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

Mesoscale eddies: Hotspots of prokaryotic activity and differential community structure in the ocean

14 pages, 9 figures, 2 tablesTo investigate the effects of mesoscale eddies on prokaryotic assemblage structure and activity, we sampled two cyclonic eddies (CEs) and two anticyclonic eddies (AEs) in the permanent eddy-field downstream the Canary Islands. The eddy stations were compared with two far-field (FF) stations located also in the Canary Current, but outside the influence of the eddy field. The distribution of prokaryotic abundance (PA), bulk prokaryotic heterotrophic activity (PHA), various indicators of single-cell activity (such as nucleic acid content, proportion of live cells, and fraction of cells actively incorporating leucine), as well as bacterial and archaeal community structure were determined from the surface to 2000 m depth. In the upper epipelagic layer (0-200 m), the effect of eddies on the prokaryotic community was more apparent, as indicated by the higher PA, PHA, fraction of living cells, and percentage of active cells incorporating leucine within eddies than at FF stations. Prokaryotic community composition differed also between eddy and FF stations in the epipelagic layer. In the mesopelagic layer (200-1000 m), there were also significant differences in PA and PHA between eddy and FF stations, although in general, there were no clear differences in community composition or single-cell activity. The effects on prokaryotic activity and community structure were stronger in AE than CE, decreasing with depth in both types of eddies. Overall, both types of eddies show distinct community compositions (as compared with FF in the epipelagic), and represent oceanic hotspots of prokaryotic activity (in the epi- and mesopelagic realms)This research was supported by two grants of the Spanish Ministry of Education and Science to JA (Oceanic Eddies and Atmospheric Deposition—RODA, CTM 2004-06842-C03/MAR, and Shelf–Ocean Exchanges in the Canaries– Iberian Large Marine Ecosystem-CAIBEX, CTM 2007- 66498-C02), a grant of the Earth and Life Science Division of the Dutch Science Foundation (ALW-NWO; ARCHIMEDES project, 835.20.023) to GJH, and a predoctoral Fellowship of the Spanish Ministry of Education and Science (AP2005-3932) to FB. IL and JMG were also supported by project MODIVUS (CTM2005-04795/MAR). The work was carried out within the frame of the EU ‘Networks of Excellence’ MarBef and EurOceansPeer Reviewe

Hiding in plain sight: the globally distributed bacterial candidate phylum PAUC34f

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chen, M. L., Becraft, E. D., Pachiadaki, M., Brown, J. M., Jarett, J. K., Gasol, J. M., Ravin, N. V., Moser, D. P., Nunoura, T., Herndl, G. J., Woyke, T., & Stepanauskas, R. Hiding in plain sight: the globally distributed bacterial candidate phylum PAUC34f. Frontiers in Microbiology, 11, (2020): 376, doi: 10.3389/fmicb.2020.00376.Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.This work was funded by the United States National Science Foundation grants 1460861 (REU site at Bigelow Laboratory for Ocean Sciences), 1441717, 1335810, and 1232982 to RS, and the Simons Foundation (Life Sciences Project Award ID 510023) to RS. NR was supported by the Ministry of Science and Higher Education of Russia. GH was supported by the Austrian Science Fund (FWF) project ARTEMIS (P28781-B21) and the European Research Council under the European Community’s Seventh Framework Program (FP7/2007-2013)/ERC (Grant Agreement No. 268595). JG was supported by Spanish project RTI2018-101025-B-I00. TW and JJ were funded by the U.S. Department of Energy, Joint Genome Institute, a DOE Office of Science User Facility supported under Contract No. DE-AC02-05CH11231

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

Depth Dependent Relationships between Temperature and Ocean Heterotrophic Prokaryotic Production

9 páginas, 2 figuras, 1 tabla.-- This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these termsCorrigendum: Depth Dependent Relationships between Temperature and Ocean Heterotrophic Prokaryotic Production, Frontiers in Marine Science 4: 91 (2017) https://doi.org/10.3389/fmars.2017.00091Marine prokaryotes play a key role in cycling of organic matter and nutrients in the ocean. Using a unique dataset (>14,500 samples), we applied a space-for-time substitution analysis to assess the temperature dependence of prokaryotic heterotrophic production (PHP) in epi- (0–200 m), meso- (201–1000 m) and bathypelagic waters (1001–4000 m) of the global ocean. Here, we show that the temperature dependence of PHP is fundamentally different between these major oceanic depth layers, with an estimated ecosystem-level activation energy (Ea) of 36 ± 7 kJ mol−1 for the epipelagic, 72 ± 15 kJ mol−1 for the mesopelagic and 274 ± 65 kJ mol−1 for the bathypelagic realm. We suggest that the increasing temperature dependence with depth is related to the parallel vertical gradient in the proportion of recalcitrant organic compounds. These Ea predict an increased PHP of about 5, 12, and 55% in the epi-, meso-, and bathypelagic ocean, respectively, in response to a water temperature increase by 1°C. Hence, there is indication that a major thus far underestimated feedback mechanism exists between future bathypelagic ocean warming and heterotrophic prokaryotic activityFinancial support for this project was provided by the Australian Institute of Marine Science (AIMS) and a grant from the Carlsberg Foundation to CL. XA, XM and JG were funded by the Malaspina expedition 2010 (grant n° CSD2008–00077) and HOTMIX (grant n° CTM2011–30010–C02–02) projects. TR was supported by the PADOM project (Austrian Science Fund grant n° P23221-B11). GH was funded by the Austrian Science Fund (FWF) project I486-B09 and by the European Research Council under the European Community's Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement No. 268595 (MEDEA project).Peer reviewe

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

Seasonal patterns of microbial diversity across the world oceans

Understanding the patterns of marine microbial diversity (Bacteria + Archaea) is essential, as variations in their alpha- and beta-diversities can affect ecological processes. Investigations of microbial diversity from global oceanographic expeditions and basin-wide transects show positive correlations between microbial diversity and either temperature or productivity, but these studies rarely captured seasonality, especially in polar regions. Here, using multiannual alpha-diversity data from eight time series in the northern and southern hemispheres, we show that marine microbial community richness and evenness generally correlate more strongly with daylength than with temperature or chlorophyll a (a proxy for photosynthetic biomass). This pattern is observable across time series found in the northern and southern hemispheres regardless of collection method, DNA extraction protocols, targeted 16S rRNA hypervariable region, sequencing technology, or bioinformatics pipeline

Hiding in plain sight: The globally distributed bacterial candidate phylum PAUC34f

Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments. © Copyright © 2020 Chen, Becraft, Pachiadaki, Brown, Jarett, Gasol, Ravin, Moser, Nunoura, Herndl, Woyke and Stepanauskas

Transient Changes in Bacterioplankton Communities Induced by the Submarine Volcanic Eruption of El Hierro (Canary Islands)

Postprint4,411