Impact of airborne algicidal bacteria on marine phytoplankton blooms.

Ocean microbes are involved in global processes such as nutrient and carbon cycling. Recent studies indicated diverse modes of algal-bacterial interactions, including mutualism and pathogenicity, which have a substantial impact on ecology and oceanic carbon sequestration, and hence, on climate. However, the airborne dispersal and pathogenicity of bacteria in the marine ecosystem remained elusive. Here, we isolated an airborne algicidal bacterium, Roseovarius nubinhibens, emitted to the atmosphere as primary marine aerosol (referred also as sea spray aerosols) and collected above a coccolithophore bloom in the North Atlantic Ocean. The aerosolized bacteria retained infective properties and induced lysis of Gephyrocapsa huxleyi cultures.This suggests that the transport of marine bacteria through the atmosphere can effectively spread infection agents over vast oceanic regions, highlighting its significance in regulating the cell fate in algal blooms.

Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems.

The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.

Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition.

Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.

Pervasive tandem duplications and convergent evolution shape coral genomes.

BACKGROUND: Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. RESULTS: In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. CONCLUSIONS: At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.

Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms.

Algal blooms are hotspots of marine primary production and play central roles in microbial ecology and global elemental cycling. Upon demise of the bloom, organic carbon is partly respired and partly transferred to either higher trophic levels, bacterial biomass production or sinking. Viral infection can lead to bloom termination, but its impact on the fate of carbon remains largely unquantified. Here, we characterize the interplay between viral infection and the composition of a bloom-associated microbiome and consequently the evolving biogeochemical landscape, by conducting a large-scale mesocosm experiment where we monitor seven induced coccolithophore blooms. The blooms show different degrees of viral infection and reveal that only high levels of viral infection are followed by significant shifts in the composition of free-living bacterial and eukaryotic assemblages. Intriguingly, upon viral infection the biomass of eukaryotic heterotrophs (thraustochytrids) rivals that of bacteria as potential recyclers of organic matter. By combining modeling and quantification of active viral infection at a single-cell resolution, we estimate that viral infection causes a 2-4 fold increase in per-cell rates of extracellular carbon release in the form of acidic polysaccharides and particulate inorganic carbon, two major contributors to carbon sinking into the deep ocean. These results reveal the impact of viral infection on the fate of carbon through microbial recyclers of organic matter in large-scale coccolithophore blooms.

Diel cycle of sea spray aerosol concentration.

Sea spray aerosol (SSA) formation have a major role in the climate system, but measurements at a global-scale of this micro-scale process are highly challenging. We measured high-resolution temporal patterns of SSA number concentration over the Atlantic Ocean, Caribbean Sea, and the Pacific Ocean covering over 42,000 km. We discovered a ubiquitous 24-hour rhythm to the SSA number concentration, with concentrations increasing after sunrise, remaining higher during the day, and returning to predawn values after sunset. The presence of dominating continental aerosol transport can mask the SSA cycle. We did not find significant links between the diel cycle of SSA number concentration and diel variations of surface winds, atmospheric physical properties, radiation, pollution, nor oceanic physical properties. However, the daily mean sea surface temperature positively correlated with the magnitude of the day-to-nighttime increase in SSA concentration. Parallel diel patterns in particle sizes were also detected in near-surface waters attributed to variations in the size of particles smaller than ~1 µm. These variations may point to microbial day-to-night modulation of bubble-bursting dynamics as a possible cause of the SSA cycle.

The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean.

Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.

Evolution of the Complex Refractive Index of Secondary Organic Aerosols during Atmospheric Aging.

The wavelength-dependence of the complex refractive indices (RI) in the visible spectral range of secondary organic aerosols (SOA) are rarely studied, and the evolution of the RI with atmospheric aging is largely unknown. In this study, we applied a novel white light-broadband cavity enhanced spectroscopy to measure the changes in the RI (400-650 nm) of ß-pinene and p-xylene SOA produced and aged in an oxidation flow reactor, simulating daytime aging under NO x-free conditions. It was found that these SOA are not absorbing in the visible range, and that the real part of the RI, n, shows a slight spectral dependence in the visible range. With increased OH exposure, n first increased and then decreased, possibly due to an increase in aerosol density and chemical mean polarizability for SOA produced at low OH exposures, and a decrease in chemical mean polarizability for SOA produced at high OH exposures, respectively. A simple radiative forcing calculation suggests that atmospheric aging can introduce more than 40% uncertainty due to the changes in the RI for aged SOA.

Changes in the optical properties of benzo[a]pyrene-coated aerosols upon heterogeneous reactions with NO2 and NO3.

Chemical reactions can alter the chemical, physical, and optical properties of aerosols. It has been postulated that nitration of aerosols can account for atmospheric absorbance over urban areas. To study this potentially important process, the change in optical properties of laboratory-generated benzo[a]pyrene (BaP)-coated aerosols following exposure to NO(2) and NO(3) was investigated at 355 nm and 532 nm by three aerosol analysis techniques. The extinction coefficient was determined at 355 nm and 532 nm from cavity ring-down aerosol spectroscopy (CRD-AS); the absorption coefficient was measured by photoacoustic spectroscopy (PAS) at 532 nm, while an on-line aerosol mass spectrometer (AMS) supplied real-time quantitative information about the chemical composition of aerosols. In this study, 240 nm polystyrene latex (PSL) spheres were thinly coated with BaP to form 300 or 310 nm aerosols that were exposed to high concentrations of NO(2) and NO(3) and measured with CRD-AS, PAS, and the AMS. The extinction efficiencies (Q(ext)) changed after exposure to NO(2) and NO(3) at both wavelengths. Prior to reaction, Q(ext) for the 355 nm and 532 nm wavelengths were 4.36 ± 0.04 and 2.39 ± 0.05, respectively, and Q(ext) increased to 5.26 ± 0.04 and 2.79 ± 0.05 after exposure. The absorption cross-section at 532 nm, determined with PAS, reached σ(abs) = (0.039 ± 0.001) × 10(-8) cm(2), indicating that absorption increased with formation of nitro-BaP, the main reaction product detected by the AMS. The single-scattering albedo (SSA), a measure of particle scattering efficiency, decreased from 1 to 0.85 ± 0.03, showing that changes in the optical properties of BaP-covered aerosols due to nitration may have implications for regional radiation budget and, hence, climate.

Effective broadband refractive index retrieval by a white light optical particle counter.

A new approach to retrieve the effective broadband refractive indices (nbroad,eff) of aerosol particles by a white light aerosol spectrometer (WELAS) optical particle counter (OPC) is presented. Using a tandem differential mobility analyzer (DMA)-OPC system, the nbroad,eff are obtained for both laboratory and field applications. This method was tested in the laboratory using substances with a wide range of optical properties. With the obtained nbroad,eff, WELAS aerosol size distributions can be corrected. Therefore, this method can be used for instrument calibration in both laboratory and field measurements. The retrieved effective broadband refractive indices for the scattering aerosols were: ammonium sulfate ((NH4)2SO4, AS) nbroad,eff=1.52(+/-0.01)+i0.0, glutaric acid (HOOC(CH2)3COOH, GA) nbroad,eff=1.45(+/-0.01)+i0.0, and sodium chloride (NaCl) nbroad,eff=1.49(+/-0.02)+i0.0, all within 4% of literature values. A lightly absorbing substance, Suwannee river fulvic acid (SRFA), was also measured, and its retrieved nbroad,eff is like that of a pure scatterer, with a value of nbroad,eff=1.53(+/-0.01)+i0.0. The retrieved real part of nbroad,eff is in accordance with literature values and the imaginary part with the behavior of the white light spectrum of the WELAS, which is not sensitive below a wavelength of 380 nm, where SRFA mainly absorbs. For absorbing substances, nigrosine and various mixtures of nigrosine with AS and GA were measured. For nigrosine, nbroad,eff=1.64(+/-0.04)+i0.20(+/-0.03) was retrieved, in very good agreement with values found in the literature. The nbroad,eff retrieved by this method for the mixtures was in accordance with the complex refractive index expected. The nbroad,eff retrieved by this method would be similar to the values obtained using the solar spectrum.