly bind to certain NoV strains, supporting the giant clams ability to bioaccumulate NoV. This was confirmed by the presence of NoV GII in one of the three batches of giant clams placed in a contaminated marine area. Overall, all sample types were positive for at least one type of virus, some of which were infectious and therefore likely to cause public health concerns. [ABSTRACT FROM AUTHOR]