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

Microbially-Mediated Fluorescent Organic Matter Transformations in the Deep Ocean. Do the chemical precursors matter?

Original research paperThe refractory nature of marine dissolved organic matter (DOM) increases while it travels from surface waters to the deep ocean. This resistant fraction is in part composed of fluorescent humic-like material, which is relatively difficult to metabolize by deep water prokaryotes, and it can also be generated by microbial activity. It has been recently argued that microbial production of new fluorescent DOM (FDOM) requires the presence of humic precursors in the surrounding environment. In order to experimentally test how the chemical quality of the available organic compounds influences the production of new FDOM, three experiments were performed with bathypelagic Atlantic waters. Microbial communities were incubated in three treatments which differed in the quality of the organic compounds added: (i) glucose and acetate; (ii) glucose, acetate, essential amino acids, and humic acids; and (iii) humic acids alone. The response of the prokaryotes and the production of FDOM were simultaneously monitored. Prokaryotic abundance was highest in treatments where labile compounds were added. The rate of humic-like fluorescence production, scaled to prokaryotic abundance, varied depending on the quality of the additions. The precursor compounds affected the generation of new humic-like FDOM, and the cell-specific production of this material was higher in the incubations amended with humic precursors. Furthermore, we observed that the protein-like fluorescence decreased only when fresh amino acids were added. These findings contribute to the understanding of FDOM variability in deep waters and provide valuable information for studies where fluorescent compounds are used in order to track water masses and/or microbial processes.Spanish Ministry of Economy and Competitivity, CSIC, ESF and Danish Research Council for Independent ResearchVersión del edito

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

En prensa8,951

Empirical leucine-to-carbon conversion factors for estimating heterothrophic bacterial production in surface waters of the world oceans

Comunicación oralBacterial biomass production is a key parameter for evaluating the role of bacterioplankton in ocean carbon cycling. However, bacterial production cannot be directly measured and is typically estimated from the incorporation rates of radiolabelled leucine. The conversion of leucine uptake rates into bacterial carbon production rates requires the use of conversion factors (CFs) which must be empirically determined. Despite the empirical leucine-to-carbon CFs vary widely across environments very little is known about its potential controlling factors. We conducted a set of 10 surface seawater cultures experiments where the growth of the natural bacterial assemblage was promoted by filtration (removal of grazers) or by both filtration and dilution. Sampling stations were located between 30 ºN and 30 ºS, including the Atlantic, Pacific and Indian oceans. CFs varied from 0.13 to 1.47 Kg C mol Leu-1, being higher in the filtrated than in the filtrated and diluted treatment. The abundance of picocyanobacteria explained 60% of the observed variability. Our results further suggest that the composition of bacterioplankton, as assessed by ARISA fingerprinting, may partially explain the observed variation in CFs

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

Sample dilution and bacterial community composition influence empirical leucine-to-carbon conversion factors in surface waters of the world's oceans

Research articleThe transformation of leucine incorporation into prokaryotic carbon production rates requires the use of either theoretical or empirically determined conversion factors. Empirical leucine-to-carbon conversion factors (eCFs) vary widely across environments, and little is known about their potential controlling factors. We conducted 10 surface seawater manipulation experiments across the world’s oceans, where the growth of the natural prokaryotic assemblages was promoted by filtration (i.e. removal of grazers; F treatment) or filtration combined with dilution (i.e. relieving also resource competition; FD treatment). The impact of sunlight exposure was also evaluated in the FD treatments, and we did not find a significant effect on the eCFs. The eCFs varied from 0.09 to 1.47 kg C mol Leu-1 and were significantly lower in the filtered and diluted (FD) than in the filtered (F) treatments. Also, changes in bacterial community composition during the incubations, as assessed by Automated Ribosomal Intergenic Spacer Analysis (ARISA), were stronger in the FD than in the F treatments, as compared to unmanipulated controls. Thus, we discourage the common procedure of diluting samples (in addition to filtration) for eCFs determination. The eCFs in the filtered treatment were negatively correlated with the initial chlorophyll a concentration, picocyanobacterial abundance (mostly Prochlorococcus) and the percentage of heterotrophic prokaryotes with high nucleic acid content (%HNA). The latter two variables explained 80% of the eCFs variability in the F treatment, supporting the view that both Prochlorococcus and HNA prokaryotes incorporate leucine in substantial amounts although resulting into relatively low carbon production rates in the oligotrophic ocean.En prensa3,829