RSS 1.0Marine Science Program
For more information visit: https://bese.kaust.edu.sa/study/Pages/MarS.aspx
Recent Submissions
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Engineered production of isoprene from the model green microalga Chlamydomonas reinhardtii(Metabolic Engineering Communications, Elsevier BV, 2023-03-23) [Article]Isoprene is a clear, colorless, volatile 5-carbon hydrocarbon that is one monomer of all cellular isoprenoids and a platform chemical with multiple applications in industry. Many plants have evolved isoprene synthases (IspSs) with the capacity to liberate isoprene from dimethylallyl diphosphate (DMADP) as part of cellular thermotolerance mechanisms. Isoprene is hydrophobic and volatile, rapidly leaves plant tissues and is one of the main carbon emission sources from vegetation globally. The universality of isoprenoid metabolism allows volatile isoprene production from microbes expressing heterologous IspSs. Here, we compared heterologous overexpression from the nuclear genome and localization into the plastid of four plant terpene synthases (TPs) in the green microalga Chlamydomonas reinhardtii. Using sealed vial mixotrophic cultivation, direct quantification of isoprene production was achieved from the headspace of living cultures, with the highest isoprene production observed in algae expressing the Ipomoea batatas IspS. Perturbations of the downstream carotenoid pathway through keto carotenoid biosynthesis enhanced isoprene titers, which could be further enhanced by increasing flux towards DMADP through heterologous co-expression of a yeast isopentenyl-PP delta isomerase. Multiplexed controlled-environment testing revealed that cultivation temperature, rather than illumination intensity, was the main factor affecting isoprene yield from the engineered alga. This is the first report of heterologous isoprene production from a eukaryotic alga and sets a foundation for further exploration of carbon conversion to this commodity chemical.
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Molecular insights into the Darwin paradox of coral reefs from the sea anemone Aiptasia(Science Advances, American Association for the Advancement of Science (AAAS), 2023-03-15) [Article]Symbiotic cnidarians such as corals and anemones form highly productive and biodiverse coral reef ecosystems in nutrient-poor ocean environments, a phenomenon known as Darwin’s paradox. Resolving this paradox requires elucidating the molecular bases of efficient nutrient distribution and recycling in the cnidarian-dinoflagellate symbiosis. Using the sea anemone Aiptasia, we show that during symbiosis, the increased availability of glucose and the presence of the algae jointly induce the coordinated up-regulation and relocalization of glucose and ammonium transporters. These molecular responses are critical to support symbiont functioning and organism-wide nitrogen assimilation through glutamine synthetase/glutamate synthase–mediated amino acid biosynthesis. Our results reveal crucial aspects of the molecular mechanisms underlying nitrogen conservation and recycling in these organisms that allow them to thrive in the nitrogen-poor ocean environments.
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Abiotic selection of microbial genome size in the global ocean(Nature Communications, Springer Science and Business Media LLC, 2023-03-13) [Article]Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little is currently known about how the size of prokaryotic genomes evolves in the global ocean and whether patterns reflect shifts in resource availability in the epipelagic and relatively stable deep-sea environmental conditions. Using 364 marine microbial metagenomes, we investigate how the average genome size of uncultured planktonic prokaryotes varies across the tropical and polar oceans to the hadal realm. We find that genome size is highest in the perennially cold polar ocean, reflecting elongation of coding genes and gene dosage effects due to duplications in the interior ocean microbiome. Moreover, the rate of change in genome size due to temperature is 16-fold higher than with depth up to 200 m. Our results demonstrate how environmental factors can influence marine microbial genome size selection and ecological strategies of the microbiome.
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Differential susceptibility of Red Sea Pocilloporidae corals to UVB highlights photoacclimation potential(Frontiers in Marine Science, Frontiers Media SA, 2023-03-13) [Article]Despite being exposed to extreme water temperatures and solar irradiances, Red Sea corals are relatively resistant to bleaching. While their thermal tolerance is well described, little is known about their resistance to ultraviolet-B radiation (UVB). Here, we performed a short-term (2 days) UVB-removal incubation with Stylophora pistillata, and in situ measurements with Pocillopora verrucosa complemented by a long-term (46 days) transplantation and UVB-removal experiment. Using a suite of physiological parameters (effective quantum yield (Fv’/Fm’), oxidative stress (lipid peroxidation, LPO), and primary production), we assessed the impacts of UVB on the physiology and acclimation capacity of Red Sea corals. Shielding S. pistillata from UVB did not change the gross primary production or Fv’/Fm’, and respiration and LPO in the host remained unaffected. In situ, P. verrucosa exhibited less varying and significantly higher Fv’/Fm’ in 8 m depth (0.61 ± 0.04) than in 4 m (0.52 ± 0.06), 2 m (0.51 ± 0.09), and 0.5 m (0.50 ± 0.11), where water temperatures ranged from 30.5–33.4, 30.6–34.0, 30.8–34.5, 30.6–37.3°C and daily UVB exposures averaged 0.9, 2.9, 11.8 and 21.4 kJ m-2, respectively. Fv’/Fm’ correlated the strongest with UVB (-0.57), followed by PAR (-0.54) and temperature (-0.40), suggesting that UVB is a key determinant of photosynthetic efficiency. Fv’/Fm’ of upward transplanted specimens (T 1m) was initially decreased but gradually increased and reached the same values as shallow corals (1 m) after 44 days. UVB removal significantly increased the Fv’/Fm’ of transplanted corals in the first 20 days. Oxidative stress was initially highest in T 1m samples under full sunlight but equalized with 1 m specimens by day 46, whereas oxidative stress was significantly reduced by day 4 in T 1m corals sheltered from UVB. Overall, UVB-removal generally had little impact on the physiology of shallow-water S. pistillata and P. verrucosa but considerably accelerated the acclimation of upward transplanted corals. Our study highlights that UVB is a crucial stressor governing the photoacclimation capacity of these Red Sea coral species.
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Phylogenetics and taxonomy of the scleractinian coral family Euphylliidae(Contributions to Zoology, Brill Academic Publishers, 2023-03-13) [Article]The family Euphylliidae consists of reef-building zooxanthellate scleractinian corals distributed across the Indo-Pacific. Seven extant genera comprising a total of 22 valid species are currently recognised. Recent studies have re-organised the taxonomy of the family at the genus level based on molecular and morphological data, including a comprehensive revision of Euphyllia and the resurrection of Fimbriaphyllia. Here, three mitochondrial loci (coi, 12S rRNA, and 16S rRNA) were sequenced and morphological examinations were conducted at three scales (macro/micromorphology and microstructure of the skeleton, and polyp morphology) to study the phylogeny and taxonomy of Euphylliidae. We analysed a total of 11 valid species collected from seven Indo-Pacific localities. The monotypic genus Coeloseris, currently in Agariciidae, was also investigated since previous molecular data suggested a close relationship with the Euphylliidae. Molecular and morphological phylogenetic trees were broadly concordant in the definition of genus-level clades. All analysed genera, i.e., Ctenella, Euphyllia, Fimbriaphyllia, Galaxea, and Gyrosmilia, were reciprocally monophyletic based on molecular results. Coeloseris was nested within the family and, therefore, is formally moved into Euphylliidae. Updated morphological diagnoses are provided for each investigated genus. This study further demonstrated that a phylogenetic classification of scleractinian corals can be achieved by applying a combined morpho-molecular approach. Finally, we encourage phylogenetic and taxonomic studies of the euphylliid taxa not yet analysed molecularly, such as the monotypic genera Montigyra and Simplastrea.
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Disparate population and holobiont structure of pocilloporid corals across the Red Sea gradient demonstrate species-specific evolutionary trajectories(Molecular Ecology, Wiley, 2023-03-03) [Article]Global habitat degradation heightens the need to better understand patterns of genetic connectivity and diversity of marine biota across geographical ranges to guide conservation efforts. Corals across the Red Sea are subject to pronounced environmental differences, but studies so far suggest that animal populations are largely connected, excepting evidence for a genetic break between the northern-central and southern regions. Here, we investigated population structure and holobiont assemblage of two common pocilloporid corals, Pocillopora verrucosa and Stylophora pistillata, across the Red Sea. We found little evidence for population differentiation in P. verrucosa, except for the southernmost site. Conversely, S. pistillata exhibited a complex population structure with evidence for within-reef and regional genetic differentiation, in line with differences in their reproductive mode (P. verrucosa is a broadcast spawner and S. pistillata is a brooder). Analysis for genomic loci under positive selection identified 85 sites (18 of which were in coding sequences) that distinguished the southern P. verrucosa population from the remainder of the Red Sea population. By comparison, we found 128 loci (24 of which were residing in coding sequences) in S. pistillata with evidence for local adaptation at various sites. Functional annotation of the underlying proteins revealed putative roles in the response to stress, lipid metabolism, transport, cytoskeletal rearrangement, and ciliary function (among others). Microbial assemblages of both coral species showed pervasive association with microalgal symbionts from the genus Symbiodinium (former clade A) and bacteria from the genus Endozoicomonas that exhibited significant differences according to host genotype and environment. The disparity of population genetic and holobiont assemblage patterns even between closely related species (family Pocilloporidae) highlights the need for multispecies investigations to better understand the role of the environment in shaping evolutionary trajectories. It further emphasizes the importance of networks of reef reserves to achieve conservation of genetic variants critical to the future survival of coral ecosystems.
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Using standardized fish-specific autonomous reef monitoring structures ( FARMS ) to quantify cryptobenthic fish communities(Methods in Ecology and Evolution, Wiley, 2023-03-03) [Article]Biodiversity inventories and monitoring techniques for marine fishes often overlook small (<5 cm), bottom-associated (‘cryptobenthic’) fishes, and few standardized, comparative assessments of cryptobenthic fish communities exist. We sought to develop a standardized, quantitative survey method for cryptobenthic fishes that permits their sampling across a variety of habitats and conditions. Fish-specific autonomous reef monitoring structures (FARMS) are designed to sample cryptobenthic fishes using a suite of accessible and affordable materials. To generate a variety of microhabitats, FARMS consist of three layers of stacked PVC pipes in three different sizes, as well as a bottom and top level of loose PVC-pipe fragments in a mesh basket. We deployed FARMS across a variety of habitats, including coral reefs, seagrass beds, oyster reefs, mangroves, and soft-bottom habitats across six locations (Hawai'i, Texas, Panama, Saudi Arabia, Brazil, and Curaçao). From shallow estuaries to coral reefs beyond 100 m depth, FARMS attracted distinct communities of native cryptobenthic fishes with strong site or habitat specificity. Comparing the FARMS to communities sampled with alternative methods (enclosed clove-oil stations on coral reefs in Panama and oyster sampling units on oyster reefs in Texas) suggests that FARMS yield a subset of cryptobenthic fish species that are representative of those present on local coral and oyster reefs. While FARMS yield fewer individuals per sample, they are efficient sampling devices relative to the sampled area. We demonstrate that FARMS represent a useful tool for standardized collections of cryptobenthic fishes. While natural substrata are bound to yield more mature communities with a larger number of individuals and wider range of specialist species, the potential to deploy and retrieve FARMS in turbid environments, beyond regular SCUBA depth, and where fish collections using anaesthetics or ichthyocides are forbidden suggests that they are a valuable complementary technique to survey fishes in aquatic ecosystems. Deploying FARMS in locations and habitats where cryptobenthic fish communities have not been studied in detail may yield many valuable specimens of unknown or poorly known species.
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Ideas and perspectives. The fluctuating nature of oxygen shapes the ecology of aquatic habitats and their biogeochemical cycles: the aquatic oxyscape(Copernicus GmbH, 2023-03-03) [Preprint]Oxygen availability is a pivotal factor for ecosystem functioning and the resistance of organisms to the effect of climate change in aquatic habitats. Although extensive work has been made to assess the effect of oxygen on marine and freshwater biota, many studies did not capture the ecological importance of oxygen variations. Overlooking the fluctuating nature of oxygen may cause potential biases in the design and implementation of management policies of aquatic habitats. Conceptual perspectives on the dynamic nature of oxygen fluctuations have been raised in the scientific community to enhance the understanding of the effect of oxygen on the physiology and the ecology of aquatic species and the biogeochemical functioning of the ecosystems. A growing number of empirical works are outlining a novel conceptual framework that considers the magnitude of oxygen fluctuation as a key variable that explains adaptation to stress conditions. Oxygen in productive aquatic habitats shows large fluctuations at diel and seasonal scales, exposing aquatic species from conditions of extreme supersaturation to anoxia. Recent research indicates that such fluctuation tunes the physiological plasticity of the animal in response to thermal stresses. In this contribution, we provide compelling evidence based on current research that the fluctuating oxygen landscape, here defined as “oxyscape”, has an important role in aquatic animal physiology and adaptation and the ecosystem biogeochemistry. We propose that the oxyscape should be considered in the modelling and managing policies of aquatic ecosystems.
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Mitigating the ecological collapse of coral reef ecosystems(EMBO reports, EMBO, 2023-03-02) [Article]Effective strategies to preserve coral reef ecosystems
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A thermophilic chemolithoautotrophic bacterial consortium suggests a mutual relationship between bacteria in extreme oligotrophic environments(Communications Biology, Springer Science and Business Media LLC, 2023-03-01) [Article]A thermophilic, chemolithoautotrophic, and aerobic microbial consortium (termed carbonitroflex) growing in a nutrient-poor medium and an atmosphere containing N2, O2, CO2, and CO is investigated as a model to expand our understanding of extreme biological systems. Here we show that the consortium is dominated by Carbonactinospora thermoautotrophica (strain StC), followed by Sphaerobacter thermophilus, Chelatococcus spp., and Geobacillus spp. Metagenomic analysis of the consortium reveals a mutual relationship among bacteria, with C. thermoautotrophica StC exhibiting carboxydotrophy and carbon-dioxide storage capacity. C. thermoautotrophica StC, Chelatococcus spp., and S. thermophilus harbor genes encoding CO dehydrogenase and formate oxidase. No pure cultures were obtained under the original growth conditions, indicating that a tightly regulated interactive metabolism might be required for group survival and growth in this extreme oligotrophic system. The breadwinner hypothesis is proposed to explain the metabolic flux model and highlight the vital role of C. thermoautotrophica StC (the sole keystone species and primary carbon producer) in the survival of all consortium members. Our data may contribute to the investigation of complex interactions in extreme environments, exemplifying the interconnections and dependency within microbial communities.
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The role of the cryptobiome and its associated microbial community in coral reef biogeochemical cycling(2023-03) [Thesis]
Advisors: Daffonchio, Daniele; Carvalho, Susana
Committee member: Rosado, Alexandre S.Tropical coral reefs are highly productive ecosystems thriving in oligotrophic waters, a phenomenon facilitated by efficient but delicate biogeochemical cycling within reef communities. Global climate change and local stressors are driving phase shifts from coral- to non-calcifier-dominated states in reefs worldwide, substantially altering reef biogeochemical functioning. While major benthic players such as coral and macroalgae have been investigated in detail regarding carbon and nutrient dynamics, the less conspicuous “reef cryptobiome” (sensu Carvalho et al., 2019) – comprising most of reef diversity – has only recently gained attention. Autonomous Reef Monitoring Structures (ARMS) have recently been developed to sample coral reef cryptobenthic communities in a non-destructive and standardised way, allowing exploration of these often overlooked biota. Here, 16 ARMS were deployed for seven months in four distinct habitats dominated by different benthic players (i.e., four units per habitat) in a nearshore Red Sea coral reef to investigate the cryptobiome associated with proxies of varying benthic states. Two of these habitats were coral-dominated, and one each dominated by turf algae or coral rubble. To assess the biogeochemical fluxes of pioneering cryptobenthic communities, ARMS were incubated in situ prior to retrieval using customised chambers. Subsequently, 16S rRNA gene amplicon and shotgun metagenomic sequencing of the ARMS sessile (i.e., encrusting) fractions were performed to link observed fluxes with prokaryotic taxonomic and functional profiles, particularly regarding nitrogen cycling. The results show that the pioneering cryptobiome represents a significant source of inorganic nutrients and that its associated microbial communities facilitate the mineralisation and assimilation of organic matter and provide crucial genetic functional pathways for nitrogen cycling. Functional similarities among habitats suggested functional redundancy despite variation in bacterial community composition. Hence, the reef cryptobiome can be considered an important biogeochemical player in coral reefs, actively shaping the abiotic conditions within niches of the reef framework and driving the recruitment and persistence of crytobenthic and other reef organisms. As communities associated with the algae-dominated reef habitat were most distinct compositionally and biogeochemically, and as non-calcifiers are becoming more dominant in many reefs, this has implications for intensifying phase shifts in coral reefs worldwide. Future ARMS studies will also benefit from adjustment of sample processing and molecular protocols, resulting in higher sample throughput and lower costs in times of increased application of ARMS. -
Mycobiome structure does not affect field litter decomposition in Eucalyptus and Acacia plantations(Frontiers in microbiology, Frontiers Media SA, 2023-02-28) [Article]Mixed tree plantations have been studied because of their potential to improve biomass production, ecosystem diversity, and soil quality. One example is a mixture of Eucalyptus and Acacia trees, which is a promising strategy to improve microbial diversity and nutrient cycling in soil. We examined how a mixture of these species may influence the biochemical attributes and fungal community associated with leaf litter, and the effects on litter decomposition. We studied the litter from pure and mixed plantations, evaluating the effects of plant material and incubation site on the mycobiome and decomposition rate using litterbags incubated in situ. Our central hypothesis was litter fungal community would change according to incubation site, and it would interfere in litter decomposition rate. Both the plant material and the incubation locale significantly affected the litter decomposition. The origin of the litter was the main modulator of the mycobiome, with distinct communities from one plant species to another. The community changed with the incubation time but the incubation site did not influence the mycobiome community. Our data showed that litter and soil did not share the main elements of the community. Contrary to our hypothesis, the microbial community structure and diversity lacked any association with the decomposition rate. The differences in the decomposition pattern are explained basically as a function of the exchange of nitrogen compounds between the litter.
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Linker histone H1 modulates defense priming and immunity in plants(Nucleic Acids Research, Oxford University Press (OUP), 2023-02-25) [Article]Linker H1 histones play an important role in animal and human pathogenesis, but their function in plant immunity is poorly understood. Here, we analyzed mutants of the three canonical variants of Arabidopsis H1 histones, namely H1.1, H1.2 and H1.3. We observed that double h1.1h1.2 and triple h1.1h1.2h1.3 (3h1) mutants were resistant to Pseudomonas syringae and Botrytis cinerea infections. Transcriptome analysis of 3h1 mutant plants showed H1s play a key role in regulating the expression of early and late defense genes upon pathogen challenge. Moreover, 3h1 mutant plants showed enhanced production of reactive oxygen species and activation of mitogen activated protein kinases upon pathogen-associated molecular pattern (PAMP) treatment. However, 3h1 mutant plants were insensitive to priming with flg22, a well-known bacterial PAMP which induces enhanced resistance in WT plants. The defective defense response in 3h1 upon priming was correlated with altered DNA methylation and reduced global H3K56ac levels. Our data place H1 as a molecular gatekeeper in governing dynamic changes in the chromatin landscape of defense genes during plant pathogen interaction.
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Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes(Nature Communications, Springer Science and Business Media LLC, 2023-02-24) [Article]Microbial communities respond to temperature with physiological adaptation and compositional turnover. Whether thermal selection of enzymes explains marine microbiome plasticity in response to temperature remains unresolved. By quantifying the thermal behaviour of seven functionally-independent enzyme classes (esterase, extradiol dioxygenase, phosphatase, beta-galactosidase, nuclease, transaminase, and aldo-keto reductase) in native proteomes of marine sediment microbiomes from the Irish Sea to the southern Red Sea, we record a significant effect of the mean annual temperature (MAT) on enzyme response in all cases. Activity and stability profiles of 228 esterases and 5 extradiol dioxygenases from sediment and seawater across 70 locations worldwide validate this thermal pattern. Modelling the esterase phase transition temperature as a measure of structural flexibility confirms the observed relationship with MAT. Furthermore, when considering temperature variability in sites with non-significantly different MATs, the broadest range of enzyme thermal behaviour and the highest growth plasticity of the enriched heterotrophic bacteria occur in samples with the widest annual thermal variability. These results indicate that temperature-driven enzyme selection shapes microbiome thermal plasticity and that thermal variability finely tunes such processes and should be considered alongside MAT in forecasting microbial community thermal response.
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Global biogeography of the glacier-fed stream microbiome(Copernicus GmbH, 2023-02-22) [Presentation]Glacier-fed streams (GFSs) serve as headwaters to many of the world’s largest river networks. Although being characterized by extreme environmental conditions (i.e., low water temperatures, oligotrophy) GFSs host an underappreciated microbial biodiversity, especially within benthic biofilms which play pivotal roles in downstream biogeochemical cycles. Yet, we still lack a global overview of the GFS biofilm microbiome. In addition, little is known on how environmental conditions shape bacterial diversity, and how these relationships drive global distribution patterns. This is particularly important as mountain glaciers are currently vanishing at a rapid pace due to global warming. Here, we used 16S rRNA gene sequencing data from the Vanishing Glaciers project to conduct a first comprehensive analysis of the benthic microbiome from 148 GFSs across 11 mountain ranges. Our analyses revealed marked biogeographic patterns in the GFS microbiome, mainly driven by the replacement of phylogenetically closely related taxa. Strikingly, the GFS microbiome was characterized by pronounced level of endemism, with >58% of the Amplicon Sequence Variants (ASVs) being specific to one mountain range. Consistent with the marked dissimilarities across mountain ranges, we found a very small taxonomic core including only 200 ASVs, yet accounting for >25% of the total relative abundance of the ASVs. Finally, we found that spatial effects such as dispersal limitation, isolation and spatially autocorrelated environmental conditions overwhelmed the effect of the environment by itself on benthic biofilm beta diversity. Our findings shed light on the previously unresolved global diversity and biogeography of the GFS microbiome now at risk across the world’s major mountain ranges because of rapidly shrinking glaciers.
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Disturbance of primary producer communities disrupts the thermal limits of the associated aquatic fauna.(The Science of the total environment, Elsevier BV, 2023-02-14) [Article]Environmental fluctuation forms a framework of variability within which species have evolved. Environmental fluctuation includes predictability, such as diel cycles of aquatic oxygen fluctuation driven by primary producers. Oxygen availability and fluctuation shape the physiological responses of aquatic animals to warming, so that, in theory, oxygen fluctuation could influence their thermal ecology. We describe annual oxygen variability in agricultural drainage channels and show that disruption of oxygen fluctuation through dredging of plants reduces the thermal tolerance of freshwater animals. We compared the temperature responses of snails, amphipods, leeches and mussels exposed to either natural oxygen fluctuation or constant oxygen in situ under different acclimation periods. Oxygen saturation in channel water ranged from c. 0 % saturation at night to >300 % during the day. Temperature showed normal seasonal variation and was almost synchronous with daily oxygen fluctuation. A dredging event in 2020 dramatically reduced dissolved oxygen variability and the correlation between oxygen and temperature was lost. The tolerance of invertebrates to thermal stress was significantly lower when natural fluctuation in oxygen availability was reduced and decoupled from temperature. This highlights the importance of natural cycles of variability and the need to include finer scale effects, including indirect biological effects, in modelling the ecosystem-level consequences of climate change. Furthermore, restoration and management of primary producers in aquatic habitats could be important to improve the thermal protection of aquatic invertebrates and their resistance to environmental variation imposed by climate change.
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Novel infrastructure for coral gardening and reefscaping(Frontiers in Marine Science, Frontiers Media SA, 2023-02-10) [Article]Since 1950, coral abundance has declined worldwide by an estimated 60%, and further dramatic declines are predicted. Although global reductions in carbon emissions are essential to prevent further loss, coral reef restoration has become imperative to maintain the ecosystem services that coral reefs provide to humans at local scales. Yet, currently coral restoration and gardening efforts are too expensive to scale up due to the labor-intensive nature of the methods and low success rates. Here, we present a suite of technologies that improve coral reef restoration and rehabilitation’s scalability, efficiency, and effectiveness. Our modular technologies are designed to streamline in and ex situ nursery workflows, reduce maintenance times, solve problems in transporting corals to outplanting sites, and enable rapid outplanting on natural and artificial substrates. These novel structures can act as coral seeding hubs, which placed strategically, can have the capacity to enhance coral reproduction and replenish degraded nearby reefs with larvae. They can be applied to coral restoration and reefscaping, complemented by unique eco-friendly, low-carbon-emission structures for the creation of architecturally and visually appealing habitats and underwater landscapes. Our technologies integrate novel monitoring approaches that support intelligent solutions to track genotypes, optimize and control stock management, apply assisted evolution approaches, and adaptive management through long-term monitoring.
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Marine picoplankton metagenomes from eleven vertical profiles obtained by the Malaspina Expedition in the tropical and subtropical oceans(Cold Spring Harbor Laboratory, 2023-02-06) [Preprint]The Ocean microbiome has a crucial role on Earth's biogeochemical cycles, but also represents a tremendous potential for biological applications as part of the blue-biotechnology. During the last decade, global cruises such as Tara Oceans or the Malaspina Expedition have expanded our knowledge on the diversity and genetic repertoire of marine microbes. Nevertheless, there is still a gap of knowledge on broad scale patterns between photic and bathypelagic dark ocean microbes derived by the lack of detailed vertical profiles covering contrasting oceans regions. Here we present 76 microbial metagenomes of the picoplankton size fraction (0.2-3.0 microns) from 11 stations along the Malaspina Expedition circumnavigation that cover vertical profiles sampling at 7 depths, from surface to the 4000m deep (or the sea floor in shallower waters). The Malaspina Microbial Vertical Profiles metagenomes (MProfile) dataset produced 1.66 Tbp of raw DNA sequences and assembled them into a total 25.3 Gbp. After gene prediction and annotation, we built a 46.3 million non-redundant gene compendium with their corresponding annotations (M-GeneDB-VP), clustered at 95% sequence similarity. This dataset will be a valuable resource for exploring the functional and taxonomic connectivity between the photic and bathypelagic ocean at a global scale, while increasing our general knowledge on the Ocean microbiome.
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PlantACT! - how to tackle the climate crisis.(Trends in plant science, Elsevier BV, 2023-02-03) [Article]Greenhouse gas (GHG) emissions have created a global climate crisis which requires immediate interventions to mitigate the negative effects on all aspects of life on this planet. As current agriculture and land use contributes up to 25% of total GHG emissions, plant scientists take center stage in finding possible solutions for a transition to sustainable agriculture and land use. In this article, the PlantACT! (Plants for climate ACTion!) initiative of plant scientists lays out a road map of how and in which areas plant scientists can contribute to finding immediate, mid-term, and long-term solutions, and what changes are necessary to implement these solutions at the personal, institutional, and funding levels.
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Ultrastructural and proteomic evidence for the presence of a putative nucleolus in an Archaeon(Frontiers in microbiology, Frontiers Media SA, 2023-02-02) [Article]Nucleoli are subcellular compartments where transcription and maturation of pre-ribosomal RNAs occur. While the transcription of ribosomal RNAs is common to all living cells, the presence and ultrastructure of nucleoli has been only documented in eukaryotes. Asgard-Archaea, the closest prokaryotic relatives of eukaryotes, and their near relatives TACK-Archaea have homologs of nucleolar proteins and RNAs in their genome, but the cellular organization of both is largely unexplored. Here we provide ultrastructural and molecular evidence for the presence of putative nucleolus-like subcellular domains in the TACK crenarchaeon Saccharolobus solfataricus (formerly known as Sulfolobus solfataricus). Transmission electron microscopy (TEM) revealed consistent electron-dense fibro-granular compartments, also positive to the specific silver staining for nucleolar organizer regions (AgNOR). TEM also confirmed that ribosomal DNA (rDNA) is spatially distributed in non-random, clustered arrays underlying fine structures, as observed by ultrastructural in situ hybridization (UISH). To further explore these observations, proteomic sequencing of isolated bands from AgNOR-stained protein gels was conducted and compared against a compiled inventory of putative nucleolar homologs from the S. solfataricus P1 genome. Sequenced AgNOR-sensitive peptides encoded homologs of eukaryotic nucleoli proteins, enriched for nucleolus-related functions. Our results provide first evidence that subcellular domains of nucleolar-like nature are not exclusive to eukaryotes. Based on our data, we propose a model for a putative nucleolus in S. solfataricus. Whereas technical limitations and further aspects remain a matter for future functional studies, our data supports the origin of nucleoli within the common ancestor of Eukarya and TACK-Archaea, based on a two-domain tree of life.
