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The microbial assemblages of marine organisms play fundamental biological roles in their eukaryotic hosts. Studies aimed at characterizing this diversity have increased over the last decade and with the availability of high-throughput sequencing, we are now able to characterize bacteria that were non-culturable and, therefore, went undetected. With the number of marine microbiome studies growing rapidly, it is increasingly important to develop a set of "best practices" in order to accurately represent the bacterial communities present, and correct for biases. To address this, we sampled the gut communities of the pan-tropical echinoid Echinometra mathaei from two environmentally distinct populations along the Arabian Peninsula. We used three common DNA extraction procedures and compared inferred bacterial diversity from each method through 16S ribosomal RNA (rRNA) gene amplicon sequencing. Our results show that the addition of a bead-beating and lysozyme step more effectively capture traditionally difficult to lyse taxa, such as gram-positive bacteria. Further, DNA extraction method plays an important role in estimates of Shannon diversity, with diversity indices significantly higher in both sites combined when a lysozyme and bead beating step was used. Finally, we conducted a literature synthesis to highlight the current diversity of approaches used to characterize the microbiome of marine invertebrates and found that the inclusion of a lysozyme treatment is uncommon (2% of surveyed studies), despite the importance of this step in recovery of rare OTUs as shown in our study.

Extreme environmental gradients represent excellent study systems to better understand the variables that mediate patterns of genomic variation between populations. They also allow for more accurate predictions of how future environmental change might affect marine species. The Persian/Arabian Gulf is extreme in both temperature and salinity while the adjacent Gulf of Oman has conditions more typical of tropical oceans. The sea urchin Echinometra sp. EZ inhabits both of these seas and plays a critical role in coral reef health as a grazer and bioeroder, but, to date, there have been no population genomic studies on this or any urchin species in this unique region. E. sp. EZ’s life history traits (e.g., large population sizes, large reproductive clutches, and long life spans), in theory, should homogenize populations unless non-neutral processes are occurring. Here, we generated a draft genome and a restriction-site associated DNA sequencing dataset from seven populations along an environmental gradient across the Persian/Arabian Gulf and the Gulf of Oman. The estimated genome size of E. sp. EZ was 609 Mb and the heterozygosity was amongst the highest recorded for an echinoderm at 4.5%. We recovered 918 high quality SNPs from 85 individuals which we then used in downstream analyses. Population structure analyses revealed a high degree of admixture between all sites, although there was population differentiation and significant pairwise FST values between the two seas. Preliminary results suggest migration is bidirectional between the seas and nine candidate loci were identified as being under putative natural selection, including one collagen gene. This study is the first to investigate the population genomics of a sea urchin from this extreme environmental gradient and is an important contribution to our understanding of the complex spatial patterns that drive genomic divergence.

The microbiome is important in shaping organismal biology in a wide range of eukaryotic species and has been shown to play critical roles in host physiological functions and susceptibility to disease (Bayer

The maintenance of coral reef framework results from a balance between skeletal accretion and bioerosion, and this balance can be disrupted by environmental stress and disturbance. Coral reefs in northeastern Arabia exist in extreme environmental conditions and have experienced severe disturbances in recent years. This study assessed the intensity of macrobioerosion in two regionally common species, Platygyra daedalea and Cyphastrea microphthalma, at three sites within the southern Persian/Arabian Gulf and at one site in the Sea of Oman. On average, bioeroders removed 9.2 ± 1.6% of the skeletal surface area in P. daedalea and 26.4 ± 1.6% in C. microphthalma, with variation between species attributed to differences in colony morphology. Bioerosion intensity varied among sites in each species. Within the southern Arabian Gulf, both P. daedalea and C. microphthalma showed the highest bioerosion intensity at Delma, in the western region, compared with that of Saadiyat or Ras Ghanada to the east, with the elevated bioerosion at Delma consistent with a history of more extreme environmental conditions and bleaching-related disturbances. The highest bioerosion in P. daedalea occurred at Fujairah in the Sea of Oman, and this site was amongst the highest in C. microphthalma. Although this site is characterized by more benign environmental conditions, reefs in this area experienced mass coral mortality due to anoxia during a large-scale harmful algal bloom in 2008/9 and the high bioerosion in Fujairah likely represents a long-term signature of this disturbance. The intensity of macrobioerosion observed here is high compared with other regions, suggesting that that chronic exposure to long-term environmental stress and a history of disturbance may lead enhanced loss of reef framework.

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