Seasonal variation of the sound-scattering zooplankton vertical distribution in the oxygen-deficient waters of the NE Black Sea

At the northeastern Black Sea research site, observations from 2010–2020 allowed us to study the dynamics and evolution of the vertical distribution of mesozooplankton in oxygen-deficient conditions via analysis of sound-scattering layers associated with dominant zooplankton aggregations. The data were obtained with profiler mooring and zooplankton net sampling. The profiler was equipped with an acoustic Doppler current meter, a conductivity–temperature–depth probe, and fast sensors for the concentration of dissolved oxygen [O2]. The acoustic instrument conducted ultrasound (2 MHz) backscatter measurements at three angles while being carried by the profiler through the oxic zone. For the lower part of the oxycline and the hypoxic zone, the normalized data of three acoustic beams (directional acoustic backscatter ratios, R) indicated sound-scattering mesozooplankton aggregations, which were defined by zooplankton taxonomic and quantitative characteristics based on stratified net sampling at the mooring site. The time series of ∼ 14 000 R profiles as a function of [O2] at depths where [O2] < 200 µm were analyzed to determine month-to-month variations of the sound-scattering layers. From spring to early autumn, there were two sound-scattering maxima corresponding to (1) daytime aggregations, mainly formed by diel-vertical-migrating copepods Calanus euxinus and Pseudocalanus elongatus and chaetognaths Parasagitta setosa, usually at [O2] = 15–100 µm, and (2) a persistent monospecific layer of the diapausing fifth copepodite stages of C. euxinus in the suboxic zone at 3 µm < [O2] < 10 µm. From late autumn to early winter, no persistent deep sound-scattering layer was observed. At the end of winter, the acoustic backscatter was basically uniform in the lower part of the oxycline and the hypoxic zone. The assessment of the seasonal variability of the sound-scattering mesozooplankton layers is important for understanding biogeochemical processes in oxygen-deficient waters.

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics

Background The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former, albeit with lower salinity and temperature. Despite its well-known hydrology and physicochemical features, this enormous water mass remains poorly studied at the microbial genomics level. Results We have sampled its different water masses and analyzed the microbiome by shotgun and genome-resolved metagenomics, generating a large number of metagenome-assembled genomes (MAGs) from them. We found various similarities with previously described Black Sea metagenomic datasets, that show remarkable stability in its microbiome. Our datasets are also comparable to other marine anoxic water columns like the Cariaco Basin. The oxic zone resembles to standard marine (e.g. Mediterranean) photic zones, with Cyanobacteria (Synechococcus but a conspicuously absent Prochlorococcus), and photoheterotrophs domination (largely again with marine relatives). The chemocline presents very different characteristics from the oxic surface with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. The euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy-generating metabolism, a few (but detectable) methanogenesis marker genes, and a large number of “dark matter” streamlined genomes of largely unpredictable ecology. Conclusions The Black Sea oxic zone presents many similarities to the global ocean while the redoxcline and euxinic water masses have similarities to other similar aquatic environments of marine (Cariaco Basin or other Black Sea regions) or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environment. We are adding critical information about this unique and important ecosystem and its microbiome.

The impact of depositional conditions on biogeochemical cycling of iron and stable iron signatures in sediments of the Argentina Continental Margin

&lt;p&gt;The Argentina Continental Margin represents a unique geologic setting to study interactions between bottom currents and sediment deposition as well as their impact on (bio)geochemical processes, particularly the cycling of iron (Fe). Our aim was to determine (1) how different depositional conditions control post-depositional (bio)geochemical processes and (2) how stable Fe isotopes (&amp;#948;&lt;sup&gt;56&lt;/sup&gt;Fe) of pore water and solid phases are affected accordingly. Furthermore, we (3) evaluated the applicability of &amp;#948;&lt;sup&gt;56&lt;/sup&gt;Fe of solid Fe pools as a proxy to trace past diagenetic alteration of Fe, which might be decoupled from current redox conditions. Sediments from two different depositional environments were sampled during RV SONNE expedition SO260: a site dominated by contouritic deposition on a terrace (Contourite Site) and the lower continental slope (Slope Site) dominated by hemipelagic sedimentation. Sequentially extracted sedimentary Fe [1] and &amp;#948;&lt;sup&gt;56&lt;/sup&gt;Fe analyses of extracts and pore water [2,3] were combined with sedimentological, radioisotope, geochemical and magnetic data. Our study presents the first sedimentary &amp;#948;&lt;sup&gt;56&lt;/sup&gt;Fe dataset at the Argentina Continental Margin.&lt;/p&gt;&lt;p&gt;The depositional conditions differed between and within both sites as evidenced by variable grain sizes, organic carbon contents and sedimentation rates. At the Contourite Site, non-steady state pore-water conditions and diagenetic overprint occurs in the post-oxic zone and the sulfate-methane transition (SMT). In contrast, pore-water profiles at the Slope Site suggest that currently steady-state conditions prevail, leading to a strong diagenetic overprint of Fe oxides at the SMT. Pore-water &amp;#948;&lt;sup&gt;56&lt;/sup&gt;Fe values at the Slope Site are mostly negative, which is typical for on-going microbial Fe reduction. At the Contourite Site the pore-water &amp;#948;&lt;sup&gt;56&lt;/sup&gt;Fe values are mostly positive and range between -0.35&amp;#8240; to 1.82&amp;#8240;. Positive &amp;#948;&lt;sup&gt;56&lt;/sup&gt;Fe values are related to high sulfate reduction rates that dominate over Fe reduction in the post-oxic zone. The HS&lt;sup&gt;- &lt;/sup&gt;liberated during organoclastic sulfate reduction or sulfate-mediated anaerobic oxidation of methane (AOM) reacts with Fe&lt;sup&gt;2+&lt;/sup&gt; to form Fe sulfides. Hereby, light Fe isotopes are preferentially removed from the dissolved pool. The isotopically light Fe sulfides drive the acetate-leached Fe pool towards negative values. Isotopic trends were absent in other extracted Fe pools, partly due to unintended dissolution of silicate Fe masking the composition of targeted Fe oxides. Significant amounts of reactive Fe phases are preserved below the SMT and are possibly available for reduction processes, such as Fe-mediated AOM [4]. Fe&lt;sup&gt;2+&lt;/sup&gt; in the methanic zone is isotopically light at both sites, which is indicative for a microbial Fe reduction process.&lt;/p&gt;&lt;p&gt;Our results demonstrate that depositional conditions exert a significant control on geochemical conditions and dominant (bio)geochemical processes in the sediments of both contrasting sites. We conclude that the applicability of sedimentary &amp;#948;&lt;sup&gt;56&lt;/sup&gt;Fe signatures as a proxy to trace diagenetic Fe overprint is limited to distinct Fe pools. The development into a useful tool depends on the refining of extraction methods or other means to analyse &amp;#948;&lt;sup&gt;56&lt;/sup&gt;Fe in specific sedimentary Fe phases.&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;References:&lt;/p&gt;&lt;p&gt;[1]Poulton and Canfield, 2005. Chemical Geology 214: 209-221.&lt;br&gt;[2]Henkel et al., 2016. Chemical Geology 421: 93-102.&lt;br&gt;[3]Homoky et al., 2013. Nature Communications 4: 1-10.&lt;br&gt;[4]Riedinger et al., 2014. Geobiology 12: 172-181.&lt;/p&gt;

Microbiome of the Black Sea Water Column Analyzed by Genome Centric Metagenomics

Background: The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former albeit with lower salinity and (mostly) temperature. In spite of its well-known hydrology and physico chemistry, this enormous water mass remains poorly studied at the microbial genomics level. Results: We have sampled its different water masses and analyzed the microbiome by classic and genome-resolved metagenomics generating a large number of metagenome-assembled genomes (MAGs) from them. The oxic zone presents many similarities to the global ocean while the euxinic water mass has similarities to other similar aquatic environments of marine or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environments and includes Cyanobacteria (Synechococcus), photoheterotrophs (largely with marine relatives), facultative/microaerophilic microbes again largely marine, chemolithotrophs (N and S oxidizers) and a large number of anaerobes, mostly sulfate reducers but also a few methanogens and a large number of “dark matter” streamlined genomes of largely unpredictable ecology. Conclusions: The Black Sea presents a mixture of similarities to other water bodies. The photic zone has many microbes in common with that of the Mediterranean with the relevant exception of the absence of Prochlorococcus. The chemocline already presents very different characteristics with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. Finally the euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy generating metabolism and a small but detectable methanogenesis.We are adding critical information about this unique and important ecosystem and its microbiome.

Microbiome of the Black Sea water column analyzed by genome centric metagenomics

BackgroundThe Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former albeit with lower salinity and (mostly) temperature. In spite of its well-known hydrology and physico chemistry, this enormous water mass remains poorly studied at the microbial genomics level.ResultsWe have sampled its different water masses and analyzed the microbiome by classic and genome-resolved metagenomics generating a large number of metagenome-assembled genomes (MAGs) from them. The oxic zone presents many similarities to the global ocean while the euxinic water mass has similarities to other similar aquatic environments of marine or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environments and includes Cyanobacteria (Synechococcus), photoheterotrophs (largely with marine relatives), facultative/microaerophilic microbes again largely marine, chemolithotrophs (N and S oxidizers) and a large number of anaerobes, mostly sulfate reducers but also a few methanogens and a large number of “dark matter” streamlined genomes of largely unpredictable ecology.ConclusionsThe Black Sea presents a mixture of similarities to other water bodies. The photic zone has many microbes in common with that of the Mediterranean with the relevant exception of the absence of Prochlorococcus. The chemocline already presents very different characteristics with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. Finally the euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy generating metabolism and a small but detectable methanogenesis.We are adding critical information about this unique and important ecosystem and its microbiome.

Quantification of Hyporheic Nitrate Removal at the Reach Scale: Exposure Times versus Residence Times

&lt;p&gt;The rate of biogeochemical processing associated with natural degradation and transformation processes in the hyporheic zone (HZ) is one of the largest uncertainties in predicting nutrient fluxes. We present a lumped parameter (LPM) model that can be used to quantify the mass loss for nitrate in the HZ operating at the scale of river reaches to entire catchments. The model is based on using exposure times (ET) to account for the effective timescales of reactive transport in the HZ. Reach scale ET distributions are derived by removing the portion of hyporheic residence times (RT) associated with flow through the oxic zone. The model was used to quantify nitrate removal for two scenarios: 1) a 100 m generic river reach and 2) a small agricultural catchment in Brittany (France). For the field site hyporheic RT are derived from measured in-stream &lt;sup&gt;222&lt;/sup&gt;Rn activities and mass balance modelling. Simulations were carried out using different types of RT distributions (exponential, power-law and gamma-type) for which ET were derived. Mass loss of nitrate in the HZ for the field site ranged from 0-0.45 kg d&lt;sup&gt;-1&lt;/sup&gt; depending on the RT distribution and the availability of oxygen in the streambed sediments. Simulations with power law ET distribution models only show very little removal of nitrate due to the heavy weighting towards shorter flow paths that are confined to the oxic sediments.&amp;#160; Based on the simulation results, we suggest that ET likely lead to more realistic estimates for nutrient removal.&lt;/p&gt;

Division of labor and growth during electrical cooperation in multicellular cable bacteria

Multicellularity is a key evolutionary innovation, leading to coordinated activity and resource sharing among cells, which generally occurs via the physical exchange of chemical compounds. However, filamentous cable bacteria display a unique metabolism in which redox transformations in distant cells are coupled via long-distance electron transport rather than an exchange of chemicals. This challenges our understanding of organismal functioning, as the link among electron transfer, metabolism, energy conservation, and filament growth in cable bacteria remains enigmatic. Here, we show that cells within individual filaments of cable bacteria display a remarkable dichotomy in biosynthesis that coincides with redox zonation. Nanoscale secondary ion mass spectrometry combined with 13C (bicarbonate and propionate) and 15N-ammonia isotope labeling reveals that cells performing sulfide oxidation in deeper anoxic horizons have a high assimilation rate, whereas cells performing oxygen reduction in the oxic zone show very little or no label uptake. Accordingly, oxygen reduction appears to merely function as a mechanism to quickly dispense of electrons with little to no energy conservation, while biosynthesis and growth are restricted to sulfide-respiring cells. Still, cells can immediately switch roles when redox conditions change, and show no differentiation, which suggests that the “community service” performed by the cells in the oxic zone is only temporary. Overall, our data reveal a division of labor and electrical cooperation among cells that has not been seen previously in multicellular organisms.

The effect of unsteady streamflow and stream-groundwater interactions on oxygen consumption in a sandy streambed

Streamflow dynamics are often ignored when studying biogeochemical processes in the hyporheic zone. We explored the interactive effects of unsteady streamflow and groundwater fluxes on the delivery and consumption of oxygen within the hyporheic zone using a recirculating flume packed with natural sandy sediments. The flume was equipped with a programmable streamflow control and drainage system that was used to impose losing and gaining fluxes. Tracer tests were used to measure hyporheic exchange flux and a planar optode was used to measure subsurface oxygen concentration patterns. It was found that the volume of the oxic zone decreased when the losing flux declined, and was drastically decreased when gaining conditions were applied. It was also found that unsteady streamflow led to a slight increase in the average volume of the oxic zone, compared to the average volume of the oxic zone under steady streamflow. However, the average oxygen consumption rates were significantly higher under unsteady streamflow compared to steady streamflow under all groundwater conditions with the exception of the highest losing flux. The present study provides the first insight into the interactions between streamflow unsteadiness and losing/gaining fluxes and improve understanding of their impact on microbial metabolism in the hyporheic zone.

On the evolution and physiology of cable bacteria

Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes of 3 marine Candidatus Electrothrix and 1 freshwater Ca. Electronema species. These genomes contain >50% unknown genes but still share their core genomic makeup with sulfate-reducing and sulfur-disproportionating Desulfobulbaceae, with few core genes lost and 212 unique genes (from 197 gene families) conserved among cable bacteria. Last common ancestor analysis indicates gene divergence and lateral gene transfer as equally important origins of these unique genes. With support from metaproteomics of a Ca. Electronema enrichment, the genomes suggest that cable bacteria oxidize sulfide by reversing the canonical sulfate reduction pathway and fix CO2 using the Wood–Ljungdahl pathway. Cable bacteria show limited organotrophic potential, may assimilate smaller organic acids and alcohols, fix N2, and synthesize polyphosphates and polyglucose as storage compounds; several of these traits were confirmed by cell-level experimental analyses. We propose a model for electron flow from sulfide to oxygen that involves periplasmic cytochromes, yet-unidentified conductive periplasmic fibers, and periplasmic oxygen reduction. This model proposes that an active cable bacterium gains energy in the anodic, sulfide-oxidizing cells, whereas cells in the oxic zone flare off electrons through intense cathodic oxygen respiration without energy conservation; this peculiar form of multicellularity seems unparalleled in the microbial world.