Direct cell mass measurements expand the role of small microorganisms in nature.

Microbial biomass is a key parameter needed for the quantification of microbial turnover rates and their contribution to the biogeochemical element cycles. However, estimates of microbial biomass rely on empirically-derived mass-to-volume relationships and large discrepancies exist between the available empirical conversion factors. Here we report a significant non-linear relationship between carbon mass and cell volume (mcarbon = 197 × V0.46.; R2 = 0.95) based on direct cell mass, volume and elemental composition measurements of twelve prokaryotic species with average volumes between 0.011 – 0.705 μm3. The carbon mass density of our measured cells ranged from 250 to 1800 fg C μm-3 for the measured cell volumes. Compared to other currently used models, our relationship yielded up to 300 % higher carbon mass values. A compilation of our and previously published data showed that cells with larger volumes (> 0.5 μm3) display a constant (carbon) mass-to-volume ratio whereas cells with volumes below 0.5 μm3 exhibit a nonlinear increase in (carbon) mass density with decreasing volume. Small microorganisms dominate marine and freshwater bacterioplankton as well as soils and marine and terrestrial subsurface. The application of our experimentally-determined conversion factors will help to quantify the true contribution of these microorganisms to ecosystem functions and global microbial biomass

Report and preliminary results of R/V POSEIDON cruise POS539, Varna (Bulgaria) - Varna (Bulgaria) November 6 - November 21, 2019

The R/V POSEIDON cruise POS539 took place in the northwestern basin of the Black Sea (42°30’N to 44°N and 29°E to 31°E). The overarching aim of the campaign was to obtain sediment and water samples, including suspended particle material, from the various redox zones of the Black Sea. The campaign lasted between November 6th and November 21st 2019 and the collected samples were taken in order to investigate the activity and physiology of microorganisms involved in the conversion of nitrogen compounds and degradation of organic carbon under various oxygen conditions. The main topics of the cruise were: (a) to quantify the contribution of archaeal nitrifiers to the nitrogen and carbon cycles, b) to measure the production and consumption of the powerful greenhouse gases CH4 and N2O, c) to record palaeoenvironmental changes in high resolution, and d) to describe the complexity and identity of biopolymers. For this, water and sediment samples were retrieved from 10 discrete shelf and slope stations. First, ‘deep water’ transect was conducted, which included three stations with water depths over 2000 m. The second perpendicular transect encompassed stations that gradually transitioned from the deep parts of the slope towards the shelf (ca. 80 m depth). Additionally, two stations were setup north and south of the shelf transect, respectively, for paleoceanographic studies. Throughout the cruise the weather conditions were overwhelmingly good, only towards the end of the campaign gusty winds of 7 Bft were recorded. The recorded oceanographic conditions were in agreement with the expected water properties at all stations. Station activities were completed on November 20th at 14:00 local board time. On November 21st at 10:30 local time, R/V POSEIDON reached the port of Varna, Bulgaria, thus concluding the POS539 expedition. Analyses and results from the samples and experiments will provide a basis for our understanding of the microbial control on the carbon and nitrogen cycle of the Black Sea.13032

Dark aerobic sulfide oxidation by anoxygenic phototrophs in anoxic waters

Anoxygenic phototrophic sulfide oxidation by green and purple sulfur bacteria (PSB) plays a key role in sulfide removal from anoxic shallow sediments and stratified waters. Although some PSB can also oxidize sulfide with nitrate and oxygen, little is known about the prevalence of this chemolithotrophic lifestyle in the environment. In this study, we investigated the role of these phototrophs in light‐independent sulfide removal in the chemocline of Lake Cadagno. Our temporally resolved, high‐resolution chemical profiles indicated that dark sulfide oxidation was coupled to high oxygen consumption rates of ~9 μM O2·h−1. Single‐cell analyses of lake water incubated with 13CO2 in the dark revealed that Chromatium okenii was to a large extent responsible for aerobic sulfide oxidation and it accounted for up to 40% of total dark carbon fixation. The genome of Chr. okenii reconstructed from the Lake Cadagno metagenome confirms its capacity for microaerophilic growth and provides further insights into its metabolic capabilities. Moreover, our genomic and single‐cell data indicated that other PSB grow microaerobically in these apparently anoxic waters. Altogether, our observations suggest that aerobic respiration may not only play an underappreciated role in anoxic environments but also that organisms typically considered strict anaerobes may be involved

Ideas and Perspectives: A Strategic Assessment of Methane and Nitrous Oxide Measurements In the Marine Environment

In the current era of rapid climate change, accurate characterization of climate-relevant gas dynamics-namely production, consumption, and net emissions-is required for all biomes, especially those ecosystems most susceptible to the impact of change. Marine environments include regions that act as net sources or sinks for numerous climateactive trace gases including methane (CH4) and nitrous oxide (N2O). The temporal and spatial distributions of CH4 and N2O are controlled by the interaction of complex biogeochemical and physical processes. To evaluate and quantify how these mechanisms affect marine CH4 and N2O cycling requires a combination of traditional scientific disciplines including oceanography, microbiology, and numerical modeling. Fundamental to these efforts is ensuring that the datasets produced by independent scientists are comparable and interoperable. Equally critical is transparent communication within the research community about the technical improvements required to increase our collective understanding of marine CH4 and N2O. A workshop sponsored by Ocean Carbon and Biogeochemistry (OCB) was organized to enhance dialogue and collaborations pertaining to marine CH4 and N2O. Here, we summarize the outcomes from the workshop to describe the challenges and opportunities for near-future CH4 and N2O research in the marine environment

Distributions and compound-specific isotopic signatures of sedimentary chlorins reflect the composition of photoautotrophic communities and their carbon and nitrogen sources in Swiss lakes and the Black Sea

We examined the distributions of tetrapyrrole pigments (i.e. intact chlorophylls and bacteriochlorophylls, pheopigments) as well as their compound-specific carbon and nitrogen isotopic compositions in the sediments of three Swiss lakes (Lakes Rotsee, Cadagno and Zurich) and the Black Sea to investigate the biogeochemical cycling of carbon and nitrogen mediated by phototrophic eukaryotes (algae) and bacteria. The factors controlling chlorin isotope variations are discussed and the feasibility to use chlorins as indicators for reconstructions of surface water environments is evaluated. Chlorophyll a and its derivatives including pheophytin a, a pheophytin a epimer, pyropheophytin a, 132,173-cyclopheophorbide-a-enol, chlorophyllone a as well as steryl and carotenol chlorin esters were detected in all sediments. The presence of bacteriochlorophylls e and their derivatives confirmed the presence of brown strains of green phototrophic sulfur bacteria (Chlorobiaceae; GSB) in all three lakes. In the shallower Lakes Rotsee and Cadagno, purple sulfur bacteria (Chromatiaceae; PSB) were also present as confirmed by bacteriochlorophyll a derivatives. Despite the different degrees of water column hypoxia at the studied sites, the chlorins in all sediments were attributed to rapid transformation of intact tetrapyrroles and the formation of related pheopigments.The scatter of compound-specific carbon isotopic compositions of Chl a and its derivatives resulted from different timing of pheopigment formation, likely due to the interaction of blooms of various phytoplankton communities at different times of the year and the variable degrees of carbon limitation and/or different contributions of recycled organic matter (OM). The nitrogen isotopic composition of the chloropigments mainly derived from nitrate assimilation in Lake Zurich and the Black Sea, whereas ammonium and nitrate assimilation were predominant in Lake Rotsee. In the epilimnion of the meromictic Lake Cadagno, dissolved organic nitrogen (DON) supplied to the surface water from ammonium assimilation in the chemocline may be the main nitrogen source. Phototrophic sulfur bacteria in Lakes Rotsee and Cadagno thrived mainly under dissolved organic carbon depleted conditions within the chemocline and in the hypolimnion. GSB may use predominantly ammonium and at least in Lake Cadagno also perform N2 fixation. In contrast, the nitrogen source of PSB could not be reconstructed with d15N values of bacteriochlorins, because nitrogen isotopic fractionation during BChl a synthesis seems to be almost independent of the assimilated substrate

An automated Raman-based platform for the sorting of live cells by functional properties

Stable-isotope probing is widely used to study the function of microbial taxa in their natural environment, but sorting of isotopically labelled microbial cells from complex samples for subsequent genomic analysis or cultivation is still in its early infancy. Here, we introduce an optofluidic platform for automated sorting of stable-isotope-probing-labelled microbial cells, combining microfluidics, optical tweezing and Raman microspectroscopy, which yields live cells suitable for subsequent single-cell genomics, mini-metagenomics or cultivation. We describe the design and optimization of this Raman-activated cell-sorting approach, illustrate its operation with four model bacteria (two intestinal, one soil and one marine) and demonstrate its high sorting accuracy (98.3 ± 1.7%), throughput (200-500 cells h-1; 3.3-8.3 cells min-1) and compatibility with cultivation. Application of this sorting approach for the metagenomic characterization of bacteria involved in mucin degradation in the mouse colon revealed a diverse consortium of bacteria, including several members of the underexplored family Muribaculaceae, highlighting both the complexity of this niche and the potential of Raman-activated cell sorting for identifying key players in targeted processes.</p

Methane-carbon flow into the benthic food web at cold seeps – a case study from the Costa Rica subduction zone

Cold seep ecosystems can support enormous biomasses of free-living and symbiotic chemoautotrophic organisms that get their energy from the oxidation of methane or sulfide. Most of this biomass derives from animals that are associated with bacterial symbionts, which are able to metabolize the chemical resources provided by the seeping fluids. Often these systems also harbor dense accumulations of non-symbiotic megafauna, which can be relevant in exporting chemosynthetically fixed carbon from seeps to the surrounding deep sea. Here we investigated the carbon sources of lithodid crabs (Paralomis sp.) feeding on thiotrophic bacterial mats at an active mud volcano at the Costa Rica subduction zone. To evaluate the dietary carbon source of the crabs, we compared the microbial community in stomach contents with surface sediments covered by microbial mats. The stomach content analyses revealed a dominance of epsilonproteobacterial 16S rRNA gene sequences related to the free-living and epibiotic sulfur oxidiser Sulfurovum sp. We also found Sulfurovum sp. as well as members of the genera Arcobacter and Sulfurimonas in mat-covered surface sediments where Epsilonproteobacteria were highly abundant constituting 10% of total cells. Furthermore, we detected substantial amounts of bacterial fatty acids such as i-C15:0 and C17:1ω6c with stable carbon isotope compositions as low as −53‰ in the stomach and muscle tissue. These results indicate that the white microbial mats at Mound 12 are comprised of Epsilonproteobacteria and that microbial mat-derived carbon provides an important contribution to the crab's nutrition. In addition, our lipid analyses also suggest that the crabs feed on other 13C-depleted organic matter sources, possibly symbiotic megafauna as well as on photosynthetic carbon sources such as sedimentary detritus

A Mississippian black shale record of redox oscillation in the Craven Basin, UK

Early diagenetic redox oscillation processes have been rarely recognised in the ancient rock record but potentially exert an important control on mineral authigenesis, hydrocarbon prospectivity and supply of metals and/or reduced S as part of associated mineral systems. The upper unit of the Mississippian Bowland Shale Formation is a candidate record of diagenetic redox oscillation processes because it was deposited under a relatively high sediment accumulation rate linked to a large delta system, and under dominantly anoxic and intermittently sulphidic bottom-water conditions. In order to characterise the syngenetic and early diagenetic processes, sedimentological and geochemical data were integrated through the Upper Bowland Shale at three sites in the Craven Basin (Lancashire, UK). Organic matter (OM) comprises a mixture of Type II, II-S, II/III and III OM. ‘Redox zones’ are defined by patterns of Fe-speciation and redox-sensitive trace element enrichment and split into two groups. ‘Sulphidic’ zones (EUX, AN-III, AN-I and AN-IT) represent sediments deposited under conditions of at least intermittently active sulphate-reduction in bottom-waters. ‘Non-sulphidic’ zones (OX-RX, OX-F and OX) represent sediments deposited under non-sulphidic (oxic to ferruginous anoxic) bottom-waters. Operation of a shelf-to-basin ‘reactive Fe’ (FeHR) shuttle, moderated by sea level fluctuation and delta proximity, controlled the position and stability of redoxclines between zones of Fe and sulphate reduction, and methanogenesis. Early diagenetic redoxclines were capable of migration through the shallow sediment column relatively quickly, in response to sea level fluctuation. Preservation of syngenetic and early diagenetic geochemical signals shows redoxclines between Fe and sulphate reduction, and the upper boundary of sulphate-methane transition zone, were positioned within decimetres (i.e., 10 s cm) of seabed. Falling sea level and increasing FeHR supply is recognised as a switch from zones EUX (high sea level), AN-III and ultimately AN-I and AN-IT (low sea level). Zone AN-I defines the operation of ‘redox oscillation’, between zones of Fe and sulphate reduction in shallow porewaters, associated with enhanced degradation of OM and complete dissolution of primary carbonate. Preservation of OM and carbonate, in this system, was a function of changing bottom and pore water redox processes. Redox oscillation operated in a siliciclastic, prodeltaic environment associated with a relatively high sediment accumulation rate and high loadings of labile organic matter and metal oxides. These findings are important for understanding Late Palaeozoic black shales in the context of hydrocarbon and mineral systems