Publications

The established approach to model seston size distributions involves the grouping of particles within logarithmic size classes and the examination of the relationship between density, or normalized biomass, and the characteristic sizes of the classes. Here we examine the distributional basis of the established approach and draw a connection between the biomass size spectrum and the Pareto distribution, a model widely used in other disciplines dealing with size‐structured systems. We provide efficient estimators of the parameters and also suggest that datasets exhibiting significant departures from a smooth power function decline can be adequately modeled using a Pareto type II distribution.

<strong class="journal-contentHeaderColor">Abstract.</strong> The measurements of dissolved organic carbon (DOC), nitrogen (DON), and phosphorus (DOP) are used to characterize the dissolved organic matter (DOM) pool and are important components of biogeochemical cycling in the coastal ocean. Here, we present the first edition of a global database (CoastDOM v1; available at <a href="https://figshare.com/s/512289eb43c4f8e8eaef" target="_blank" rel="noopener">https://figshare.com/s/512289eb43c4f8e8eaef</a>) compiling previously published and unpublished measurements of DOC, DON, and DOP collected in coastal waters. These data are complemented by hydrographic data such as temperature and salinity and, to the extent possible, other biogeochemical variables (e.g., Chlorophyll-<em>a</em>, inorganic nutrients) and the inorganic carbon system (e.g., dissolved inorganic carbon and total alkalinity). Overall, CoastDOM v1 includes observations from all continents however, most data were collected in the Northern Hemisphere, with a clear gap in coastal water DOM measurements from the Southern Hemisphere. The data included were collected from 1978 to 2022 and consist of 62339 data points for DOC, 20360 for DON and 13440 for DOP. The number of measurements decreases progressively in the sequence DOC &gt; DON &gt; DOP, reflecting both differences in the maturity of the analytical methods and the greater focus on carbon cycling by the aquatic science community. The global database shows that the average DOC concentration in coastal waters (average (standard deviation; SD): 182 (314) &micro;mol C L^&minus;1; median: 103 &micro;mol C L^&minus;1), is 13-fold greater than the average coastal DON concentrations (average (SD): 13.6 (30.4) &micro;mol N L^&minus;1; median: 8.0 &micro;mol N L^&minus;1), which was itself 39-fold greater than the average coastal DOP concentrations (average (SD): 0.34 &plusmn; 1.11 &micro;mol P L^&minus;1; median: 0.18 &micro;mol P L^&minus;1). This dataset will be useful to identify global spatial and temporal patterns in DOM and to facilitate reuse of DOC, DON and DOP data in studies aimed at better characterising local biogeochemical processes, closing nutrient budgets, estimating carbon, nitrogen and phosphorous pools, as well as identifying a baseline for modelling future changes in coastal waters.

Abstract Background Recent epidemic of novel coronavirus (SARS-CoV-2) has triggered a rising global health emergency that demands urgent analysis of its genome and solutions for detection and therapy. Methods We used a comparative pangenomic analysis of Betacoronavirus sequenced thus far to detect the core and accessory gene clusters of this genus including SARS-CoV-2. We then annotate the functions, which are confirmed by structural analysis, and predict the potential location within the host cells of these proteins. Findings We found five accessory gene clusters common to the SARS clade, including SARS-CoV-2, that perform functions supporting their pathogenicity. Phylogenetic analysis showed one of the accessory gene clusters, the protein E, to be present across the inferred evolutionary pathway of the SARS clade, including that of the horseshoe bat virus (Hp-betacoronavirus/Zhejiang2013), inferred to be the parental member of the clade. The E protein is highly conserved in the clade, differing between SARS and SARS-Cov2 with a difference of single amino acid substitution and a single amino acid insertion present in SARS but absent from SARS-CoV-2. Betacoronavirus pangenomedb is available at http://pangenomedb.cbrc.kaust.edu.sa. Interpretation The characterization and functional assessment of SARS-CoV-2 envelope, E, protein in gene cluster 6, together with previous findings on this protein for SARS, leads us to recommend that detection of COVID-2019 be developed based on the SARS-CoV-2 E protein and that treatment using mutated SARS-Cov-2 lacking the E protein be explored as a promising candidate for a vaccine. Funding This research was funded by the King Abdullah University of Science and Technology (KAUST) through funding allocated to Computational Bioscience Research Center (CBRC) and another KAUST award under the award number FCC/1/1976-25-01. Research in context Evidence before this study The response to the recent epidemic of novel coronavirus 2019-nCoV, now named SARS-CoV-2, and its disease named COVID-2019, require elucidating the possible origin, gene functions and potential treatment options. The genome sequence released for SARS-CoV-2 is a key resource to these efforts. We used all available whole-virus genomes released for the Betacoronavirus to conduct a functional pangenomic analysis of these viruses, including that of SARS-CoV-2. SARS-CoV-2 was previously reported in publications as 2019-nCoV. NCBI produced a dedicated resource for SARS-CoV-2 related publications and sequence data (https://www.ncbi.nlm.nih.gov/genbank/SARS-CoV-2-seqs/). We searched this resource for terms “2019-nCoV AND envelope” (1 hit), or “2019-nCoV AND orf10” (0 hits) or “2019-nCoV pangenome” (0 hits) to find any published work related to these genes in SARS-CoV-2. We retrieved all Betacoronavirus (taxon id 694002) whole genome sequences from NCBI (January 26, 2020 from web page https://www.ncbi.nlm.nih.gov/assembly) using the search term “txid694002[Organism:exp]”. This search retrieved a total of 22 whole genomes, of which 18 were unique genomes, including 4 that for SARS-CoV-2, see supplementary table 1. Added value of this study We report and make available an interactive pangenome analysis resource (defining core and accessory genome components) for the genus Betacoronavirus (https://pangenomedb.cbrc.kaust.edu.sa), including SARS-CoV-2. We identify and define all core and accessory gene alignments and phylogenetic trees for this genus. We then explore these data to provide insights into potential functions for uncharacterized genes (ORFs 6,8,10) unique to SARS-like coronaviruses, and suggest potential options for detection and therapy of COVID-2019. This analysis points at protein E, highly conserved across all SARS-like coronaviruses, as a promising candidate for COVID-2019 detection and therapy. Implications of all the available evidence The Betacoronavirus pangenome data we made public allows exploration of core and accessory elements of these viruses to understand the pathogenicity of SARS-CoV-2, thereby expediting progress in responding to the pandemic. The characterization and functional assessment of SARS-CoV-2 envelope, E, protein, in gene cluster 6 together with previous findings on this protein for SARS, leads us to recommend that detection of COVID-2019 be developed based on the SARS-CoV-2 E protein and that treatment using mutated SARS-Cov-2 lacking the E protein be explored as a promising candidate for a vaccine.

Climate-driven range-shifts create evolutionary opportunities for allopatric divergence and subsequent contact, leading to genetic structuration and hybrid zones. We investigate how these processes influenced the evolution of a complex of three closely related Cystoseira spp., which are a key component of the Mediterranean-Atlantic seaweed forests that are undergoing population declines. The C. tamariscifolia complex, composed of C. tamariscifolia s.s., C. amentacea and C. mediterranea, have indistinct boundaries and natural hybridization is suspected. Our aims are to (1) infer the genetic structure and diversity of these species throughout their distribution ranges using microsatellite markers to identify ancient versus recent geographical populations, contact zones and reproductive barriers, and (2) hindcast past distributions using niche models to investigate the influence of past range shifts on genetic divergence at multiple spatial scales. Results supported a single, morphologically plastic species the genetic structure of which was incongruent with a priori species assignments. The low diversity and low singularity in northern European populations suggest recent colonization after the LGM. The southern Iberian genetic hotspot most likely results from the role of this area as a climatic refugium or a secondary contact zone between differentiated populations or both. We hypothesize that life-history traits (selfing, low dispersal) and prior colonization effects, rather than reproductive barriers, might explain the observed genetic discontinuities.

<title>Abstract</title> Background The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have largescale consequences. Yet, the underlying ecological mechanisms structuring it are unclear. Here we investigate how fundamental ecological mechanisms ( selection , dispersal and ecological drift ) shape the smallest members of the tropical and subtropical surface-ocean microbiota: prokaryotes and minute eukaryotes (picoeukaryotes). Furthermore, we investigate the agents exerting abiotic selection on this assemblage as well as the spatial patterns emerging from the action of ecological mechanisms. To explore the previous, we analysed the composition of surface-ocean prokaryotic and picoeukaryotic communities using DNA-sequence data (16S- and 18S-rRNA genes) collected during the circumglobal expeditions Malaspina-2010 and TARA-Oceans . Results We found that the two main components of the tropical and subtropical surface-ocean microbiota, prokaryotes and picoeukaryotes, appear to be structured by different ecological mechanisms. Picoeukaryotic communities were predominantly structured by dispersal-limitation, while prokaryotic counterparts appeared to be shaped by the combined action of dispersal-limitation, selection and drift. Temperature-driven selection appeared as a major factor, out of a few selected factors, influencing species co-occurrence networks in prokaryotes but not in picoeukaryotes, indicating that association patterns may contribute to understand ocean microbiota structure and response to selection. Other measured abiotic variables seemed to have limited selective effects on community structure in the tropical and subtropical ocean. Picoeukaryotes displayed a higher spatial differentiation between communities and a higher distance decay when compared to prokaryotes, consistent with a scenario of higher dispersal limitation in the former after considering environmental heterogeneity. Lastly, random dynamics or drift seemed to have a more important role in structuring prokaryotic communities than picoeukaryotic counterparts. Conclusions The differential action of ecological mechanisms seems to cause contrasting biogeography, in the tropical and subtropical ocean, among the smallest surface plankton, prokaryotes and picoeukaryotes. This suggests that the idiosyncrasy of the main constituents of the ocean microbiota should be considered in order to understand its current and future configuration, which is especially relevant in a context of global change, where the reaction of surface ocean plankton to temperature increase is still unclear.

Abstract. Red Sea mangroves have a lower carbon burial rate than the global average, whereby small greenhouse gas fluxes may offset a large proportion of carbon burial. Monthly soil core sampling was conducted across 2 years at two sites within a central Eastern Red Sea mangrove stand to examine carbon dioxide (CO2) and methane (CH4) fluxes under dry and inundated conditions. Fluxes were highly variable, characterized by a prevalence of low emissions punctuated by bursts of high emissions. At the landward site, average ± SE (median) flux from the soil-air interface was 3111 ± 929 (811) µmol CO2 m−2 d−1 and 1.68 ± 0.63 (0.26) µmol CH4 m−2 d−1 under light conditions, and 8657 ± 2269 (1615) µmol CO2 m−2 d−1 and 0.84 ± 0.79 (0.59) µmol CH4 m−2 d−1 under dark conditions. Average ± SE (median) sea-air fluxes were –55 ± 165 (-79) µmol CO2 m−2 d−1 and 0.12 ± 0.23 (0.08) µmol CH4 m−2 d−1 under light conditions, and 27 ± 48 (53) µmol CO2 m−2 d−1 and 0.16 ± 0.13 (0.09) µmol CH4 m−2 d−1 in dark conditions. The seaward site recorded higher CH4 flux, averaging 18.7 ± 8.18 (1.7) and 17.1 ± 4.55 (7.7) µmol CH4 m−2 d−1 in light and dark conditions. Mean fluxes offset 94.5 % of carbon burial, with a median of 4.9 % skewed by extreme variability. However, reported CO2 removal by total alkalinity emission from carbonate dissolution greatly exceeded both processes and drives the role of these ecosystems as intense CO2 sinks.

Disentangling the effects of temperature, bottom-up (resource availability) and top-down (viral lysis and protistan grazing) controls on the biomass and growth rates of heterotrophic bacterioplankton has remained challenging, especially in the underexplored tropical and subtropical oceans. Here we combine a dataset gathered in the subtropical and tropical Atlantic, Indian and Pacific oceans with inshore and offshore surface observations in the central Red Sea, a substantially warmer (28.8 ± 0.4°C) basin compared with the other sites (24.7 ± 0.2°C). Heterotrophic bacteria and phytoplankton stocks covaried positively except in the Red Sea, which showed significantly lower bacterial abundances (typically <5 x 106 cells mL-1). Oligotrophy was shared among all sites, characterized by similar chlorophyll a and inorganic and organic nutrient concentrations. The higher relative abundances of viruses and heterotrophic nanoflagellates in the Red Sea suggest a tight top-down control preventing the accumulation of larger bacterial numbers. Red Sea bacteria showed variable specific growth rates but almost 2-fold higher than their oceanic counterparts (0.81 vs. 0.47 ± 0.03 d-1) and were less responsive to temperature than to trophic state. The contribution of the typically copiotrophic high nucleic acid content cells explained 41% of the variance in specific growth rates of the pooled dataset. We suggest that the balance between widespread resource limitation and local peaks in protistan and viral mortality will largely impact potential future temperature-driven increases in heterotrophic bacteria biomass in low latitude waters.