Biology subjects

Duarte, C. M.

Publications and source records attributed to Duarte, C. M..

At least 19 recordsLinked to original sources

bioRxiv2026

A cold-adapted Cas9 nuclease from the deep ocean

The abundance of CRISPR systems in bacteria and archaea fuels the search for Cas nucleases that perform where established enzymes fail. Deep Ocean 1 Cas9 (DO1Cas9) is to our knowledge the first Cas9 nuclease characterized from the deep ocean, recovered from a metagenomic sample at 1,500 m depth in the Atlantic Ocean. DO1Cas9 shows cold-adapted structural flexibility, thermal susceptibility, salt-dependent stability, higher specificity than SpCas9 and cleaves double-stranded DNA efficiently under cold conditions where mesophilic SpCas9 retains only residual activity. DO1Cas9 edits genomes in diverse organisms such as Caenorhabditis elegans, zebrafish, the marine tunicate Oikopleura dioica, and the malaria parasite Plasmodium falciparum. In the marine bacterium Marinomonas mediterranea, DO1Cas9 programmed against an invading phage reduced plaquing efficiency about 10-fold more than SpCas9. These results expand the CRISPR-Cas9 toolbox with a nuclease for cold-chain editing and marine biotechnology.

genetics↗

bioRxiv2026

Self-generated oxygen limitation drives coral outcomes during marine heatwaves

Marine heatwaves cause massive, but often patchy coral bleaching. Why neighboring colonies often respond differently remains unresolved. Here, we show that interactions between metabolic demand and flow-mediated resupply generate heterogeneous oxygen microenvironments inside branching corals under heat stress. During the 2023 and 2024 Red Sea heatwaves, high-frequency in situ measurements revealed hypoxic to near-anoxic interbranch conditions despite well-oxygenated surrounding seawater. In 2023, neighboring colonies developed divergent oxygen regimes preceding paling and bleaching; in 2024, stronger and earlier thermal stress was associated with recurrent nighttime near-anoxia before tissue disintegration and mortality. A physics-based three-dimensional fluid-metabolism model reproduced these patterns. Oxygen depletion and coral impacts emerged when metabolic oxygen demand exceeded flow-mediated resupply. Organism-scale variability in oxygen regimes may explain divergent coral fate under shared heatwave exposure.

ecology↗

bioRxiv2026

Thermal stress drives seagrass fragmentation in the Mediterranean Sea

Posidonia oceanica meadows, which underpin Mediterranean coastal ecosystems, are undergoing accelerated decline, partly driven by thermal stress. While previous quantitative studies have identified temperature thresholds beyond which seagrass mortality increases sharply, we show the cumulative and sublethal impacts of prolonged warming under fluctuating subthreshold conditions. To capture these effects, we introduce Stress Degree Days (SDD), a physiologically grounded index derived from an experimentally validated mortality rate function. Using sea surface temperature (SST) data, we quantified the cumulative thermal exposure across the Mediterranean Basin from 2000 to 2020. Leveraging high-resolution satellite imagery and deep learning-based habitat mapping, we linked SDD-derived thermal exposure to meadow fragmentation, which is a proxy for seagrass health. Our results show that high thermal stress (> 50%) is concentrated along the southern and eastern Mediterranean, where meadows exhibit more than 40% cover loss and elevated fragmentation, even though maximum SSTs remained below lethal limits (LT50 = 28.9 {degrees}C). This finding highlights the critical role of chronic sublethal thermal stress in driving structural degradation. Future projections under the RCP8.5, business as usual, and the more moderate RCP4.5 climatic scenarios indicate basin-wide regression, with expected cover losses of approximately 80% and 40%, respectively, by 2100, and near-total habitat suitability collapse in the southern regions. Consequently, fragmentation indices are projected to double or triple, further disrupting clonal connectivity, sediment retention, and oxygen export. In summary, by integrating physiological mechanisms, large-scale remote sensing, and climate modeling, the SDD framework identifies thermal hotspots, reveals emergent vulnerability patterns, and offers a predictive tool to guide conservation strategies in warming oceans.

ecology↗

bioRxiv2025

Widespread and Abundant CRISPR-Cas Systems in the Deep Ocean

CRISPR-Cas systems have revolutionized modern biology. Most CRISPR-Cas systems in use for biotechnological applications derive from cultivated bacteria, but evidence suggests that environmental microbiomes harbor a large untapped diversity of these systems. Yet, our understanding of which environmental and biological factors drive the prevalence of CRISPR-Cas systems in the oceans remains limited. A search for CRISPR-Cas systems was conducted among 176 globally-distributed marine microbial metagenomes from the Malaspina expedition, which sampled both free-living and particle-attached microbiomes with emphasis on the deep ocean. We show that CRISPR-Cas systems are proportionally more abundant among microbiomes from the deep ocean than in the photic layers and among free-living microbes compared to those attached to particles, reflecting the higher concentrations of archaea and their viruses in these habitats. We identified 1,146 CRISPR-cas loci, some of which displayed unique loci architectures. From these loci, a total of 48 Cas9 proteins were identified, many of which are potentially novel. These discoveries expand the scope of CRISPR-Cas diversity and point at the deep-sea as a rich reservoir of these resources, which helps guide future bioprospecting efforts.

microbiology↗

bioRxiv2025

Seagrass arabinogalactan-proteins: Are they important for adaptation to the marine environment?

During the late cretaceous period several lineages of angiosperm plants transitioned from land to the sea by successfully adapting to life in salt water, forming the polyphyletic group of seagrasses. Today, four seagrass families inhabit coastal systems and are deeply intertwined with health and welfare of these ecosystems. Adaptation to the ocean environment included changes in the composition of plant cell walls and associated glycoproteins. We have asked the question whether or not there is a convergent and similar arabinogalactan-protein glycan repertoire in all seagrasses, given initial findings of arabinogalactan-proteins with unique features in the well-studied eelgrass, Zostera marina. We isolated and characterized arabinogalactan-proteins from seven species covering the four major seagrass families using carbohydrate analysis and glycan immunoassays, along with a bioinformatic search for relevant gene pathways in newly published seagrass genomes and transcriptomes. Glycan parts of all seagrass arabinogalactan-proteins shared a high proportion of 1,4-linked glucuronic acids and terminal 4-O-methyl glucuronic acid residues. Trait-based dendrograms generated to inform phylogenetic-relatedness showed there was no phylogenetic signal among seagrass families and arabinogalactan-protein features. Transcriptomic datasets from Cymodocea nodosa and Thalassia hemprichii growing under hypersaline conditions showed an upregulation of enzymes involved in 4O-methylation and glucuronic acid transfer. We therefore conclude that environmental factors, especially salinity with higher monovalent ion concentration, influence seagrass arabinogalactan-proteins structure more intensely than phylogenetic history.

plant biology↗

bioRxiv2024

Unravelling the universal spatial properties of coral reefs

Coral reefs are under rapid decline due to human pressures such as climate change. Achieving the Kunming-Montreal Global Biodiversity Framework goals, which include restoring 30% of degraded habitats like coral reefs by 2030, requires a comprehensive understanding of their extent and structure, which has been hitherto lacking. We address this limitation based on the unprecedented canonical inventory of coral reefs extracted from the Allen Coral Atlas of shallow-water tropical reefs. We identified a total of 1,579,772 individual reefs globally, extending over a total of 52,423 km2 of ocean area with mean and median sizes of 3.32 ha and 0.3 ha, respectively. We unravelled three universal laws that are common to all coral reef provinces: the size-frequency distribution, the inter-reef distance distribution and the area-perimeter relation, which follow power laws with an exponent of 1.8, 2.33 and 1.26, respectively. We demonstrate that coral reefs develop universal fractal patterns characterised by a perimeter fractal dimension of DP = 1.3 and a surface fractal dimension of DA = 1.6. Our analysis shows that coral reefs display intricate fractal-like geometries and exhibit universal macroecological patterns, largely independent of their geographical location. The universality of the observed patterns suggests that these features possibly stem from the highly conserved interactions of biological, physical, and chemical processes. Over geological scales, these processes lead to reef landscape patterns common among all provinces, providing new information relevant to reef growth modelling.

ecology↗

bioRxiv2024

Oxygen deprivation implicated in rapid coral mortality -- an emerging perilous threat to coral reefs

Tropical coral reefs are undergoing unprecedented degradation1, primarily due to the increasing intensity and frequency of marine heatwaves with climate change2-4. Coral bleaching is a well-known ramification of marine heatwaves, but rapid coral mortality is an emerging paradigm that visually manifests as the sloughing of tissue from the coral skeleton. Unlike coral bleaching, coral tissue sloughing precludes any prospect of holobiont recovery beyond the initial onset1,5,6, indicating a life-or-death tipping point. Here, we experimentally confirm this phenomenon occurs when temperatures increase within temporal windows of hours to days, consistent with field observations7,8. Through microscale measurements of dissolved oxygen in the diffusive boundary layers of two abundant, keystone reef-building corals, we demonstrate that rapid temperature increases coincide with intrinsic oxygen deprivation, occurring before gross tissue disintegration or coral tissue sloughing. We propose that this distinct phenomenon arises from rapid heating, rendering the coral holobiont incapable of engaging in reactive processes to counteract the combined effects of heightened aerobic demands and impaired photosynthetic function. The passive diffusion of O2 from the surrounding bulk water is likely insufficient to meet the holobionts requirements, as explained by the Einstein-Smoluchowski kinetic theory of gases and Brownian motion9,10. These insights into coral tissue sloughing underscore the complexity of holobiont responses to stress and biophysical consequences of heatwaves. A granular understanding of these mechanisms is urgently needed, particularly regarding how heating rates may change under future climate scenarios, to re-evaluate the potentially under-recognised threats facing coral reefs.

ecology↗

bioRxiv2023

Marine picoplankton metagenomes from eleven vertical profiles obtained by the Malaspina Expedition in the tropical and subtropical oceans

The Ocean microbiome has a crucial role on Earths biogeochemical cycles, but also represents a tremendous potential for biological applications as part of the bluebiotechnology. 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 from the lack of detailed vertical profiles covering contrasting oceans depth regions. Here we present a dataset of 76 microbial metagenomes of the picoplankton size fraction (0.2-3.0 m) collected in 11 stations along the Malaspina Expedition circumnavigation that cover vertical profiles sampling at 7 depths, from the surface to the 4000 m deep (or the sea floor in shallower waters). This Malaspina Microbial Vertical Profiles metagenomes (MProfile) dataset produced 1.66 Tbp of raw DNA sequences that assembled 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 tropical and subtropical ocean at a global scale, while increasing our general knowledge on the Ocean microbiome.

microbiology↗

bioRxiv2023

Global biogeography of the smallest plankton across ocean depths

Tiny ocean plankton (picoplankton) are fundamental for the functioning of the biosphere, but the ecological mechanisms shaping their biogeography are partially understood. Comprehending whether these microorganisms are structured by niche vs. neutral processes is highly relevant in the context of global change. The ecological drivers structuring picoplankton communities differ between prokaryotes and minute eukaryotes (picoeukaryotes) in the global surface ocean: while prokaryotic communities are shaped by a balanced combination of dispersal, selection, and drift, picoeukaryotic communities are mainly shaped by dispersal limitation. Yet, whether or not the relative importance of these processes in structuring picoplankton varies as we dive into the deep ocean was unknown. Here we investigate the mechanisms structuring picoplanktonic communities inhabiting different ocean depths. We analyzed 451 samples from the tropical and subtropical global ocean and the Mediterranean Sea covering the epi- (0-200m), meso- (200- 1,000m), and bathypelagic (1,000-4,000m) depth zones. We found that selection decreased with depth possibly due to lower habitat heterogeneity. In turn, dispersal limitation increased with depth, possibly due to dispersal barriers such as water masses and bottom topography. Picoplankton {beta}-diversity positively correlated with environmental heterogeneity and water mass variability in both the open-ocean and the Mediterranean Sea. However, this relationship tended to be weaker for picoeukaryotes than for prokaryotes. Community patterns were generally more pronounced in the Mediterranean Sea, probably because of its substantial cross-basin environmental heterogeneity and deep-water isolation. Altogether, we found that different combinations of ecological mechanisms shape the biogeography of the smallest members of the ocean microbiome across ocean depths.

ecology↗

bioRxiv2022

The SLAPTAG: A new molecular tag adapted for the development of a high-performance, low-cost, affinity chromatography system

The SLAPTAG is a novel molecular TAG derived from a protein domain present in the sequence of Lactobacillus acidophilus SlpA (SlpA284-444). Proteins from different biological sources, with different molecular weights or biochemical functions, can be fused in frame to the SLAPTAG and efficiently purified by the specific binding to a bacterial-derived chromatographic matrix named here Bio-Matrix (BM). Different binding and elution conditions were evaluated to set an optimized protocol for the SLAPTAG-based affinity chromatography (SAC). The binding equilibrium between SLAPTAG and BM was reached after a few minutes at 4{degrees}C, being the apparent dissociation constant (KD) of 4.3 {micro}M, a value which is similar to different Kd determined for other S-layer proteins and their respective bacterial cell walls. A reporter protein was generated (H6-GFP-SLAPTAG) to compare the efficiency of the SAC against a commercial system based on a Ni2+-charged agarose matrix, observing no differences in the H6-GFP-SLAPTAG purification performance. The stability and reusability of the BM were evaluated, and it was determined that the matrix was stable for more than a year, being possible to reuse it five times without a significant loss in the efficiency for protein purification. Alternatively, we explored the recovery of bound SLAP-tagged proteins by proteolysis using the SLAPASE (a SLAP-tagged version of the HRV-3c protease) that released a tag-less GFP (SLAPTAG-less). Additionally, iron nanoparticles were linked to the BM and the resulting BMmag was successfully adapted for a magnetic SAC, a technique that can be potentially applied for high-throughput-out protein production and purification.

biochemistry↗

bioRxiv2022

Abundant deep ocean heterotrophic bacteria are culturable

Traditional culture techniques usually retrieve only a small fraction of the environmental marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured isolates of heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 22 samples used for isolation. These global datasets represent 60,322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers reaching up to a 28% of the 16S TAGs of the bathypelagic microbial communities, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the genera Sulfitobacter, Halomonas and Erythrobacter. These cultured isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living size fraction (0.2-0.8 m) and up to 45% in the largest plankton size fraction (20-200 m) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic realm act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria.

ecology↗

bioRxiv2022

Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities

Viruses play important roles on the biogeochemical cycles that take place in the ocean.Yet, deep ocean viruses are one of the most under-explored fractions of the global biosphere. Little is known about the environmental factors that control the composition and functioning of their communities, or how they interact with their free-living or particle-attached microbial hosts. Thus, we analysed 58 viral communities associated to size fractionated free-living (0.2-0.8 m) and particle-attached (0.8-20 m) cellular metagenomes from bathypelagic (2,150-4,018 m deep) microbiomes obtained during the Malaspina expedition. These metagenomes yielded 6,631 viral sequences, 91% of which were novel, and 67 represented high-quality genomes. Taxonomic classification assigned 53% of the viral sequences to families of tailed viruses from the order Caudovirales. Computational host prediction associated 886 viral sequences to dominant members of the deep ocean microbiome, such as Alphaproteobacteria (284), Gammaproteobacteria (241), SAR324 (23), Marinisomatota (39), and Chloroflexota (61). Free-living and particle-attached viral communities had markedly distinct taxonomic composition, host prevalence, and auxiliary metabolic gene content, which led to the discovery of novel viral encoded metabolic genes involved in the folate and nucleotide metabolisms. Water mass age emerged as an important factor driving viral community composition. We postulated this was due to changes in quality and concentration of dissolved organic matter acting on the host communities, leading to an increase of viral auxiliary metabolic genes associated with energy metabolism among older water masses. These results shed light on the mechanisms by which environmental gradients of deep ocean ecosystems structure the composition and functioning of free-living and particle-attached viral communities.

microbiology↗

bioRxiv2021

Disentangling marine microbial networks across space

Microbial interactions underpin ocean ecosystem function, but they remain barely known. Multiple studies have analyzed microbial interactions using static association networks based on omics data, yet microbial interactions are dynamic and can change across spatiotemporal scales. Understanding the dynamics of microbial interactions is needed for a better comprehension of ocean ecosystems. Here, we explored associations between archaea, bacteria, and picoeukaryotes along the water column, from the surface to the deep ocean, across the northern subtropical to the southern temperate ocean and the Mediterranean Sea by defining sample-specific subnetworks, which allowed us to examine changes in microbial associations across space. We found that associations tend to change with depth as well as with geographical scale, with a few associations being global (i.e., present across regions within the same depth layer) and 11-36% being regional within specific water layers. The lowest fraction of global associations was found in the bathypelagic zone, while associations restricted to certain regions increased with depth. The majority of associations observed in surface waters disappeared with depth, suggesting that surface ocean associations are not transferred to the deep sea, despite microbial sinking. Altogether, our results suggest that microbial associations have highly heterogeneous distributions in the horizontal and vertical dimensions of the ocean and that such distributions do not mirror taxonomic distributions. Our work contributes to better understand the dynamics of microbial interactions in the global ocean, which is urgently needed in a context of global change.

microbiology↗

bioRxiv2021

The quality of dissolved organic matter shapes the biogeography of the active bathypelagic microbiome

The bathypelagic ocean (1000-4000 m depth) is the largest aquatic biome on Earth but it is still largely unexplored. Due to its prevalent low dissolved organic carbon concentrations, most of the prokaryotic metabolic activity is assumed to be associated to particles. The role of free-living prokaryotes has thus been mostly ignored, except that of some chemolithoautotrophic lineages. Here we used a global bathypelagic survey of size-fractionated metagenomic and 16S (genes and transcripts) data and performed a differential abundance analysis to explore the functional traits of the different prokaryotic life-strategies, their contribution to the active microbiome, and the role that the quality of the dissolved organic matter (DOM) plays in driving this contribution. We found that free-living prokaryotes have limited capacity to uplift their metabolism in response to environmental changes and display comparatively lower growth rates than particle associated prokaryotes, but are responsible for the synthesis of vitamins in the bathypelagic. Furthermore, their contribution to the active prokaryotic microbiome increased towards waters depleted of labile DOM, which represented a large fraction of the tropical and subtropical ocean sampled stations. This points to a relevant yet overlooked role of free-living prokaryotes in DOM cycling in the vast bathypelagic desert.

ecology↗

bioRxiv2021

Rapid Evolution of SARS-CoV-2 Challenges Human Defenses

Evolutionary ecology theory provides an avenue to anticipate the future behavior of SARS-CoV-2. Here we quantify the accelerating evolution of SARS-CoV-2 by tracking the SARS-CoV-2 mutation globally, with a focus on the Receptor Binding Domain (RBD) of the spike protein believed to determine infectivity. We estimate that 384 million people were infected by March 1st, 2021, producing up to 1021 copies of the virus, with one new RBD variant appearing for every 600,000 human infections, resulting in approximately three new effective RBD variants produced daily. Doubling the number of RBD variants every 71.67 days followed by selection of the most infective variants challenges our defenses and calls for a shift to anticipatory, rather than reactive tactics. One-Sentence SummaryAccelerating evolution of SARS-CoV-2 demands formulating universal vaccines and treatments based on big-data simulations of possible new variants.

evolutionary biology↗

bioRxiv2020

Rapid Evolution of Plastic-degrading Enzymes Prevalent in the Global Ocean

Estimates of marine plastic stocks, a major threat to marine life (1), are far lower than expected from exponentially-increasing litter inputs, suggesting important loss factors (2, 3). These may involve microbial degradation, as the plastic-degrading polyethylene terephthalate enzyme (PETase) has been reported in marine microbial communities (4). An assessment of 416 metagenomes of planktonic communities across the global ocean identifies 68 oceanic PETase variants (oPETase) that evolved from ancestral enzymes degrading polycyclic aromatic hydrocarbons. Twenty oPETases show predicted efficiencies comparable to those of laboratory-optimized PETases, suggesting strong selective pressures directing the evolution of these enzymes. We found oPETases in 90.1% of samples across all oceans and depths, particularly abundant at 1,000 m depth, with a strong dominance of Pseudomonadales containing putative highly-efficient oPETase variants in the dark ocean. Enzymatic degradation may be removing plastic from the marine environment while providing a carbon source for bathypelagic microbial communities.

evolutionary biology↗

bioRxiv2020

Forces experienced by instrumented animals depend on lifestyle

Animal-attached devices have transformed our understanding of vertebrate ecology. However, to be acceptable, researchers must minimize tag-related harm. The long-standing recommendation that tag masses should not exceed 3% of the animals body mass ignores tag forces generated by movement. We used collar-attached accelerometers on four free-ranging carnivores, spanning two orders of magnitude in mass, to reveal that during movement, forces exerted by 3% tags were generally equivalent to 4-19% of the animals masses, with a record of 54% in a hunting cheetah. Controlled studies on domestic dogs revealed how the tag forces are dictated by animal gait and speed but appear largely invariant of body mass. This fundamentally changes how acceptable tag mass limits should be determined, requiring cognizance of animal athleticism. One Sentence SummaryThere can be no universal rule for collar-tag masses as a percentage of carrier mass since tag forces depend on lifestyle.

ecology↗

bioRxiv2020

Light into the darkness: Unifying the known and unknown coding sequence space in microbiome analyses

Genes of unknown function are among the biggest challenges in molecular biology, especially in microbial systems, where 40%-60% of the predicted genes are unknown. Despite previous attempts, systematic approaches to include the unknown fraction into analytical workflows are still lacking. Here, we propose a conceptual framework and a computational workflow that bridge the known-unknown gap in genomes and metagenomes. We showcase our approach by exploring 415,971,742 genes predicted from 1,749 metagenomes and 28,941 bacterial and archaeal genomes. We quantify the extent of the unknown fraction, its diversity, and its relevance across multiple biomes. Furthermore, we provide a collection of 283,874 lineage-specific genes of unknown function for Cand. Patescibacteria, being a significant resource to expand our understanding of their unusual biology. Finally, by identifying a target gene of unknown function for antibiotic resistance, we demonstrate how we can enable the generation of hypotheses that can be used to augment experimental data.

microbiology↗