Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 40579, doi:10.1038/srep40579.Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.This research was supported by a KAUST-WHOI Post-doctoral Partnership Award to M.J.N. and a KAUST-WHOI Special Academic Partnership Funding Reserve Award to C.R.V. and A.A. Additional research was supported from baseline funds to C.R.V. by the King Abdullah University of Science and Technology (KAUST)

Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Applied Microbiology and Biotechnology 100 (2016): 8315–8324, doi:10.1007/s00253-016-7777-0.Endozoicomonas bacteria are emerging as extremely diverse and flexible symbionts of numerous marine hosts inhabiting oceans worldwide. Their hosts range from simple invertebrate species, such as sponges and corals, to complex vertebrates, such as fish. Although widely distributed, the functional role of Endozoicomonas within their host microenvironment is not well understood. In this review, we provide a summary of the currently recognized hosts of Endozoicomonas and their global distribution. Next, the potential functional roles of Endozoicomonas, particularly in light of recent microscopic, genomic, and genetic analyses, are discussed. These analyses suggest that Endozoicomonas typically reside in aggregates within host tissues, have a free-living stage due to their large genome sizes, show signs of host and local adaptation, participate in host-associated protein and carbohydrate transport and cycling, and harbour a high degree of genomic plasticity due to the large proportion of transposable elements residing in their genomes. This review will finish with a discussion on the methodological tools currently employed to study Endozoicomonas and host interactions and review future avenues for studying complex host-microbial symbioses.This work was supported by a KAUST-WHOI Post-doctoral Partnership Award to MJN and a KAUST-WHOI Special Academic Partnership Funding Reserve Award to CRV and AA. Research in this study was further supported by baseline research funds to CRV by KAUST and NSF award OCE-1233612 to AA

From cholera to corals: viruses as drivers of virulence in a major coral bacterial pathogen

Disease is an increasing threat to reef-building corals. One of the few identified pathogens of coral disease is the bacterium Vibrio coralliilyticus. In Vibrio cholerae, infection by a bacterial virus (bacteriophage) results in the conversion of non-pathogenic strains to pathogenic strains and this can lead to cholera pandemics. Pathogenicity islands encoded in the V. cholerae genome play an important role in pathogenesis. Here we analyse five whole genome sequences of V. coralliilyticus to examine whether virulence is similarly driven by horizontally acquired elements. We demonstrate that bacteriophage genomes encoding toxin genes with homology to those found in pathogenic V. cholerae are integrated in V. coralliilyticus genomes. Virulence factors located on chromosomal pathogenicity islands also exist in some strains of V. coralliilyticus. The presence of these genetic signatures indicates virulence in V. coralliilyticus is driven by prophages and other horizontally acquired elements. Screening for pathogens of coral disease should target conserved regions in these elements

Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISME Journal 11 (2017): 186–200, doi:10.1038/ismej.2016.95.Reef-building corals are well regarded not only for their obligate association with endosymbiotic algae, but also with prokaryotic symbionts, the specificity of which remains elusive. To identify the central microbial symbionts of corals, their specificity across species and conservation over geographic regions, we sequenced partial SSU ribosomal RNA genes of Bacteria and Archaea from the common corals Stylophora pistillata and Pocillopora verrucosa across 28 reefs within seven major geographical regions. We demonstrate that both corals harbor Endozoicomonas bacteria as their prevalent symbiont. Importantly, catalyzed reporter deposition–fluorescence in situ hybridization (CARD–FISH) with Endozoicomonas-specific probes confirmed their residence as large aggregations deep within coral tissues. Using fine-scale genotyping techniques and single-cell genomics, we demonstrate that P. verrucosa harbors the same Endozoicomonas, whereas S. pistillata associates with geographically distinct genotypes. This specificity may be shaped by the different reproductive strategies of the hosts, potentially uncovering a pattern of symbiont selection that is linked to life history. Spawning corals such as P. verrucosa acquire prokaryotes from the environment. In contrast, brooding corals such as S. pistillata release symbiont-packed planula larvae, which may explain a strong regional signature in their microbiome. Our work contributes to the factors underlying microbiome specificity and adds detail to coral holobiont functioning.This research was supported by a KAUST-WHOI Post-doctoral Partnership Award to MN and a KAUST-WHOI Special Academic Partnership Funding Reserve Award to CRV and AA. Research in this study was further supported by baseline research funds to CRV by KAUST and NSF award OCE-1233612 to AA. RR was supported by the ct-PIRE Project, Robert Lemelson Fellowship, Graduate Research Award (UCLA), Women Divers Hall of Fame—Sister Fund Conservation Award and a Betty and E. P. Franklin Grant in Tropical Biology and Conservation

Analytical solution of generalized Burton--Cabrera--Frank equations for growth and post--growth equilibration on vicinal surfaces

We investigate growth on vicinal surfaces by molecular beam epitaxy making use of a generalized Burton--Cabrera--Frank model. Our primary aim is to propose and implement a novel analytical program based on a perturbative solution of the non--linear equations describing the coupled adatom and dimer kinetics. These equations are considered as originating from a fully microscopic description that allows the step boundary conditions to be directly formulated in terms of the sticking coefficients at each step. As an example, we study the importance of diffusion barriers for adatoms hopping down descending steps (Schwoebel effect) during growth and post-growth equilibration of the surface.Comment: 16 pages, REVTeX 3.0, IC-DDV-94-00

Reflection High Energy Electron Diffraction (RHEED) Intensity Oscillations: Growth Modes and Growth Rates: A Critique

The origin of and diffraction effects associated with reflection high energy electron diffraction (RHEED) intensity oscillations which occur during layer-by-layer growth of epitaxial thin films of III-V compounds by molecular beam epitaxy (MBE) are explained. It is shown that on (001) oriented substrates the period of the oscillations is in general a direct measure of the film growth rate which corresponds to the group III element flux. There are, however, exceptions to this simple concept including growth under group III rich-conditions, vicinal plane growth and growth from pulsed beams; each is considered. On non-(001) low index orientations, the RHEED oscillation period only provides a measure of the growth rate over a very limited range of conditions. The fundamental reason appears to be the more restricted reactivity between the group III and V elements, so the oscillations are induced by the group V element, not the group III, which is quite different from (001) surfaces, at least for conventional growth conditions. Finally, growth modes and strain relaxation differences between (001) and (110)-based growth of InAs on GaAs are illustrated. It is shown that there is no real relationship between strain and growth mode and it is suggested that adatom mobility is the essential parameter which determines growth mode. In more general terms, it appears that kinetic factors rather than equilibrium considerations are responsible for the growth mode. Models based on purely equilibrium concepts are therefore unlikely to have general validity

Fabrication and Characterization of Modulation-Doped ZnSe/(Zn,Cd)Se (110) Quantum Wells: A New System for Spin Coherence Studies

We describe the growth of modulation-doped ZnSe/(Zn,Cd)Se quantum wells on (110) GaAs substrates. Unlike the well-known protocol for the epitaxy of ZnSe-based quantum structures on (001) GaAs, we find that the fabrication of quantum well structures on (110) GaAs requires significantly different growth conditions and sample architecture. We use magnetotransport measurements to confirm the formation of a two-dimensional electron gas in these samples, and then measure transverse electron spin relaxation times using time-resolved Faraday rotation. In contrast to expectations based upon known spin relaxation mechanisms, we find surprisingly little difference between the spin lifetimes in these (110)-oriented samples in comparison with (100)-oriented control samples.Comment: To appear in Journal of Superconductivity (Proceedings of 3rd Conference on Physics and Applications of Spin-dependent Phenomena in Semiconductors

On the Feasibility of Imaging Carbonatite-Hosted Rare Earth Element Deposits Using Remote Sensing

Rare earth elements (REEs) generate characteristic absorption features in visible to shortwave infrared (VNIR-SWIR) reflectance spectra. Neodymium (Nd) has among the most prominent absorption features of the REEs and thus represents a key pathfinder element for the REEs as a whole. Given that the world’s largest REE deposits are associated with carbonatites, we present spectral, petrographic, and geochemical data from a predominantly carbonatitic suite of rocks that we use to assess the feasibility of imaging REE deposits using remote sensing. Samples were selected to cover a wide range of extents and styles of REE mineralization, and encompass calcio-, ferro- and magnesio-carbonatites. REE ores from the Bayan Obo (China) and Mountain Pass (United States) mines, as well as REE-rich alkaline rocks from the Motzfeldt and Ilímaussaq intrusions in Greenland, were also included in the sample suite. The depth and area of Nd absorption features in spectra collected under laboratory conditions correlate positively with the Nd content of whole-rock samples. The wavelength of Nd absorption features is predominantly independent of sample lithology and mineralogy. Correlations are most reliable for the two absorption features centered at ~744 and ~802 nm that can be observed in samples containing as little as ~1,000 ppm Nd. By convolving laboratory spectra to the spectral response functions of a variety of remote sensing instruments we demonstrate that hyperspectral instruments with capabilities equivalent to the operational Airborne Visible-Infrared Imaging Spectrometer (AVIRIS) and planned Environmental Mapping and Analysis Program (EnMAP) systems have the spectral resolutions necessary to detect Nd absorption features, especially in high-grade samples with economically relevant REE accumulations (Nd > 30,000 ppm). Adding synthetic noise to convolved spectra indicates that correlations between Nd absorption area and whole-rock Nd content only remain robust when spectra have signal-to-noise ratios in excess of ~250:1. Although atmospheric interferences are modest across the wavelength intervals relevant for Nd detection, most REE-rich outcrops are too small to be detectable using satellite-based platforms with >30-m spatial resolutions. However, our results indicate that Nd absorption features should be identifiable in high-quality, airborne, hyperspectral datasets collected at meter-scale spatial resolutions. Future deployment of hyperspectral instruments on unmanned aerial vehicles could enable REE grade to be mapped at the centimeter scale across whole deposits

National innovation and knowledge performance: The role of higher education teaching and training

This paper acknowledges the role of the higher education system (HES) in the production of knowledge and human capital. However, most of the literature attributes this production to the second (research activities) and third (exploitation of teaching and research activities) mission. This paper proposes to investigate the under explored role of the first mission (teaching) of HES in the production of national innovation