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

Anterior talofibular ligament's superior fascicle as a cause of ankle microinstability can be routinely identified by ultrasound.

PURPOSE: Chronic pain can affect up to 40% of patients after ankle inversion sprains. The current hypothesis to explain this high percentage of chronic pain is a partial/total rupture of anterior talofibular ligament (ATFL) superior fascicle, a structure that has recently been described as intra-articular and as having a different function than ATFL's inferior fascicle. This has created the need for diagnosing ATFL superior and inferior fascicles independently. Therefore, the objective of this study is to investigate if the ATFL's superior fascicle can be visualized on ultrasound, and to describe its ultrasonographic appearance. METHODS: Twenty fresh-frozen ankle specimens were used in this 4-phases study. First, the specimens were scanned on US to identify what was believed to be ATFL's superior fascicle. Second, ATFL's superior fascicle was sutured under direct arthroscopic vision. Next, the specimens were scanned on US to obtain an image of the sutured structure. Finally, the specimens were dissected to confirm that the suture was indeed placed on ATFL's superior fascicle. RESULTS: On the 20 specimens studied, full correlation was obtained between US, arthroscopic suture and specimen dissection. ATFL's superior fascicle US appearance is provided. CONCLUSION: ATFL's superior fascicle can be visualized on US, which will allow to undergo diagnosis of isolated injuries to that fascicle, a common finding in ankle microinstability. The results of this study will facilitate the diagnosis of partial or complete rupture of ATFL's superior fascicle, likely increasing the amount of ankle microinstability diagnosis, impacting clinical management of ankle sprain consequences

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

Postprint4,411

Diel vertical migrants and the ocean carbon pump: is there a ladder of migration?

Active flux performed by migrant biota is still a gap in the knowledge of the biological pump in the ocean. These organisms mainly feed upon epipelagic zooplankton and transport this carbon due to their feeding at the shallower layers and their defecation, respiration, excretion and mortality at depth. The recent finding that mesopelagic fish biomass in the ocean is one order of magnitude higher indicates that the active flux should be thoroughly evaluated. Here, we show enhanced plankton biomass, ranging from bacteria to zooplankton, reaching down to 4,000 m depth below the Atlantic and Pacific equatorial upwelling systems. We also found a striking close relationship between the zooplankton backscatter enhancement in the epi-, meso- and bathypelagic zones. Backscatter increased in a similar proportion along the subtropical, tropical, and equatorial areas in the three zones. Literature, recent data in subtropical waters, and these results suggest an intense active carbon transport from the epipelagic layer to the deep sea driven by zooplankton and micronekton, enhancing the efficiency of the biological pump and promoting true carbon sequestration beyond 1000 m depth.MALASPINA (CSD2008 00077) MAFIA (CTM2012-39587-C04

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