This study characterizes the microbial community composition over Haas Mound, one of the most prominent cold-water coral mounds of the Logachev Mound province (Rockall Bank, NE Atlantic). We outline patterns of distribution vertically -from the seafloor to the water column -and laterally -across the mound -and couple these to mound topography and hydrography. Samples of water, sediment and Lophelia pertusa were collected in 2012 and 2013 from locations that were chosen based on high definition video surveys. Temperature and current measurements were obtained at two sites at the summit and foot of Haas Mound to study near-bed hydrodynamic conditions. Overlaying water was collected from depths of 400 m as well as 5 and 10 m above the bottom using a CTD/Rosette system. Near-bottom water, sediment and L. pertusa mucus and skeleton samples were obtained with a box corer. Of all these biotopes, Roche GS-FLX amplicon sequencing targeting both Bacteria and Archaea was carried out, augmenting our understanding of deep sea microbial consortia. The pattern of similarities between samples, visualized by multi-dimensional scaling (MDS), indicates a strong link between the distribution of microbes and the specific biotopes. The microbial operational taxonomic unit (OTU) diversity was the highest in near-bottom water, which was sampled in the coral framework. For the first time, Thaumarchaeota marine group I (MGI) were found in L. pertusa mucus; Endozoicomonas was detected in skeleton, mucus and near-bottom water, whereas Mycoplasma was only detected in skeleton and near-bottom water, however not in mucus. Analysis of similarities (ANOSIM) indicates that overlaying water is well-mixed at 400 m depth but less so at 5 and 10 m above the bottom, where the composition of microbial communities differed significantly between summit, slope and off-mound. At all locations, the near-bottom water differed significantly from water at 5 m above the bottom, illustrating that the near-bottom water in between the coral framework represents a separate microbial habitat. Furthermore, the observed spatial heterogeneity in microbial communities is discussed in relation to environmental conditions. Published by CopernicusPublications on behalf of the European Geosciences Union. J. D. L. van Bleijswijk et al.: Microbial assemblages on a cold-water coral mound 1000 m 12 9 11 8 24 15 25 46 72 lander

Regeneration is an essential process for all multicellular organisms, allowing them to recover effectively from internal and external injury. This process has been studied extensively in a medical context in vertebrates, with pathways often investigated mechanistically, both to derive increased understanding and as potential drug targets for therapy. Several species from other parts of the metazoan tree of life, including Hydra, planarians and echinoderms, noted for their regenerative capabilities, have previously been targeted for study. Less well-documented for their regenerative abilities are sponges. This is surprising, as they are both one of the earliest-branching extant metazoan phyla on Earth, and are rapidly able to respond to injury. Their sessile lifestyle, lack of an external protective layer, inability to respond to predation and filter-feeding strategy all mean that regeneration is often required. In particular the demosponge genus Halisarca has been noted for its fast cell turnover and ability to quickly adjust its cell kinetic properties to repair damage through regeneration. However, while the rate and structure of regeneration in sponges has begun to be investigated, the molecular mechanisms behind this ability are yet to be catalogued. Here we describe the assembly of a reference transcriptome for Halisarca caerulea, along with additional transcriptomes noting response to injury before, shortly following (2h post-), and 12h after trauma. RNAseq reads were assembled using Trinity, annotated, and samples compared, to allow initial insight into the transcriptomic basis of sponge regenerative processes. These resources are deep, with our reference assembly containing >92.6% of the BUSCO Metazoa set of genes, and well-assembled (N50s of 836, 957, 1688 and 2032 for untreated, 2h, 12h and reference transcriptomes respectively), and therefore represent excellent qualitative resources as a bedrock for future study. The generation of transcriptomic resources from sponges before and following deliberate damage has allowed us to study particular pathways within this species responsible for repairing damage. We note particularly the involvement of the Wnt cascades in this process in this species, and detail the contents of this cascade, along with cell cycle, extracellular matrix and apoptosis-linked genes in this work. This resource represents an initial starting point for the continued development of this knowledge, given H. caerulea's ability to regenerate and position as an outgroup for comparing the process of regeneration across metazoan lineages. With this resource in place, we can begin to infer the regenerative capacity of the common ancestor of all extant animal life, and unravel the elements of regeneration in an often-overlooked clade.

Abstract. This study shows the microbial community composition over Haas Mound, one of the most prominent cold-water coral mounds of the Logachev Mound Province (Rockall Bank, NE Atlantic), outlining distribution patterns both vertically from the seafloor to the water column and laterally across the mound and coupling this to mound topography and hydrography. Samples were collected in 2012 and 2013 from biotopes that were partially chosen based on high definition video surveys that were conducted prior to sampling and included overlaying water (400 m depth and 5+10 m above the bottom (m ab)) collected with a CTD/Rosette system and near-bottom water, sediment, Lophelia pertusa mucus, and L. pertusa skeleton samples collected with a box-core. Furthermore, temperature and current measurements were obtained at two sites at the summit and foot of Haas Mound to study near-bed hydrodynamic conditions. Community composition was determined by next generation Roche 454 sequencing yielding high-resolution records of 16 S rRNA genotypes, improving our understanding of deep-sea microbial consortia. With the methods we employed we were able to report for the first time Archaea in association with L. pertusa. The pattern of similarities between samples visualized by multi-dimensional scaling (MDS), indicates a strong link between the distribution of microbes and specific biotopes. All biotopes share a number of taxa, but biotopes are distinct on basis of relative abundances and a small number of unique taxa. Similarity in microbes indicates that water is well-mixed at 400 m depth, but less so at 5 + 10 m above the bottom, where microbial communities differed between summit, slope and off mound. Even more variability was observed in the near-bottom water samples, which group according to sampling station. Likely the coral framework prevents the near-bottom water in between the branches to be vigorously mixed with the water overlaying the reef. The microbial consortium on Haas Mound appears strongly linked with the surrounding environment, making cold-water coral communities sensitive to outside environmental influences.

Abstract:Regeneration is an essential process for all multicellular organisms, allowing them to recover effectively from internal and external injury. This process has been studied extensively in a medical context in vertebrates, with pathways often investigated mechanistically, both to derive increased understanding and as potential drug targets for therapy. Several species from other parts of the metazoan tree of life, noted for their regenerative prowess, have previously been targeted for study. This allows us to understand their regenerative mechanisms and see how they could be adapted for use in medicine.Species in clades such as Hydra, planarians and echinoderms can regenerate large portions of their body, the former two clades being able to completely regenerate from even a small portion of their somatic tissue. Less well-documented for their regenerative abilities are sponges. This is surprising, as they are both one of the earliest-branching extant metazoan phyla on Earth, and are rapidly able to respond to injury. Their sessile lifestyle, lack of an external protective layer, inability to respond to predation and filter-feeding strategy all mean that regeneration is often required. In particular the demosponge genus Halisarca has been noted for its fast cell turnover and ability to quickly adjust its cell kinetic properties to repair damage through regeneration. However, while the rate and structure of regeneration in sponges has begun to be investigated, the molecular mechanisms behind this ability are yet to be catalogued.Here we describe the assembly of a reference transcriptome for Halisarca caerulea, along with additional transcriptomes noting response to injury before, shortly following (2 hrs post-), and 12 hrs after trauma. RNAseq reads were assembled using Trinity, annotated, and samples compared, to allow initial insight into the transcriptomic basis of sponge regenerative processes. These resources are deep, with our reference assembly containing more than 92.6% of the BUSCO Metazoa set of genes, and well-assembled (N50s of 836, 957, 1,688 and 2,032 for untreated, 2h, 12h and reference transcriptomes respectively), and therefore represent excellent initial resources as a bedrock for future study. The generation of transcriptomic resources from sponges before and following deliberate damage has allowed us to study particular pathways within this species responsible for repairing damage. We note particularly the involvement of the Wnt cascades in this process in this species, and detail the contents of this cascade, along with cell cycle, extracellular matrix and apoptosis-linked genes in this work.This resource represents an excellent starting point for the continued development of this knowledge, given H. caerulea's ability to regenerate and position as an outgroup for comparing the process of regeneration across metazoan lineages. With this resource in place, we can begin to infer the regenerative capacity of the common ancestor of all extant animal life, and unravel the elements of regener...

 All techniques have biases and limitations which may shape our view of holobionts  Tackling the complexity of holobionts will depend on continued technological advances especially in DNA sequencing and imaging. AbstractIt is now recognised that the biology of almost any organism cannot be fully understood without recognising the existence and potential functional importance of associated microbes. Arguably, the emergence of this holistic viewpoint may never have occurred without the development of a crucial molecular technique, 16S rDNA gene amplicon sequencing, which allowed microbial communities to be easily profiled across a broad range of contexts. A diverse array of molecular techniques are now used to profile microbial communities, infer their evolutionary histories, visualise them in host tissues, and measure their molecular activity. In this review, we examine each of these categories of measurement and inference with a focus on the questions they make tractable, and the degree to which their capabilities and limitations shape our view of the holobiont.