Publications

The ocean surface microlayer (SML), with physicochemical characteristics different from those of subsurface waters (SSW), results in dense and active viral and microbial communities that may favor virus–host interactions. Conversely, wind speed and/or UV radiation could adversely affect virus infection. Furthermore, in polar regions, organic and inorganic nutrient inputs from melting ice may increase microbial activity in the SML. Since the role of viruses in the microbial food web of the SML is poorly understood in polar oceans, we aimed to study the impact of viruses on prokaryotic communities in the SML and in the SSW in Arctic and Antarctic waters. We hypothesized that a higher viral activity in the SML than in the SSW in both polar systems would be observed. We measured viral and prokaryote abundances, virus-mediated mortality on prokaryotes, heterotrophic and phototrophic nanoflagellate abundance, and environmental factors. In both polar zones, we found small differences in environmental factors between the SML and the SSW. In contrast, despite the adverse effect of wind, viral and prokaryote abundances and virus-mediated mortality on prokaryotes were higher in the SML than in the SSW. As a consequence, the higher carbon flux released by lysed cells in the SML than in the SSW would increase the pool of dissolved organic carbon (DOC) and be rapidly used by other prokaryotes to grow (the viral shunt). Thus, our results suggest that viral activity greatly contributes to the functioning of the microbial food web in the SML, which could influence the biogeochemical cycles of the water column.

ABSTRACT 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 μm) and up to 45% in the largest plankton size fraction (20-200 μm) 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.

The Red Sea has been recognized as a coral reef refugia, but it is vulnerable to warming and pollution. Here we investigated the spatial and temporal trends of 15 element concentrations (Na, Mg, P, S, Ca, Cr, Mn, Fe, Co, Ni, Cu, Zn, Sr, Mo, and Cd) from 9 central Saudi Arabian Red Sea coral reef sediment cores (aged from the 1460s to the 1980s). We found several element concentrations were higher in the northern (Na, Ca, Cr, Fe, Co, Ni, and Sr) or southern (Mg, P, S, Mn, and Cd) Red Sea reef sediments, respectively (p < 0.05). In the central (i.e., Thuwal) to southern (i.e., Al Lith) Red Sea, the temporal trends of element concentrations were diverse, but the reef sedimentation rates (-36.4% and -80.5%, respectively) and all elemental accumulation rates (-49.4% for Cd to -12.2% for Zn, and -86.2% for Co to -61.4% for Cu, respectively) declined over time, potentially caused by warming-induced thermal bleaching. In the central to northern Red Sea (i.e., Yanbu), the severity of thermal bleaching is low, while the reef sedimentation rates (187%), element concentrations (6.7% for S to 764% for Co; except Na, Mg, Ca, Sr, and Cd), and all elemental accumulation rates (190% for Mg to 2697% for Co) exponentially increased from the 1970s, probably due the rapid industrialization in Yanbu. Our study also observed increased trace metal concentrations (e.g., Cu, Zn, and Ni) in the Thuwal and Al Lith coral reefs with severe bleaching histories, consistent with previous reports that trace metals might result in decreased resistance of corals to thermal stress under warming scenarios. Our study points to the urgent need to slow down global ocean warming and reduce the local discharge of trace metal pollutants to protect this biodiversity hotspot.

Abstract Background Using environmental DNA (eDNA) to detect taxa is quickly becoming an important technique to determine the distribution and diversity of macroorganisms. Assessing differences in communities based on eDNA extracted from sediment could enhance our understanding of marine communities among the many different marine habitats both from the present and from the past using sediment cores. Although the effect of extraction methods on metabarcoding results has been tested for both water and sediment samples, less is known about how sediment types may affect the extraction and sequencing of eDNA. Methods and Results We used two extraction methods to assess if the amount of extracted DNA was different among three marine habitats: coral reefs, mangrove forests, and seagrass meadows. First, an equal amount of DNA was added to sterilized sediment and there was no difference in the DNA extracted from the different habitats. Second, an equal amount of DNA from a species that did not occur naturally was added to the sediment and the number of sequenced reads of this species was not different among habitats. A concomitant test found that a commercial extraction kit, the MO BIO PowerSoil DNA isolation kit, and published extraction protocol from Lever et al. (2015, Frontiers in Microbiology, 6, 476) had similar results. Conclusions Although different environmental conditions within the habitats will likely affect the degradation of eDNA, these findings suggest that diverse characteristic of the sediments from different habitats does not affect the extraction of DNA. This is an important step in determining whether eDNA within sediment can be utilized to compare the communities from different marine habitats.

Marine protected areas (MPAs) have emerged as potentially important conservation tools for the conservation of biodiversity and mitigation of climate impacts. Among MPAs, a large percentage has been created with the implicit goal of protecting shark populations, including 17 shark sanctuaries which fully protect sharks throughout their jurisdiction. The Commonwealth of the Bahamas represents a long-term MPA for sharks, following the banning of commercial longlining in 1993 and subsequent designation as a shark sanctuary in 2011. Little is known, however, about the long-term behavior and space use of sharks within this protected area, particularly among reef-associated sharks for which the sanctuary presumably offers the most benefit. We used acoustic telemetry to advance our understanding of the ecology of such sharks, namely Caribbean reef sharks ( Carcharhinus perezi ) and tiger sharks ( Galeocerdo cuvier ), over two discrete islands (New Providence and Great Exuma) varying in human activity level, over 2 years. We evaluated which factors influenced the likelihood of detection of individuals, analyzed patterns of movement and occurrence, and identified variability in habitat selection among species and regions, using a dataset of 23 Caribbean reef sharks and 15 tiger sharks which were passively monitored in two arrays with a combined total of 13 acoustic receivers. Caribbean reef sharks had lower detection probabilities than tiger sharks, and exhibited relatively low habitat connectivity and high residency, while tiger sharks demonstrated wider roaming behavior across much greater space. Tiger sharks were associated with shallow seagrass habitats where available, but frequently transited between and connected different habitat types. Our data support the notion that large MPAs afford greater degrees of protection for highly resident species such as Caribbean reef sharks, yet still may provide substantial benefits for more migratory species such as tiger sharks. We discuss these findings within the context of species-habitat linkages, ecosystem services, and the establishment of future MPAs.

Abstract. Nitrogen loads in coastal areas have increased dramatically, with detrimental consequences for coastal ecosystems. Shallow sediments and seagrass meadows are hotspots for denitrification, favoring N loss. However, atmospheric dinitrogen (N2) fixation has been reported to support seagrass growth. Therefore, the role of coastal marine systems dominated by seagrasses in the net N2 flux remains unclear. Here, we measured denitrification, anaerobic ammonium oxidation (anammox), and N2 fixation in a tropical seagrass (Enhalus acoroides) meadow and the adjacent bare sediment in a coastal lagoon in the central Red Sea. We detected high annual mean rates of denitrification (34.9±10.3 and 31.6±8.9 mg N m−2 d−1) and anammox (12.4±3.4 and 19.8±4.4 mg N m−2 d−1) in vegetated and bare sediments. The annual mean N loss was higher (between 8 and 63-fold) than the N2 fixed (annual mean = 5.9±0.2 and 0.8±0.3 mg N m−2 d−1) in the meadow and bare sediment, leading to a net flux of N2 from sediments to the atmosphere. Despite the importance of this coastal lagoon in removing N from the system, N2 fixation can contribute substantially to seagrass growth since N2 fixation rates found here could contribute up to 36 % of plant N requirements. In vegetated sediments, anammox rates decreased with increasing organic matter (OM) content, while N2 fixation increased with OM content. Denitrification and anammox increased linearly with temperature, while N2 fixation showed a maximum at intermediate temperatures. Therefore, the forecasted warming could further increase the N2 flux from sediments to the atmosphere, potentially impacting seagrass productivity and their capacity to mitigate climate change but also enhancing their potential N removal.

Without an adequate supply of dissolved vitamins, many species of phytoplankton do not grow. Additions of inorganic nutrients like phosphorus and nitrogen, and trace metals like iron, are not alone adequate to sustain life—a practical lesson learned quickly by experimental biologists when they try to keep eukaryotic phytoplankton cultures alive in their labs. The reason is that coenzymes such as B vitamins are also required for many metabolic pathways. For example, vitamin B, serves as a cofactor for a large number of enzymatic systems, including the pyruvate dehydrogenase complex required for the metabolism of carbohydrates (glycolysis) and amino acid synthesis [Vandamme, 1989]. Vitamin B 12 is used primarily to assist two enzymes: methionine synthase, which is involved in DNA synthesis, and methylmalonyl CoA mutase, which is required for inorganic carbon assimilation [ Lindemans and Abels , 1985].

This database consists of methane fluxes and ancillary data compiled from the literature for aquatic ecosystems including rivers and streams, lakes, ponds and reservoirs, estuaries, mangroves, saltmarshes, seagrasses, tidal flats, aquaculture ponds, continental shelfs, and summarises previous published freshwater wetlands, rice cultivation (Saunois et al 2020) and slope and open ocean (Weber et al. 2019).