Recent Submissions

  • Apocarotenoids Involved in Plant Development and Stress Response.

    Felemban, Abrar; Braguy, Justine; Zurbriggen, Matias D; Al-Babili, Salim (Frontiers in plant science, Frontiers Media SA, 2019-10-16) [Article]
    Carotenoids are isoprenoid pigments synthesized by all photosynthetic organisms and many heterotrophic microorganisms. They are equipped with a conjugated double-bond system that builds the basis for their role in harvesting light energy and in protecting the cell from photo-oxidation. In addition, the carotenoids polyene makes them susceptible to oxidative cleavage, yielding carbonyl products called apocarotenoids. This oxidation can be catalyzed by carotenoid cleavage dioxygenases or triggered nonenzymatically by reactive oxygen species. The group of plant apocarotenoids includes important phytohormones, such as abscisic acid and strigolactones, and signaling molecules, such as β-cyclocitral. Abscisic acid is a key regulator of plant's response to abiotic stress and is involved in different developmental processes, such as seed dormancy. Strigolactone is a main regulator of plant architecture and an important signaling molecule in the plant-rhizosphere communication. β-Cyclocitral, a volatile derived from β-carotene oxidation, mediates the response of cells to singlet oxygen stress. Besides these well-known examples, recent research unraveled novel apocarotenoid growth regulators and suggests the presence of yet unidentified ones. In this review, we describe the biosynthesis and biological functions of established regulatory apocarotenoids and touch on the recently identified anchorene and zaxinone, with emphasis on their role in plant growth, development, and stress response.
  • Apocarotenoids: Old and New Mediators of the Arbuscular Mycorrhizal Symbiosis.

    Fiorilli, Valentina; Wang, Jian You; Bonfante, Paola; Lanfranco, Luisa; Al-Babili, Salim (Frontiers in plant science, Frontiers Media SA, 2019-10-16) [Article]
    Plants utilize hormones and other small molecules to trigger and coordinate their growth and developmental processes, adapt and respond to environmental cues, and communicate with surrounding organisms. Some of these molecules originate from carotenoids that act as universal precursors of bioactive metabolites arising through oxidation of the carotenoid backbone. This metabolic conversion produces a large set of compounds known as apocarotenoids, which includes the plant hormones abscisic acid (ABA) and strigolactones (SLs) and different signaling molecules. An increasing body of evidence suggests a crucial role of previously identified and recently discovered carotenoid-derived metabolites in the communication with arbuscular mycorrhizal (AM) fungi and the establishment of the corresponding symbiosis, which is one of the most relevant plant-fungus mutualistic interactions in nature. In this review, we provide an update on the function of apocarotenoid hormones and regulatory metabolites in AM symbiosis, highlighting their effect on both partners.
  • Single-Molecule Förster Resonance Energy Transfer Methods for Real-Time Investigation of the Holliday Junction Resolution by GEN1.

    Sobhy, Mohamed Abdelmaboud; Bralic, Amer; Raducanu, Vlad-Stefan; Tehseen, Muhammad; Ouyang, Yujing; Takahashi, Masateru; Rashid, Fahad; Zaher, Manal; Hamdan, Samir (Journal of visualized experiments : JoVE, MyJove Corporation, 2019-10-15) [Article]
    Bulk methods measure the ensemble behavior of molecules, in which individual reaction rates of the underlying steps are averaged throughout the population. Single-molecule Förster resonance energy transfer (smFRET) provides a recording of the conformational changes taking place by individual molecules in real-time. Therefore, smFRET is powerful in measuring structural changes in the enzyme or substrate during binding and catalysis. This work presents a protocol for single-molecule imaging of the interaction of a four-way Holliday junction (HJ) and gap endonuclease I (GEN1), a cytosolic homologous recombination enzyme. Also presented are single-color and two-color alternating excitation (ALEX) smFRET experimental protocols to follow the resolution of the HJ by GEN1 in real-time. The kinetics of GEN1 dimerization are determined at the HJ, which has been suggested to play a key role in the resolution of the HJ and has remained elusive until now. The techniques described here can be widely applied to obtain valuable mechanistic insights of many enzyme-DNA systems.
  • A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells.

    Cali, Corrado; Kare, Kalpana; Agus, Marco; Veloz Castillo, Maria Fernanda; Boges, Daniya; Hadwiger, Markus; Magistretti, Pierre J. (Journal of visualized experiments : JoVE, MyJove Corporation, 2019-10-15) [Article]
    Serial sectioning and subsequent high-resolution imaging of biological tissue using electron microscopy (EM) allow for the segmentation and reconstruction of high-resolution imaged stacks to reveal ultrastructural patterns that could not be resolved using 2D images. Indeed, the latter might lead to a misinterpretation of morphologies, like in the case of mitochondria; the use of 3D models is, therefore, more and more common and applied to the formulation of morphology-based functional hypotheses. To date, the use of 3D models generated from light or electron image stacks makes qualitative, visual assessments, as well as quantification, more convenient to be performed directly in 3D. As these models are often extremely complex, a virtual reality environment is also important to be set up to overcome occlusion and to take full advantage of the 3D structure. Here, a step-by-step guide from image segmentation to reconstruction and analysis is described in detail.
  • Plasmodium kinesin-8X associates with mitotic spindles and is essential for oocyst development during parasite proliferation and transmission.

    Zeeshan, Mohammad; Shilliday, Fiona; Liu, Tianyang; Abel, Steven; Mourier, Tobias; Ferguson, David J P; Rea, Edward; Stanway, Rebecca R; Roques, Magali; Williams, Desiree; Daniel, Emilie; Brady, Declan; Roberts, Anthony J; Holder, Anthony A.; Pain, Arnab; Le Roch, Karine G; Moores, Carolyn A; Tewari, Rita (PLoS pathogens, Public Library of Science (PLoS), 2019-10-11) [Article]
    Kinesin-8 proteins are microtubule motors that are often involved in regulation of mitotic spindle length and chromosome alignment. They move towards the plus ends of spindle microtubules and regulate the dynamics of these ends due, at least in some species, to their microtubule depolymerization activity. Plasmodium spp. exhibit an atypical endomitotic cell division in which chromosome condensation and spindle dynamics in the different proliferative stages are not well understood. Genome-wide shared orthology analysis of Plasmodium spp. revealed the presence of two kinesin-8 motor proteins, kinesin-8X and kinesin-8B. Here we studied the biochemical properties of kinesin-8X and its role in parasite proliferation. In vitro, kinesin-8X has motility and depolymerization activities like other kinesin-8 motors. To understand the role of Plasmodium kinesin-8X in cell division, we used fluorescence-tagging and live cell imaging to define its location, and gene targeting to analyse its function, during all proliferative stages of the rodent malaria parasite P. berghei life cycle. The results revealed a spatio-temporal involvement of kinesin-8X in spindle dynamics and an association with both mitotic and meiotic spindles and the putative microtubule organising centre (MTOC). Deletion of the kinesin-8X gene revealed a defect in oocyst development, confirmed by ultrastructural studies, suggesting that this protein is required for oocyst development and sporogony. Transcriptome analysis of Δkinesin-8X gametocytes revealed modulated expression of genes involved mainly in microtubule-based processes, chromosome organisation and the regulation of gene expression, supporting a role for kinesin-8X in cell division. Kinesin-8X is thus required for parasite proliferation within the mosquito and for transmission to the vertebrate host.
  • Adhesion to coral surface as a potential sink for marine microplastics.

    Martin, Cecilia; Corona, Elena; Mahadik, Gauri A; Duarte, Carlos M. (Environmental pollution (Barking, Essex : 1987), Elsevier BV, 2019-10-11) [Article]
    Only 1% of plastic entering the ocean is found floating on its surface, with high loads in ocean accumulation zones and semi-enclosed seas, except for the Red Sea, which supports one of the lowest floating plastic loads worldwide. Given the extension of reefs in the Red Sea, we hypothesize a major role of scleractinian corals as sinks, through suspension-feeding, and assessed microplastic removal rates by three Red Sea coral species. Experimental evidence showed removal rates ranging from 0.25 × 10-3 to 14.8 × 10-3 microplastic particles polyp-1 hour-1, among species. However, this was only 2.2 ± 0.6% of the total removal rate, with passive removal through adhesion to the coral surface being 40 times higher than active removal through suspension-feeding. These results point at adhesion of plastic to coral reef structures as a major sink for microplastics suspended in the water column after sinking, helping explain low concentrations in Red Sea surface waters.
  • Remotely sensing phytoplankton size structure in the Red Sea

    Gittings, John; Brewin, Robert J.W.; Raitsos, Dionysios E.; Kheireddine, Malika; Ouhssain, Mustapha; Jones, Burton; Hoteit, Ibrahim (Remote Sensing of Environment, Elsevier BV, 2019-10-09) [Article]
    Phytoplankton size structure impacts ocean food-web dynamics and biogeochemical cycling, and is thus an important ecological indicator that can be utilised to quantitatively evaluate the state of marine ecosystems. Potential alterations to size structure are predicted to occur in tropical regions under future scenarios of climate change. Therefore, there is an increasing requirement for the synoptic monitoring of phytoplankton size structure in marine systems. The Red Sea remains a comparatively unexplored tropical marine ecosystem, particularly with regards to its large-scale biological dynamics. Using an in situ pigment dataset acquired in the Red Sea, we parameterise a two-component, abundance-based phytoplankton size model and apply it to remotely-sensed observations of chlorophyll-a (Chl-a) concentration, to infer Chl-a in two size classes of phytoplankton, small cells <2 μm in size (picophytoplankton) and large cells >2 μm in size. Satellite-derived estimates of phytoplankton size structure are in good agreement with corresponding in situ measurements and also capture the spatial variability related to regional mesoscale dynamics. Our analysis reveals that, for the estimation of Chl-a in the two size classes, the model performs comparably or in some cases better, to validations in other oceanic regions. Our model parameterisation will be useful for future studies on the seasonal and interannual variability of phytoplankton size classes in the Red Sea, which may ultimately be relevant for understanding trophic linkages between phytoplankton size structure and fisheries, and the development of marine management strategies.
  • Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs.

    Alam, Tanvir; Alazmi, Meshari; Naser, Rayan Mohammad Mahmoud; Huser, Franceline; Momin, Afaque Ahmad Imtiyaz; Astro, Veronica; Hong, Seungbeom; Walkiewicz, Katarzyna Wiktoria; Canlas, Christian G; Huser, Raphaël; Ali, Amal J.; Merzaban, Jasmeen; Adamo, Antonio; Jaremko, Mariusz; Jaremko, Lukasz; Bajic, Vladimir B.; Gao, Xin; Arold, Stefan T. (Bioinformatics (Oxford, England), Oxford University Press (OUP), 2019-10-05) [Article]
    MOTIVATION:Leucine-aspartic acid (LD) motifs are short linear interaction motifs (SLiMs) that link paxillin family proteins to factors controlling cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood. RESULTS:To enable a proteome-wide assessment of LD motifs, we developed an active-learning based framework (LDmotif finder; LDMF) that iteratively integrates computational predictions with experimental validation. Our analysis of the human proteome revealed a dozen new proteins containing LD motifs. We found that LD motif signalling evolved in unicellular eukaryotes more than 800 Myr ago, with paxillin and vinculin as core constituents, and nuclear export signal (NES) as a likely source of de novo LD motifs. We show that LD motif proteins form a functionally homogenous group, all being involved in cell morphogenesis and adhesion. This functional focus is recapitulated in cells by GFP-fused LD motifs, suggesting that it is intrinsic to the LD motif sequence, possibly through their effect on binding partners. Our approach elucidated the origin and dynamic adaptations of an ancestral SLiM, and can serve as a guide for the identification of other SLiMs for which only few representatives are known. AVAILABILITY:LDMF is freely available online at www.cbrc.kaust.edu.sa/ldmf; Source code is available at https://github.com/tanviralambd/LD/. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.
  • Disruption of the coordination between host circadian rhythms and malaria parasite development alters the duration of the intraerythrocytic cycle

    Subudhi, Amit; O'Donnell, Aidan John; Ramaprasad, Abhinay; Abkallo, Hussein M.; Kaushik, Abhinav; Ansari, Hifzur Rahman; Abdel-Haleem, Alyaa M.; Rached, Fathia Ben; Kaneko, Osamu; Culleton, Richard; Reece, Sarah E.; Pain, Arnab (Cold Spring Harbor Laboratory, 2019-10-03) [Preprint]
    Malaria parasites complete their intra-erythrocytic developmental cycle (IDC) in multiples of 24 hours (depending on the species), suggesting a circadian basis to the asexual cell cycle, but the mechanism controlling this periodicity is unknown. Combining in vivo and in vitro approaches using rodent and human malaria parasites, we reveal that: (i) 57% of Plasmodium chabaudi genes exhibit 24 h circadian periodicity in transcription; (ii) 58% of these genes lose transcriptional rhythmicity when the IDC is out-of-synchrony with host rhythms; (iii) 9% of Plasmodium falciparum genes show circadian transcription under free-running conditions; (iv) Serpentine receptor 10 (SR10) has a circadian transcription profile and disrupting it in rodent malaria parasites shortens the IDC by 2-3 hours; (v) Multiple processes including DNA replication and the ubiquitin and proteasome pathways are affected by loss of coordination with host rhythms and by disruption of SR10. Our results show that malaria parasites are at least partly responsible for scheduling their IDCs explaining the fitness benefits of coordination with host rhythms.
  • Can Fish and Cell Phones Teach Us about Our Health?

    Lee, Michael A; Duarte, Carlos M.; Eguíluz, V. M.; Heller, Daniel A; Langer, Robert; Meekan, Mark G; Sikes, Hadley D; Srivastava, Mani; Strano, Michael S; Wilson, Rory P (ACS sensors, American Chemical Society (ACS), 2019-10-03) [Article]
    Biologging is a scientific endeavor that studies the environment and animals within it by outfitting the latter with sensors of their dynamics as they roam freely in their natural habitats. As wearable technologies advance for the monitoring of human health, it may be instructive to reflect on the successes and failures of biologging in field biology over the past few decades. Several lessons may be of value. Physiological sensors can
  • An improved indirect evaporative cooler experimental investigation

    Shahzad, Muhammad Wakil; Burhan, Muhammad; Ybyraiymkul, Doskhan; Oh, Seung Jin; Ng, Kim Choon (Applied Energy, Elsevier BV, 2019-10-01) [Article]
    Air conditioning has enhanced the work efficiency and improved life style by maintaining comfortable environment. The growing demand of air conditioning has negative impact on energy and environment. In 2015, air conditioning consumed 6% of total global electricity produced and it is expected to increase to 20% by 2050. The leveling-off conventional chiller’s efficiency at 0.85 ± 0.03 kW/Rton due to pairing of dehumidification and cooling processes in one machine is not only the major reason of high energy consumption but also the key limitation in efficiency improvement. The de-coupling of dehumidification and cooling processes can be one of the solution to achieve the quantum jump in the performance, 0.6 ± 0.03 kW/Rton, by improving individual processes. We proposed an improved indirect evaporative cooler system for sensible cooling that can be combined with dehumidification processes to achieve sustainable cooling goals. The experimentation on 800 mm long and 280 mm wide generic cell showed that it can produce temperature differential up to 10 °C with small area of heat transfer. It was showed that the proposed vertical heat exchanger configuration with multi point injection of working air is the best configuration of the indirect evaporative cooler, achieving coefficient of performance level of 78 for cooling alone. We expect that overall coefficient of performance level of 7–8 is achievable by incorporating efficient dehumidification processes. We also presented detailed design parameters that can be used as a reference for commercial system design.
  • 3D Analysis of Ordered Porous Polymeric Particles using Complementary Electron Microscopy Methods

    Alvarez, Juan; Saudino, Giovanni; Musteata, Valentina-Elena; Madhavan, Poornima; Genovese, Alessandro; Behzad, Ali Reza; Sougrat, Rachid; Boi, Cristiana; Peinemann, Klaus-Viktor; Nunes, Suzana Pereira (Scientific Reports, Springer Science and Business Media LLC, 2019-09-27) [Article]
    Highly porous particles with internal triply periodic minimal surfaces were investigated for sorption of proteins. The visualization of the complex ordered morphology requires complementary advanced methods of electron microscopy for 3D imaging, instead of a simple 2D projection: transmission electron microscopy (TEM) tomography, slice-and-view focused ion beam (FIB) and serial block face (SBF) scanning electron microscopy (SEM). The capability of each method of 3D image reconstruction was demonstrated and their potential of application to other synthetic polymeric systems was discussed. TEM has high resolution for details even smaller than 1 nm, but the imaged volume is relatively restricted (2.5 μm)3. The samples are pre-sliced in an ultramicrotome. FIB and SBF are coupled to a SEM. The sample sectioning is done in situ, respectively by an ion beam or an ultramicrotome, SBF, a method so far mostly applied only to biological systems, was particularly highly informative to reproduce the ordered morphology of block copolymer particles with 32-54 nm nanopores and sampling volume (20 μm)3.
  • Factors Regulating the Relationship Between Total and Size-Fractionated Chlorophyll-a in Coastal Waters of the Red Sea.

    Brewin, Robert J W; Moran, Xose Anxelu G.; Raitsos, Dionysios E; Gittings, John A; Calleja Cortes, Maria de Lluch; Viegas, Miguel; Ansari, Mohd Ikram; Al-otaibi, Najwa Aziz; Huete-Stauffer, Tamara M; Hoteit, Ibrahim (Frontiers in microbiology, Frontiers Media SA, 2019-09-26) [Article]
    Phytoplankton biomass and size structure are recognized as key ecological indicators. With the aim to quantify the relationship between these two ecological indicators in tropical waters and understand controlling factors, we analyzed the total chlorophyll-a concentration, a measure of phytoplankton biomass, and its partitioning into three size classes of phytoplankton, using a series of observations collected at coastal sites in the central Red Sea. Over a period of 4 years, measurements of flow cytometry, size-fractionated chlorophyll-a concentration, and physical-chemical variables were collected near Thuwal in Saudi Arabia. We fitted a three-component model to the size-fractionated chlorophyll-a data to quantify the relationship between total chlorophyll and that in three size classes of phytoplankton [pico- (<2 μm), nano- (2-20 μm) and micro-phytoplankton (>20 μm)]. The model has an advantage over other more empirical methods in that its parameters are interpretable, expressed as the maximum chlorophyll-a concentration of small phytoplankton (pico- and combined pico-nanophytoplankton, Cpm and Cp,nm , respectively) and the fractional contribution of these two size classes to total chlorophyll-a as it tends to zero (D p and D p,n ). Residuals between the model and the data (model minus data) were compared with a range of other environmental variables available in the dataset. Residuals in pico- and combined pico-nanophytoplankton fractions of total chlorophyll-a were significantly correlated with water temperature (positively) and picoeukaryote cell number (negatively). We conducted a running fit of the model with increasing temperature and found a negative relationship between temperature and parameters Cpm and Cp,nm and a positive relationship between temperature and parameters D p and D p,n . By harnessing the relative red fluorescence of the flow cytometric data, we show that picoeukaryotes, which are higher in cell number in winter (cold) than summer (warm), contain higher chlorophyll per cell than other picophytoplankton and are slightly larger in size, possibly explaining the temperature shift in model parameters, though further evidence is needed to substantiate this finding. Our results emphasize the importance of knowing the water temperature and taxonomic composition of phytoplankton within each size class when understanding their relative contribution to total chlorophyll. Furthermore, our results have implications for the development of algorithms for inferring size-fractionated chlorophyll from satellite data, and for how the partitioning of total chlorophyll into the three size classes may change in a future ocean.
  • Functional metagenomic analysis of dust-associated microbiomes above the Red Sea.

    Aalismail, Nojood; Ngugi, David K; Diaz Rua, Ruben; Alam, Intikhab; Cusack, Michael; Duarte, Carlos M. (Scientific reports, Springer Science and Business Media LLC, 2019-09-26) [Article]
    Atmospheric transport is a major vector for the long-range transport of microbial communities, maintaining connectivity among them and delivering functionally important microbes, such as pathogens. Though the taxonomic diversity of aeolian microorganisms is well characterized, the genomic functional traits underpinning their survival during atmospheric transport are poorly characterized. Here we use functional metagenomics of dust samples collected on the Global Dust Belt to initiate a Gene Catalogue of Aeolian Microbiome (GCAM) and explore microbial genetic traits enabling a successful aeolian lifestyle in Aeolian microbial communities. The GCAM reported here, derived from ten aeolian microbial metagenomes, includes a total of 2,370,956 non-redundant coding DNA sequences, corresponding to a yield of ~31 × 106 predicted genes per Tera base-pair of DNA sequenced for the aeolian samples sequenced. Two-thirds of the cataloged genes were assigned to bacteria, followed by eukaryotes (5.4%), archaea (1.1%), and viruses (0.69%). Genes encoding proteins involved in repairing UV-induced DNA damage and aerosolization of cells were ubiquitous across samples, and appear as fundamental requirements for the aeolian lifestyle, while genes coding for other important functions supporting the aeolian lifestyle (chemotaxis, aerotaxis, germination, thermal resistance, sporulation, and biofilm formation) varied among the communities sampled.
  • 3D cellular reconstruction of cortical glia and parenchymal morphometric analysis from Serial Block-Face Electron Microscopy of juvenile rat.

    Cali, Corrado; Agus, Marco; Kare, Kalpana; Boges, Daniya J; Lehväslaiho, Heikki; Hadwiger, Markus; Magistretti, Pierre J. (Progress in neurobiology, Elsevier BV, 2019-09-25) [Article]
    With the rapid evolution in the automation of serial electron microscopy in life sciences, the acquisition of terabyte-sized datasets is becoming increasingly common. High resolution serial block-face imaging (SBEM) of biological tissues offers the opportunity to segment and reconstruct nanoscale structures to reveal spatial features previously inaccessible with simple, single section, two-dimensional images, with a particular focus on glial cells, whose reconstruction efforts in literature are still limited, compared to neurons. Here, we imaged a 750000 cubic micron volume of the somatosensory cortex from a juvenile P14 rat, with 20 nm accuracy. We recognized a total of 186 cells using their nuclei, and classified them as neuronal or glial based on features of the soma and the processes. We reconstructed for the first time 4 almost complete astrocytes and neurons, 4 complete microglia and 4 complete pericytes, including their intracellular mitochondria, 186 nuclei and 213 myelinated axons. We then performed quantitative analysis on the three-dimensional models. Out of the data that we generated, we observed that neurons have larger nuclei, which correlated with their lesser density, and that astrocytes and pericytes have a higher surface to volume ratio, compared to other cell types. All reconstructed morphologies represent an important resource for computational neuroscientists, as morphological quantitative information can be inferred, to tune simulations that take into account the spatial compartmentalization of the different cell types.
  • Effect of D-ring C-3’ methylation of strigolactone analogs on their transcription regulating activity in rice

    Jamil, Muhammad; Haider, Imran; Kountche, Boubacar Amadou; Al-Babili, Salim (Plant Signaling & Behavior, Informa UK Limited, 2019-09-25) [Article]
    Strigolactones (SLs) are a well-known class of plant hormones, which are involved in a number of developmental and adaptation processes and mediate different interspecific interactions. In spite of the growing knowledge on SL biosynthesis and signal transduction, effects of structural modifications on the activity and efficiency of SLs and their analogs remain largely elusive. SLs are characterized by the presence of a lactone ring (D-ring) that is connected by an enol ether bridge to a second moiety. In this study, we investigated the effect of additional D-ring methylation of SL analogs on their transcription regulating activity. For this purpose, we compared the SL analogs MP13 and AR8, which differ only by the presence of a methyl group at the C-3ʹ atom in the latter. Transcription regulating activity was determined by quantitative real-time PCR measurement of transcript levels of SL-dependent, feed-back regulated genes in treated wild type and ccd7 mutant rice seedlings. Results obtained indicate that C-3ʹ methylation reduces the transcription regulating activity, as shown by the more pronounced suppression of the SL biosynthesis genes DWARF27 (D27) and CAROTENOID CLEAVAGE DIOXYGENASES (CCD7 and CCD8) and higher induction of the SL signaling repressor gene DWARF53 (D53) in MP13 treated seedlings. These results are consistent with a recent study on the biological activities of MP13 and AR8.
  • A genomic view of the reef-building coral Porites lutea and its microbial symbionts

    Robbins, Steven J.; ReFuGe2020 Consortium; Chan, Cheong Xin; Chan, Cheong Xin; Messer, Lauren F.; Messer, Lauren F.; Ying, Hua; Baker, Alexander; Bell, Sara C.; Ragan, Mark A.; Ragan, Mark A.; Miller, David J.; Foret, Sylvain; Voolstra, Christian R.; Tyson, Gene W.; Bourne, David G. (Nature Microbiology, Springer Science and Business Media LLC, 2019-09-23) [Article]
    Corals and the reef ecosystems that they support are in global decline due to increasing anthropogenic pressures such as climate change. However, effective reef conservation strategies are hampered by a limited mechanistic understanding of coral biology and the functional roles of the diverse microbial communities that underpin coral health. Here, we present an integrated genomic characterization of the coral species Porites lutea and its microbial partners. High-quality genomes were recovered from P. lutea, as well as a metagenome-assembled Cladocopium C15 (the dinoflagellate symbiont) and 52 bacterial and archaeal populations. Comparative genomic analysis revealed that many of the bacterial and archaeal genomes encode motifs that may be involved in maintaining association with the coral host and in supplying fixed carbon, B-vitamins and amino acids to their eukaryotic partners. Furthermore, mechanisms for ammonia, urea, nitrate, dimethylsulfoniopropionate and taurine transformation were identified that interlink members of the holobiont and may be important for nutrient acquisition and retention in oligotrophic waters. Our findings demonstrate the critical and diverse roles that microorganisms play within the coral holobiont and underscore the need to consider all of the components of the holobiont if we are to effectively inform reef conservation strategies.
  • Similar bacterial communities on healthy and injured skin of black tip reef sharks

    Pogoreutz, Claudia; Gore, Mauvis A.; Perna, Gabriela; Millar, Catriona; Nestler, Robert; Ormond, Rupert F.; Clarke, Christopher R.; Voolstra, Christian R. (Animal Microbiome, Springer Science and Business Media LLC, 2019-09-16) [Article]
    Background Sharks are in severe global decline due to human exploitation. The additional concern of emerging diseases for this ancient group of fish, however, remains poorly understood. While wild-caught and captive sharks may be susceptible to bacterial and transmissible diseases, recent reports suggest that shark skin may harbor properties that prevent infection, such as a specialized ultrastructure or innate immune properties, possibly related to associated microbial assemblages. To assess whether bacterial community composition differs between visibly healthy and insulted (injured) shark skin, we compared bacterial assemblages of skin covering the gills and the back from 44 wild-caught black-tip reef sharks (Carcharhinus melanopterus) from the Amirante Islands (Seychelles) via 16S rRNA gene amplicon sequencing. Results Shark skin-associated bacterial communities were diverse (5971 bacterial taxa from 375 families) and dominated by three families of the phylum Proteobacteria typical of marine organisms and environments (Rhodobacteraceae, Alteromonadaceae, Halomonadaceae). Significant differences in bacterial community composition of skin were observed for sharks collected from different sites, but not between healthy or injured skin samples or skin type (gills vs. back). The core microbiome (defined as bacterial taxa present in ≥50% of all samples) consisted of 12 bacterial taxa, which are commonly observed in marine organisms, some of which may be associated with animal host health. Conclusion The conserved bacterial community composition of healthy and injured shark skin samples suggests absence of severe bacterial infections or substantial pathogen propagation upon skin insult. While a mild bacterial infection may have gone undetected, the overall conserved bacterial community implies that bacterial function(s) may be maintained in injured skin. At present, the contribution of bacteria, besides intrinsic animal host factors, to counter skin infection and support rapid wound healing in sharks are unknown. This represents clear knowledge gaps that should be addressed in future work, e.g. by screening for antimicrobial properties of skin-associated bacterial isolates.
  • The many faced symbiotic snakelocks anemone (Anemonia viridis, Anthozoa): host and symbiont genetic differentiation among colour morphs

    Porro, Barbara; Mallien, Cédric; Hume, Benjamin; Pey, Alexis; Aubin, Emilie; Christen, Richard; Voolstra, Christian R.; Furla, Paola; Forcioli, Didier (Heredity, Springer Science and Business Media LLC, 2019-09-16) [Article]
    How can we explain morphological variations in a holobiont? The genetic determinism of phenotypes is not always obvious and could be circumstantial in complex organisms. In symbiotic cnidarians, it is known that morphology or colour can misrepresent a complex genetic and symbiotic diversity. Anemonia viridis is a symbiotic sea anemone from temperate seas. This species displays different colour morphs based on pigment content and lives in a wide geographical range. Here, we investigated whether colour morph differentiation correlated with host genetic diversity or associated symbiotic genetic diversity by using RAD sequencing and symbiotic dinoflagellate typing of 140 sea anemones from the English Channel and the Mediterranean Sea. We did not observe genetic differentiation among colour morphs of A. viridis at the animal host or symbiont level, rejecting the hypothesis that A. viridis colour morphs correspond to species level differences. Interestingly, we however identified at least four independent animal host genetic lineages in A. viridis that differed in their associated symbiont populations. In conclusion, although the functional role of the different morphotypes of A. viridis remains to be determined, our approach provides new insights on the existence of cryptic species within A. viridis.
  • Monitoring of the toxic dinoflagellate Alexandrium catenella in Osaka Bay, Japan using a massively parallel sequencing (MPS)-based technique

    Nagai, Satoshi; Chen, Hungyen; Kawakami, Yoko; Yamamoto, Keigo; Sildever, Sirje; Kanno, Nanako; Oikawa, Hiroshi; Yasuike, Motoshige; Nakamura, Yoji; Hongo, Yuki; Fujiwara, Atushi; Kobayashi, Takanori; Gojobori, Takashi (Harmful Algae, Elsevier BV, 2019-09-12) [Article]
    Since 2002, blooms of Alexandrium catenella sensu Fraga et al. (2015) and paralytic shellfish toxicity events have occurred almost yearly in Osaka Bay, Japan. To better understand the triggers for reoccurring A. catenella blooms in Osaka Bay, phytoplankton community was monitored during the spring seasons of 2012–2015. Monitoring was performed using massively parallel sequencing (MPS)-based technique on amplicon sequences of the 18S rRNA gene. Dense blooms of A. catenella occurred every year except in 2012, however, there was no significant correlation with the environmental parameters investigated. Plankton community diversity decreased before and middle of the A. catenella blooms, suggesting that the decline in diversity could be an indicator for the bloom occurrence. The yearly abundance pattern of A. catenella cells obtained by morphology-based counting coincided with the relative sequence abundances, which supports the effectiveness of MPS-based phytoplankton monitoring.

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