Dynamic prokaryotic communities in the dark western Mediterranean Sea

Dark ocean microbial dynamics are fundamental to understand ecosystem metabolism and ocean biogeochemical processes. Yet, the ecological response of deep ocean communities to environmental perturbations remains largely unknown. Temporal and spatial dynamics of the meso- and bathypelagic prokaryotic communities were assessed throughout a 2-year seasonal sampling across the western Mediterranean Sea. A common pattern of prokaryotic communities’ depth stratification was observed across the different regions and throughout the seasons. However, sporadic and drastic alterations of the community composition and diversity occurred either at specific water masses or throughout the aphotic zone and at a basin scale. Environmental changes resulted in a major increase in the abundance of rare or low abundant phylotypes and a profound change of the community composition. Our study evidences the temporal dynamism of dark ocean prokaryotic communities, exhibiting long periods of stability but also drastic changes, with implications in community metabolism and carbon fluxes. Taken together, the results highlight the importance of monitoring the temporal patterns of dark ocean prokaryotic communities.Versión del editor2,92

High dark CO2 fixation rates by active chemolithoautotrophic microbes along the water column (100-5000m) off Galicia (NW Iberian margin)

Poster communicationOur results provide evidence for the significant contribution to chemolithotrophy by specific archaeal and bacterial groups in the dark ocean

Assessing the apparent imbalance between geochemical and biochemical indicators of meso- and bathypelagic biological activity: What the @$#! is wrong with present calculations of carbon budgets?

Metabolic activity in the water column below the euphotic zone is ultimately fuelled by the vertical flux of organic material from the surface. Over time, the deep ocean is presumably at steady state, with sources and sinks balanced. But recently compiled global budgets and intensive local field studies suggest that estimates of metabolic activity in the dark ocean exceed the influx of organic substrates. This imbalance indicates either the existence of unaccounted sources of organic carbon or that metabolic activity in the dark ocean is being over-estimated. Budgets of organic carbon flux and metabolic activity in the dark ocean have uncertainties associated with environmental variability, measurement capabilities, conversion parameters, and processes that are not well sampled. We present these issues and quantify associated uncertainties where possible, using a Monte Carlo analysis of a published data set to determine the probability that the imbalance can be explained purely by uncertainties in measurements and conversion factors. A sensitivity analysis demonstrates that the bacterial growth efficiencies and assumed cell carbon contents have the greatest effects on the magnitude of the carbon imbalance. Two poorly quantified sources, lateral advection of particles and a population of slowly settling particles, are discussed as providing a means of closing regional carbon budgets. Finally, we make recommendations concerning future research directions to reduce important uncertainties and allow a better determination of the magnitude and causes of the unbalanced carbon budgets. (C) 2010 Elsevier Ltd. All rights reserved

Prokaryotic respiration and production in the meso- and bathypelagic realm of the eastern and western North Atlantic basin

We measured prokaryotic production and respiration in the major water masses of the North Atlantic down to a depth of,4,000 m by following the progression of the two branches of North Atlantic Deep Water (NADW) in the oceanic conveyor belt. Prokaryotic abundance decreased exponentially with depth from 3 to 0.4 3 105 cells mL21 in the eastern basin and from 3.6 to 0.3 3 105 cells mL21 in the western basin. Prokaryotic production measured via 3H-leucine incorporation showed a similar pattern to that of prokaryotic abundance and decreased with depth from 9.2 to 1.1 mmol C m23 d21 in the eastern and from 20.6 to 1.2 mmol C m23 d21 in the western basin. Prokaryotic respiration, measured via oxygen consumption, ranged from about 300 to 60 mmol C m23 d21 from,100 m depth to the NADW. Prokaryotic growth efficiencies of,2 % in the deep waters (depth range 1,200–4,000 m) indicate that the prokaryotic carbon demand exceeds dissolved organic matter input and surface primary production by 2 orders of magnitude. Cell-specific prokaryotic production was rather constant throughout the water column, ranging from 15 to 32 3 1023 fmol C cell21 d21 in the eastern and from 35 to 58

Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump

The role of the ocean as a sink for CO2 is partially dependent on the downward transport of phytoplankton cells packaged within fast-sinking particles. However, whether such fast-sinking mechanisms deliver fresh organic carbon down to the deep bathypelagic sea and whether this mechanism is prevalent across the ocean requires confirmation. Here we report the ubiquitous presence of healthy photosynthetic cells, dominated by diatoms, down to 4,000 m in the deep dark ocean. Decay experiments with surface phytoplankton suggested that the large proportion (18%) of healthy photosynthetic cells observed, on average, in the dark ocean, requires transport times from a few days to a few weeks, corresponding to sinking rates (124–732 m d−1) comparable to those of fast-sinking aggregates and faecal pellets. These results confirm the expectation that fast-sinking mechanisms inject fresh organic carbon into the deep sea and that this is a prevalent process operating across the global oligotrophic ocean

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

Dark CO2 fixation by chemolithoautotrophic prokaryotes in the deep-water masses of the north-west coast of the Iberian Peninsule

Recent studies suggest that the prokaryotes inhabiting the dark ocean present higher chemolithoautotrophic activity than assumed previously. These chemolithoautotrophic microbes incorporate dissolved inorganic carbon (DIC) as carbon source for biomass production and use reduced inorganic compound as an energy source. We have quantified DIC fixation in the meso- and bathypelagic waters of the northwestern coast of the Iberian Peninsula, ranging from 1.04 to 46.83 mmol C m-2 d-1. Combining microautoradiography and fluorescence in situ hybridization (MICRO-CARD-FISH), we confirmed that both Thaumarchaeota and some bacterial groups such as SAR-11, SAR-202, SAR-406, Alteromonas take up bicarbonate uptake, particularly in the mesopelagic waters. Quantitative PCR analyses clearly showed a higher abundance of thaumarchaeal 16S and low ammonia concentration (LAC)- amoA genes in meso- and lower bathypelagic waters than in surface waters. In contrast, high ammonia concentration (HAC)- amoA genes dominated the subsurface samples. Taken together, both genomic and physiological evidences indicate that some archaeal and bacterial groups may be significant contributors to dark ocean chemoautolithotrophy

Chromophoric signatures of microbial by-products in the dark ocean

En prensa3,792

Diversity and abundance of planktonic communities in the deep waters off the galician coast (NW Spain)

Comunicación oralPlanktonic communities play pivotal roles within marine ecosystems, affecting their structure, functioning and services. Although they have been extensively studied in the epipelagic ocean, the knowledge about these communities in the dark ocean is rather short. In this study, we explored patterns of abundance and biomass of a wide variety of taxonomic groups from the prokaryotes to mesozooplankton in the epi-, meso- and bathypelagic waters off the Galician coast. As expected, ciliate and zooplankton abundances are depleted in the bathypelagic waters relative to abundances of prokaryotes and nanoflagellates. The rate of decrease of zooplankton biomass with depth is twice as that of prokaryotes and nanoflagellates, indicating that relative contribution of mesozooplancton to the total plankton biomass decreases with depth. Overall, the diversity of prokaryotes in the dark ocean is almost as high as in the epipelagic layer, although the phylotypes are different. The major fraction of epipelagic ciliates belongs to alloricate genera, whereas tintinnids dominate the deep ciliate populations. Small copepods were dominant in the epi- and meso-pelagic zone. By contrast, foraminiferans, big copepods and myctophic fishes were more abundant in the deep ocean

A device for assesing microbial activity under ambient hydrostatic pressure: The in situ microbial incubator (ISMI)

Research articleMicrobes in the dark ocean are exposed to hydrostatic pressure increasing with depth. Activity rate measurements and biomass production of dark ocean microbes are, however, almost exclusively performed under atmospheric pressure conditions due to technical constraints of sampling equipment maintaining in situ pressure conditions. To evaluate the microbial activity under in situ hydrostatic pressure, we designed and thoroughly tested an in situ microbial incubator (ISMI). The ISMI allows autonomously collecting and incubating seawater at depth, injection of substrate and fixation of the samples after a preprogramed incubation time. The performance of the ISMI was tested in a high-pressure tank and in several field campaigns under ambient hydrostatic pressure by measuring prokaryotic bulk 3H-leucine incorporation rates. Overall, prokaryotic leucine incorporation rates were lower at in situ pressure conditions than under to depressurized conditions reaching only about 50% of the heterotrophic microbial activity measured under depressurized conditions in bathypelagic waters in the North Atlantic Ocean off the northwestern Iberian Peninsula. Our results show that the ISMI is a valuable tool to reliably determine the metabolic activity of deep-sea microbes at in situ hydrostatic pressure conditions. Hence, we advocate that deep-sea biogeochemical and microbial rate measurements should be performed under in situ pressure conditions to obtain a more realistic view on deep-sea biotic processes.IEO-CSIC, FWF, KAKENHI, ERC and GAI