Dissolved inorganic carbon fixation of Thaumarchaeota vs. Bacteria in the meso- and upper bathypelagic waters of the world’s oceans differentiated with the use of metabolic inhibitors

Recent studies suggest that the dark ocean prokaryotes fix inorganic carbon at rates substantially higher than assumed. We have studied the contribution of Archaea vs. Bacteria to total prokaryotic fixation of dissolved inorganic carbon (DIC) in the meso- and upper bathypelagic waters of the world’s oceans during the Malaspina circumnavigation expedition carried out between December 2010 and July 2011. We used the metabolic inhibitor Erythromycin, an antibiotic specifically inhibiting growth of Bacteria but not affecting Archaea. Bacteria dominated throughout the water column in the three major ocean basins (54% of the total DAPI counts), decreasing in their relative contribution to total prokaryotic abundance from the surface to the meso- and bathypelagic waters. By contrast, the relative contribution of Thaumarchaeota was generally higher in the meso- and bathypelagic layers than in the surface waters (up to 29% of the total DAPI counts in the Pacific Ocean). Averaged over the entire water column, Thaumarchaeota contributed 8%, 33% and 18% to the total prokaryotic DIC fixation in the Indian, Pacific and Atlantic Ocean, respectively. The contribution of Thaumarchaeota to total prokaryotic DIC fixation increased with depth, particularly in the Atlantic below 1000 m depth and in the lower mesopelagic zone of the Pacific Ocean. Preliminary results from an station in the Atlantic Ocean, combining microautoradiography and fluorescence in situ hybridization (MICRO-CARD-FISH), confirmed that both Thaumarchaeota and some bacterial groups such as SAR 324 take up DIC. Thaumarchaeota and SAR 324 accounted for 7 % and 12% of DIC-positive DAPI-stained cells, respectively, as revealed by MICRO-CARD-FISH. Our results suggest that some phylogenetic groups may be significant contributors to the dark ocean chemoautotrophy

Assessment of microbial plankton diversity as an ecological indicator in the NW Mediterranean coast

High-throughput sequencing of microbial assemblages has been proposed as an alternative methodology to the traditional ones used in marine monitoring and environmental assessment. Here, we evaluated pico- and nanoplankton diversity as ecological indicators in NW Mediterranean coastal waters by comparing their diversity in samples subjected to varying degrees of continental pressures. Using metabarcoding of the 16S and 18S rRNA genes, we explored whether alphadiversity indices, abundance of Operational Taxonomic Units and taxonomic groups (and their ratios) provide information on the ecological quality of coastal waters. Our results revealed that only eukaryotic diversity metrics and a limited number of prokaryotic and eukaryotic taxa displayed potential in assessing continental influences in our surveyed area, resulting thus in a restrained potential of microbial plankton diversity as an ecological indicator. Therefore, incorporating microbial plankton diversity in environmental assessment could not always result in a significant improvement of current marine monitoring strategies.Preprint2,35

Global diversity and biogeography of deep-sea pelagic prokaryotes

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Wind-induced changes in the dynamics of fluorescent organic matter in the coastal NW Mediterranean

Original research paperMarine biogeochemistry dynamics in coastal marine areas is strongly influenced by episodic events such as rain, intense winds, river discharges and anthropogenic activities. We evaluated in this study the importance of these forcing events on modulating seasonal changes in the marine biogeochemistry of the northwestern coast of the Mediterranean Sea, based on data gathered from a fixed coastal sampling station in the area. A 4-year (2011–2014) monthly sampling at four depths (0.5 m, 20 m, 50 m and 80 m) was performed to examine the time variability of several oceanographic variables: seawater temperature, salinity, inorganic nutrient concentrations (NO3−, PO43 − and SiO2), chlorophyll a (Chl a), dissolved organic carbon (DOC) and fluorescent dissolved organic matter (FDOM). FDOM dynamics was predominantly influenced by upwelling events and mixing processes, driven by strong and characteristic wind episodes. SW wind episodes favored the upwelling of deeper and denser waters into the shallower shelf, providing a surplus of autochthonous humic-like material and inorganic nutrients, whereas northerlies favored the homogenization of the whole shelf water column by cooling and evaporation. These different wind-induced processes (deep water intrusion or mixing), reported along the four sampled years, determined a high interannual environmental variability in comparison with other Mediterranean sampling sites. Graphical abstract Image 1 Download : Download high-res image (344KB)Download : Download full-size imageECOSER (CTM2011-15937-E), DOREMI (CTM2012-342949), SUAVE (CTM2014/ 23456/1) and ANIMA (CTM2015-65720) from the Spanish Ministerio de Economía y Competitividad (MINECO) and the Grup de Recerca Consolidat 2014SGR1179 and 2014SGR1029 financed by the Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR) from the Generalitat de Catalunya; (JAEPre_2011_00923) from the Agencia Estatal Consejo Su perior de Investigaciones Científicas (CSIC) and the project FERMIO (MINECO, CTM2014-57334-JIN) co-financed with FEDER fundsVersión del editor3,25

Seasonality of biogeohemically relevant genes in the NW Mediterranean coastal microbiome

Marine biogeochemical processes are mediated by microorganisms through protein encoding genes, some being solely present in prokaryotes. During the last decade, genomic site-specific and large-scale expeditions have discovered millions of genes, unveiling new putative functions and large gene phylogenetic heterogeneity. Nonetheless, little still is known about the genomic basis of key biogeochemical processes, the taxonomic groups mediating them and whether seasonal patterns occur across taxonomic levels. For these reasons, we conducted temporal analyses of the functional diversity for 18 key functional genes in a model coastal marine microbiome. We analyzed a 3-year metagenomic time-series from the Blanes Bay Microbial Observatory (NW Mediterranean Sea) through state-of-the-art omics’ tools and time series statistics. Using a new Protein-Level ASSembler (PLASS), based in assembling at the protein space, a large number of potentially new and potentially biogeochemically relevant genes were recovered, which were missed by standard metagenomic analyses. This allowed us to explore the seasonal trends and gene heterogeneity in various key genes involved in the four major marine biogeochemical cycles (carbon, phosphorus, sulfur and nitrogen). Preliminary results show some key functions as seasonal, although with heterogeneity across the different taxonomical ranks. Our results define the seasonality of gene presence in that coastal environment and are the basis to discuss the implications of the seasonality of such genes for ecosystem functionin

Microbiomes of Western Australian marine environments

27 pages, 5 figures, 1 appendixMicrobes are fundamentally important to the maintenance of all habitats, including those in the ocean: they govern biogeochemical cycles, contribute to resistance from disease and nutritional requirements of macroorganisms and provide enormous biological and genetic diversity. The oceanic environment of the west coast of Australia is dominated by the Leeuwin Current, a poleward flowing boundary current that brings warm water down the coastline from the north. Due to the influence of the current, tropical species exist further south than they would otherwise, and stretches of the coastline host unique assortments of tropical and temperate species. Seawater itself, as well as the benthic macroorganisms that inhabit ocean environments, form habitats such as extensive areas of seagrass beds, macroalgal forests, coral reefs, sponge gardens, benthic mats including stromatolites, continental slopes and canyons and abyssal plain enviroments. These environments, and the macroorganisms that inhabit them, are all intrinsically linked with highly abundant and diverse consortiums of microorganisms. To date, there has been little research aimed at understanding these critical organisms within Western Australia. Here we review the current literature from the dominant coastal types (seagrass, coral, temperate macroalgae, vertebrates and stromatolites) in Western Australia. The most well researched are pelagic habitats and those with stromatolites, whereas data on all the other environments are slowly beginning to emerge. We urge future research efforts to be directed toward understanding the diversity, function, resilience and connectivity of coastal microorganisms in Western AustraliaPeer Reviewe

Primer design for an accurate view of picocyanobacterial community structure by using high-throughput sequencing

High-throughput sequencing (HTS) of the 16S rRNA gene has been used successfully to describe the structure and dynamics of microbial communities. Picocyanobacteria are important members of bacterioplankton communities, and, so far, they have predominantly been targeted using universal bacterial primers, providing a limited resolution of the picocyanobacterial community structure and dynamics. To increase such resolution, the study of a particular target group is best approached with the use of specific primers. Here, we aimed to design and evaluate specific primers for aquatic picocyanobacterial genera to be used with high-throughput sequencing. Since the various regions of the 16S rRNA gene have different degrees of conservation in different bacterial groups, we therefore first determined which hypervariable region of the 16S rRNA gene provides the highest taxonomic and phylogenetic resolution for the genera Synechococcus, Prochlorococcus, and Cyanobium. An in silico analysis showed that the V5, V6, and V7 hypervariable regions appear to be the most informative for this group. We then designed primers flanking these hypervariable regions and tested them in natural marine and freshwater communities. We successfully detected that most (97%) of the obtained reads could be assigned to picocyanobacterial genera. We defined operational taxonomic units as exact sequence variants (zero-radius operational taxonomic units [zOTUs]), which allowed us to detect higher genetic diversity and infer ecologically relevant information about picocyanobacterial community composition and dynamics in different aquatic systems. Our results open the door to future studies investigating picocyanobacterial diversity in aquatic systems

Quantifying long-term recurrence in planktonic microbial eukaryotes

How much temporal recurrence is present in microbial assemblages is still an unanswered ecological question. Even though marked seasonal changes have been reported for whole microbial communities, less is known on the dynamics and seasonality of individual taxa. Here, we aim at understanding microbial recurrence at three different levels: community, taxonomic group and operational taxonomic units (OTUs). For that, we focused on a model microbial eukaryotic community populating a long-term marine microbial observatory using 18S rRNA gene data from two organismal size fractions: the picoplankton (0.2–3 µm) and the nanoplankton (3–20 µm). We have developed an index to quantify recurrence in particular taxa. We found that community structure oscillated systematically between two main configurations corresponding to winter and summer over the 10 years studied. A few taxonomic groups such as Mamiellophyceae or MALV-III presented clear recurrence (i.e., seasonality), whereas 13%–19% of the OTUs in both size fractions, accounting for ~40% of the relative abundance, featured recurrent dynamics. Altogether, our work links long-term whole community dynamics with that of individual OTUs and taxonomic groups, indicating that recurrent and non-recurrent changes characterize the dynamics of microbial assemblages

Factors controlling the community structure of picoplankton in contrasting marine environments.

The effect of inorganic nutrients on planktonic assemblages has traditionally relied on concentrations rather than estimates of nutrient supply. We combined a novel dataset of hydrographic properties, turbulent mixing, nutrient concentration, and picoplankton community composition with the aims of (i) quantifying the role of temperature, light, and nitrate fluxes as factors controlling the distribution of autotrophic and heterotrophic picoplankton subgroups, as determined by flow cytometry, and (ii) describing the ecological niches of the various components of the picoplankton community. Data were collected at 97 stations in the Atlantic Ocean, including tropical and subtropical open-ocean waters, the northwestern Mediterranean Sea, and the Galician coastal upwelling system of the northwest Iberian Peninsula. A generalized additive model (GAM) approach was used to predict depth-integrated biomass of each picoplankton subgroup based on three niche predictors: sea surface temperature, averaged daily surface irradiance, and the transport of nitrate into the euphotic zone, through both diffusion and advection. In addition, niche overlap among different picoplankton subgroups was computed using nonparametric kernel density functions. Temperature and nitrate supply were more relevant than light in predicting the biomass of most picoplankton subgroups, except for Prochlorococcus and lownucleic-acid (LNA) prokaryotes, for which irradiance also played a significant role. Nitrate supply was the only factor that allowed the distinction among the ecological niches of all autotrophic and heterotrophic picoplankton subgroups. Prochlorococcus and LNA prokaryotes were more abundant in warmer waters ( > 20 ◦C) where the nitrate fluxes were low, whereas Synechococcus and high-nucleic-acid (HNA) prokaryotes prevailed mainly in cooler environments characterized by intermediate or high levels of nitrate supply. Finally, the niche of picoeukaryotes was defined by low temperatures and high nitrate supply. These results support the key role of nitrate supply, as it not only promotes the growth of large phytoplankton, but it also controls the structure of marine picoplankton communitie