Effects of Mergers and Core Structure on the Bulk Properties of Nearby Galaxy Clusters

We use morphological measurements and the scatter of clusters about observed and simulated scaling relations to examine the impact of merging and core-related phenomena on the structure of galaxy clusters. All relations constructed from emission-weighted mean temperature and intracluster medium mass, X-ray luminosity, isophotal size, or near-IR luminosity show a separation between cool core (CC) and non-cool core (NCC) clusters. We attribute this partially to a temperature bias in CC clusters, and partially to other cool core-related structural changes. We attempt to minimize CC/NCC separation in scaling relations by applying a uniform scale factor to CC cluster temperatures and determining the scale factor for each relation that minimizes the separation between CC and NCC populations, and by introducing central surface brightness as a third parameter in relations. The latter approach reduces scatter in relations more than temperature scaling. We compare the scatter within subsamples split by CC/NCC and morphological merger indicators. CC clusters and clusters with less substructure generally exhibit higher scatter about relations. The larger structural variations in CC clusters exit well outside the core, suggesting that a process more global than core radiative instability is at work. Simulations without cooling mechanisms also show no correlation between substructure and larger scatter about relations, indicating that any merger-related scatter increases are subtle. The results indicate that cool core related phenomena, not merging processes, are the primary contributor to scatter in scaling relations. Our analysis does not appear to support the scenario in which clusters evolve cool cores over time unless they experience major mergers. (Abridged)Comment: 18 pages, 17 figures; minor changes to text to match accepted version. To appear in Ap

Benthic megafauna of the western Clarion-Clipperton Zone, Pacific Ocean

There is a growing interest in the exploitation of deep-sea mineral deposits, particularly on the abyssal seafloor of the central Pacific Clarion-Clipperton Zone (CCZ), which is rich in polymetallic nodules. In order to effectively manage potential exploitation activities, a thorough understanding of the biodiversity, community structure, species ranges, connectivity, and ecosystem functions across a range of scales is needed. The benthic megafauna plays an important role in the functioning of deep-sea ecosystems and represents an important component of the biodiversity. While megafaunal surveys using video and still images have provided insight into CCZ biodiversity, the collection of faunal samples is needed to confirm species identifications to accurately estimate species richness and species ranges, but faunal collections are very rarely carried out. Using a Remotely Operated Vehicle, 55 specimens of benthic megafauna were collected from seamounts and abyssal plains in three Areas of Particular Environmental Interest (APEI 1, APEI 4, and APEI 7) at 3100–5100 m depth in the western CCZ. Using both morphological and molecular evidence, 48 different morphotypes belonging to five phyla were found, only nine referrable to known species, and 39 species potentially new to science. This work highlights the need for detailed taxonomic studies incorporating genetic data, not only within the CCZ, but in other bathyal, abyssal, and hadal regions, as representative genetic reference libraries that could facilitate the generation of species inventories

Expression of the blood-group-related glycosyltransferase B4galnt2 influences the intestinal microbiota in mice

Glycans on mucosal surfaces have an important role in host–microbe interactions. The locus encoding the blood-group-related glycosyltransferase β-1,4-N-acetylgalactosaminyltransferase 2 (B4galnt2) is subject to strong selective forces in natural house-mouse populations that contain a common allelic variant that confers loss of B4galnt2 gene expression in the gastrointestinal (GI) tract. We reasoned that altered glycan-dependent intestinal host–microbe interactions may underlie these signatures of selection. To determine whether B4galnt2 influences the intestinal microbial ecology, we profiled the microbiota of wild-type and B4galnt2-deficient siblings throughout the GI tract using 16S rRNA gene pyrosequencing. This revealed both distinct communities at different anatomic sites and significant changes in composition with respect to genotype, indicating a previously unappreciated role of B4galnt2 in host–microbial homeostasis. Among the numerous B4galnt2-dependent differences identified in the abundance of specific bacterial taxa, we unexpectedly detected a difference in the pathogenic genus, Helicobacter, suggesting Helicobacter spp. also interact with B4galnt2 glycans. In contrast to other glycosyltransferases, we found that the host intestinal B4galnt2 expression is not dependent on presence of the microbiota. Given the long-term maintenance of alleles influencing B4galnt2 expression by natural selection and the GI phenotypes presented here, we suggest that variation in B4galnt2 GI expression may alter susceptibility to GI diseases such as infectious gastroenteritis

Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements

Tripartite integrative and conjugative elements (ICE3) are a novel form of ICE that exist as three separate DNA regions integrated within the genomes of Mesorhizobium spp. Prior to conjugative transfer the three ICE3 regions of M. ciceri WSM1271 ICEMcSym1271 combine and excise to form a single circular element. This assembly requires three coordinated recombination events involving three site-specific recombinases IntS, IntG and IntM. Here, we demonstrate that three excisionases–or recombination directionality factors—RdfS, RdfG and RdfM are required for ICE3 excision. Transcriptome sequencing revealed that expression of ICE3 transfer and conjugation genes was induced by quorum sensing. Quorum sensing activated expression of rdfS, and in turn RdfS stimulated transcription of both rdfG and rdfM. Therefore, RdfS acts as a “master controller” of ICE3 assembly and excision. The dependence of all three excisive reactions on RdfS ensures that ICE3 excision occurs via a stepwise sequence of recombination events that avoids splitting the chromosome into a non-viable configuration. These discoveries expose a surprisingly simple control system guiding molecular assembly of these novel and complex mobile genetic elements and highlight the diverse and critical functions of excisionase proteins in control of horizontal gene transfer

Correction to: Cluster identification, selection, and description in Cluster randomized crossover trials: the PREP-IT trials

An amendment to this paper has been published and can be accessed via the original article

Biogeography and taxonomy of Ophiuroidea (Echinodermata) from the Îles Saint-Paul and Amsterdam in the southern Indian Ocean

The ophiuroid fauna of the Île Amsterdam and Île Saint-Paul territories (SPA) is reviewed. Four new species are described: Ophiolebes felli, Ophiolebes paulensis, Ophiocomina arnaudi and Amphiura remota. Recent phylogenetic results required a partial reorganisation of Ophiacanthidae and Amphiuridae genera, including the transfer of some Ophiacantha and Ophiomitrella species to a new genus Ophiosabine (O. rosea, O. anomala, O. aristata, O. cuspidata, O. densispina, O. nodosa, O. notata, O. parcita, O. pentactis, O. vivipara, O. wolfarntzi) and existing genera Ophiosemnotes (O. conferta, O. ingrata, O. corynephora, O. clavigera, O. hamata) and Ophiolebes (O. yaldwyni), Ophiacantha spectabilis to Ophiotreta in the Ophiotomidae, and some Amphioplus species to Amphiura (A, acutus, A. ctenacantha, A. cipus). The combination Ophiophycis nixastrum is restored. The SPA endemic species Ophiocten lymani and Amphiura brevispina, and the southern Australian/New Zealand species Ophiactis cuspidata and Ophiocten australis, are recognised as valid species. The North Atlantic species Ophiura ljungmani, Ophiacantha veterna, Ophiosabine cuspidata, Ophiolimna bairdi and Ophiactis nidarosiensis are recorded from the southern Indian Ocean. Shallow water specimens of Ophiura ljungmani from the Western Atlantic are re-identified as O. fallax and O. acervata. The monotypic Ophiothauma heptactis from northern Australia is synonymised with Ophiocomella sexradia and thus the genus Ophiothauma with Ophiocomella. The biogeography of the ophiuroid fauna reflects the position of the islands near the eastward-flowing currents of the South Indian Ocean gyre. The closest affinities are with faunas in the SW Indian Ocean and SE Atlantic Ocean. Despite its proximity, no species are shared with the Kerguelen Plateau to the south. The large temperature gradient across the subtropical front between Île Saint-Paul and Kerguelen appears to be a distribution limit for littoral and upper bathyal invertebrates

Convergent Evolution and Structural Adaptation to the Deep Ocean in the Protein-Folding Chaperonin CCTα

The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations; however, their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 individuals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including chaperonin-containing TCP-1 subunit α (CCTα), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examined in silico local protein stability of CCTα across the ophiuroid tree of life (967 individuals from 725 species) in a phylogenetically corrected context and found that deep-sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed by in silico global protein stability analyses. This suggests that CCTα displays not only structural but also functional adaptations to deep-water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as a “cold-shock” protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, is a key metabolic deep-sea adaptation

Dark Ophiuroid Biodiversity in a Prospective Abyssal Mine Field

The seafloor contains valuable mineral resources, including polymetallic (or manganese) nodules that form on offshore abyssal plains. The largest and most commercially attractive deposits are located in the Clarion Clipperton Fracture Zone (CCZ), in the eastern Pacific Ocean (EP) between Hawaii and Mexico, where testing of a mineral collection system is set to start soon [1]. The requirement to establish pre-mining environmental management plans has prompted numerous recent biodiversity and DNA barcoding surveys across these remote regions. Here we map DNA sequences from sampled ophiuroids (brittle stars, including post-larvae) of the CCZ and Peru Basin onto a substantial tree of life to show unprecedented levels of abyssal ophiuroid phylogenetic diversity including at least three ancient (>70 Ma), previously unknown clades. While substantial dark (unobserved) biodiversity has been reported from various microbial meta-barcoding projects [2, 3], our data show that we have considerably under-estimated the biodiversity of even the most conspicuous mega-faunal invertebrates [4] of the EP abyssal plain

Ophiotholia (Echinodermata: Ophiuroidea): A little-known deep-sea genus present in polymetallic nodule fields with the description of a new species

The Clarion Clipperton Zone (CCZ) in the Northeast Pacific Ocean holds the largest deposits of polymetallic nodules at abyssal depths. These nodules are rock formations containing valuable metals and minerals targeted for mining. They further provide diverse habitat for a range of deep-sea species. Little is known so far on the taxonomy, natural history and biogeography of these deep-sea animals which is vital for accurate assessment of the risk of species extinctions from large-scale mining. One of the most abundant megafaunal groups in the CCZ is the Ophiuroidea (brittle stars), of which Ophiotholia is one of the more abundant genera found in the area. The genus Ophiotholia has a world-wide distribution and currently holds six species