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The oceanic waters below a depth of 200 m represent, in terms of volume, the largest habitat of the biosphere, harboring approximately 70% of the prokaryotic biomass in the oceanic water column. These waters are characterized by low temperature, increasing hydrostatic pressure, and decreasing organic matter supply with depth. Recent methodological advances in microbial oceanography have refined our view of the ecology of prokaryotes in the dark ocean. Here, we review the ecology of prokaryotes of the dark ocean, present data on the biomass distribution and heterotrophic and chemolithoautotrophic prokaryotic production in the major oceanic basins, and highlight the phylogenetic and functional diversity of this part of the ocean. We describe the connectivity of surface and deep-water prokaryotes and the molecular adaptations of piezophilic prokaryotes to high hydrostatic pressure. We also highlight knowledge gaps in the ecology of the dark ocean's prokaryotes and their role in the biogeochemical cycles in the largest habitat of the biosphere.

Background: Heterotrophic microbes in the Southern Ocean are challenged by the double constraint of low con?centrations of organic carbon (C) and iron (Fe). These essential elements are tightly coupled in cellular processes; however, the prokaryotic requirements of C and Fe under varying environmental settings remain poorly studied. Here, we used a combination of metatranscriptomics and metaproteomics to identify prokaryotic membrane transport?ers for organic substrates and Fe in naturally iron-fertilized and high-nutrient, low-chlorophyll waters of the Southern Ocean during spring and late summer.Results Pronounced diferences in membrane transporter profles between seasons were observed at both sites, both at the transcript and protein level. When specifc compound classes were considered, the two approaches revealed diferent patterns. At the transcript level, seasonal patterns were only observed for subsets of genes belong?ing to each transporter category. At the protein level, membrane transporters of organic compounds were relatively more abundant in spring as compared to summer, while the opposite pattern was observed for Fe transporters. These observations suggest an enhanced requirement for organic C in early spring and for Fe in late summer. Mapping transcripts and proteins to 50 metagenomic-assembled genomes revealed distinct taxon-specifc seasonal diferences pointing to potentially opportunistic clades, such as Pseudomonadales and Nitrincolaceae , and groups with a more restricted repertoire of expressed transporters, such as Alphaproteobacteria and Flavobacteriaceae.Conclusion The combined investigations of C and Fe membrane transporters suggest seasonal changes in the microbial requirements of these elements under diferent productivity regimes. The taxon-specifc acquisition strategies of diferent forms of C and Fe illustrate how diverse microbes could shape transcript and protein expres?sion profles at the community level

The oceanic waters below a depth of 200 m represent, in terms of volume, the largest habitat of the biosphere, harboring approximately 70% of the prokaryotic biomass in the oceanic water column. These waters are characterized by low temperature, increasing hydrostatic pressure, and decreasing organic matter supply with depth. Recent methodological advances in microbial oceanography have refined our view of the ecology of prokaryotes in the dark ocean. Here, we review the ecology of prokaryotes of the dark ocean, present data on the biomass distribution and heterotrophic and chemolithoautotrophic prokaryotic production in the major oceanic basins, and highlight the phylogenetic and functional diversity of this part of the ocean. We describe the connectivity of surface and deep-water prokaryotes and the molecular adaptations of piezophilic prokaryotes to high hydrostatic pressure. We also highlight knowledge gaps in the ecology of the dark ocean's prokaryotes and their role in the biogeochemical cycles in the largest habitat of the biosphere.

Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that—like for AOB—ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.

29 maart 2021, Contains fulltext : 232776.pdf (Publisher’s version ) (Open Access)

Over seventy years ago, Niels Bohr described how the charge state of an atomic ion moving through a solid changes dynamically as a result of electron capture and loss processes, eventually resulting in an equilibrium charge state. Although obvious, this process has so far eluded direct experimental observation. By peeling a solid, such as graphite, layer by layer, and studying the transmission of highly charged ions through single-, bi- and trilayer graphene, we can now observe dynamical changes in ion charge states with monolayer precision. In addition we present a new first-principles approach based on the virtual photon model for interparticle energy transfer to corroborate our findings. Our model that uses a Gaussian shaped dynamic polarisability rather than a spatial delta function is a major step in providing a self-consistent description for interparticle de-excitation processes at the limit of small separations.

As surface-only materials, freestanding 2D materials are known to have a high level of contamination—mostly in the form of hydrocarbons, water, and residuals from production and exfoliation. For well-designed experiments, it is of particular importance to develop effective clean- ing procedures, especially since standard surface science techniques are typically not applicable. We perform ion spectroscopy with highly charged ions transmitted through freestanding atomically thin materials and present two techniques to achieve clean samples, both based on thermal treatment. Ion charge exchange and energy loss are used to analyze the degree of sample contamination. We find that even after cleaning, heavily contaminated spots remain on single layer graphene. The contamination coverage, however, clusters in strand-like structures leaving large clean areas. We present a way to discriminate clean from contaminated areas with our ion beam spectroscopy if the heterogeneity of the surface is increased sufficiently enough. We expect a similar discrimination to be necessary in most other experimental techniques.

To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70–100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL−1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L−1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a re

Ammonia‐oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20%–40% of the ocean's prokaryotic plankton. However, it remains enigmatic to what extent these chemolithoautotrophic archaea release dissolved organic carbon (DOC). A combination of targeted and untargeted metabolomics was used to characterize the exometabolomes of three model AOA strains of the Nitrosopumilus genus. Our results indicate that marine AOA exude a suite of organic compounds with potentially varying reactivities, dominated by nitrogen‐containing compounds. A significant fraction of the released dissolved organic matter (DOM) consists of labile compounds, which typically limit prokaryotic heterotrophic activity in open ocean waters, including amino acids, thymidine and B vitamins. Amino acid release rates corresponded with ammonia oxidation activity and the three Nitrosopumilus strains predominantly released hydrophobic amino acids, potentially as a result of passive diffusion. Despite the low contribution of DOC released by AOA (~0.08%–1.05%) to the heterotrophic prokaryotic carbon demand, the release of physiologically relevant metabolites could be crucial for microbes that are auxotrophic for some of these compounds, including members of the globally abundant and ubiquitous SAR11 clade.

Ammonia-oxidizing archaea (AOA) play an important role in the nitrogen cycle and account for a considerable fraction of the prokaryotic plankton in the ocean. Most AOA lack the hydrogen peroxide (H2O2)-detoxifying enzyme catalase, and some AOA have been shown to grow poorly under conditions of exposure to H2O2. However, differences in the degrees of H2O2 sensitivity of different AOA strains, the physiological status of AOA cells exposed to H2O2, and their molecular response to H2O2 remain poorly characterized. Further, AOA might rely on heterotrophic bacteria to detoxify H2O2, and yet the extent and variety of costs and benefits involved in these interactions remain unclear. Here, we used a proteomics approach to compare the protein profiles of three Nitrosopumilus strains grown in the presence and absence of catalase and in coculture with the heterotrophic alphaproteobacterium Oceanicaulis alexandrii. We observed that most proteins detected at a higher relative abundance in H2O2-exposed Nitrosopumilus cells had no known function in oxidative stress defense. Instead, these proteins were putatively involved in the remodeling of the extracellular matrix, which we hypothesize to be a strategy limiting the influx of H2O2 into the cells. Using RNA-stable isotope probing, we confirmed that O. alexandrii cells growing in coculture with the Nitrosopumilus strains assimilated Nitrosopumilus-derived organic carbon, suggesting that AOA could recruit H2O2-detoxifying bacteria through the release of labile organic matter. Our results contribute new insights into the response of AOA to H2O2 and highlight the potential ecological importance of their interactions with heterotrophic free-living bacteria in marine environments.

To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70–100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL−1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L−1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metab

SummaryThaumarchaeota are globally distributed and abundantmicroorganisms occurring in diverse habitats and thusrepresent a major source of archaeal lipids. The scopeof lipids as taxonomic markers in microbial ecologicalstudies is limited by the scarcity of comparative dataon the membrane lipid composition of cultivated representatives,including the phylum Thaumarchaeota.Here, we comprehensively describe the core and intactpolar lipid (IPL) inventory of ten ammonia-oxidisingthaumarchaeal cultures representing all four characterizedphylogenetic clades. IPLs of these thaumarchaealstrains are generally similar and consist of membranespanning,glycerol dibiphytanyl glycerol tetraetherswith monoglycosyl, diglycosyl, phosphohexose andhexose-phosphohexose headgroups. However, the relativeabundances of these IPLs and their core lipidcompositions differ systematically between the phylogeneticsubgroups, indicating high potential forchemotaxonomic distinction of thaumarchaeal clades.Comparative lipidomic analyses of 19 euryarchaeal andcrenarchaeal strains suggested that the lipid methoxyarchaeol is synthesized exclusively by Thaumarchaeotaand may thus represent a diagnostic lipidbiomarker for this phylum. The unprecedented diversityof the thaumarchaeal lipidome with 118 differentlipids suggests that membrane lipid composition andadaptation mechanisms in Thaumarchaeota are morecomplex than previously thought and include uniquelipids with as yet unresolved properties.

The way conduction electrons respond to ultrafast external perturbations in low dimensional materials is at the core of the design of future devices for (opto)electronics, photodetection and spintronics. Highly charged ions provide a tool for probing the electronic response of solids to extremely strong electric fields localized down to nanometre-sized areas. With ion transmission times in the order of femtoseconds, we can directly probe the local electronic dynamics of an ultrathin foil on this timescale. Here we report on the ability of freestanding single layer graphene to provide tens of electrons for charge neutralization of a slow highly charged ion within a few femtoseconds. With values higher than 1012 A cm 2, the resulting local current density in graphene exceeds previously measured breakdown currents by three orders of magnitude. Surprisingly, the passing ion does not tear nanometre-sized holes into the single layer graphene. We use time-dependent density functional theory to gain insight into the multielectron dynamics.

The way conduction electrons respond to ultrafast external perturbations in low dimensional materials is at the core of the design of future devices for (opto)electronics, photodetection and spintronics. Highly charged ions provide a tool for probing the electronic response of solids to extremely strong electric fields localized down to nanometre-sized areas. With ion transmission times in the order of femtoseconds, we can directly probe the local electronic dynamics of an ultrathin foil on this timescale. Here we report on the ability of freestanding single layer graphene to provide tens of electrons for charge neutralization of a slow highly charged ion within a few femtoseconds. With values higher than 1012 A cm 2, the resulting local current density in graphene exceeds previously measured breakdown currents by three orders of magnitude. Surprisingly, the passing ion does not tear nanometre-sized holes into the single layer graphene. We use time-dependent density functional theory to gain insight into the multielectron dynamics.

Nanocomposite thin films comprised of metastable metal carbides in a carbon matrix have a wide variety of applications ranging from hard coatings to magnetics and energy storage and conversion. While their deposition using nonequilibrium techniques is established, the understanding of the dynamic evolution of such metastable nanocomposites under thermal equilibrium conditions at elevated temperatures during processing and during device operation remains limited. Here, we investigate sputterdeposited nanocomposites of metastable nickel carbide (Ni3C) nanocrystals in an amorphous carbon (a-C) matrix during thermal postdeposition processing via complementary in situ X-ray diffractometry, in situ Raman spectroscopy, and in situ Xray photoelectron spectroscopy. At low annealing temperatures (300 °C) we observe isothermal Ni3C decomposition into face-centered-cubic Ni and amorphous carbon, however, without changes to the initial finely structured nanocomposite morphology. Only for higher temperatures (400−800 °C) Ni-catalyzed isothermal graphitization of the amorphous carbon matrix sets in, which we link to bulk-diffusion-mediated phase separation of the nanocomposite into coarser Ni and graphite grains. Upon natural cooling, only minimal precipitation of additional carbon from the Ni is observed, showing that even for highly carbon saturated systems precipitation upon cooling can be kinetically quenched. Our findings demonstrate that phase transformations of the filler and morphology modifications of the nanocomposite can be decoupled, which is advantageous from a manufacturing perspective. Our in situ study also identifies the high carbon content of the Ni filler crystallites at all stages of processing as the key hallmark feature of such metal−carbon nanocomposites that governs their entire thermal evolution. In a wider context, we also discuss our findings with regard to the much debated potential role of metastable Ni3C as a catalyst phase in graphene and carbon nano

Close control over the active catalyst phase and hence carbon nanotube structure remains challenging in catalytic chemical vapor deposition since multiple competing active catalyst phases typically co-exist under realistic synthesis conditions. Here, using in-situ X-ray diffractometry, we show that the phase of supported iron catalyst particles can be reliably controlled via the addition of NH3 during nanotube synthesis. Unlike polydisperse catalyst phase mixtures during H2 diluted nanotube growth, nitrogen addition controllably leads to phase-pure c-Fe during pre-treatment and to phase-pure Fe3C during growth. We rationalize these findings in the context of ternary Fe-C-N phase diagram calculations and, thus, highlight the use of pre-treatment- and add-gases as a key parameter towards controlled carbon nanotube growth.

Using a combination of complementary in situ X-ray photoelectron spectroscopy and X-ray diffraction, we study the fundamental mechanisms underlying the chemical vapor deposition (CVD) of hexagonal boron nitride (h-BN) on polycrystalline Cu. The nucleation and growth of h-BN layers is found to occur isothermally, i.e., at constant elevated temperature, on the Cu surface during exposure to borazine. A Cu lattice expansion during borazine exposure and B precipitation from Cu upon cooling highlight that B is incorporated into the Cu bulk, i.e., that growth is not just surface-mediated. On this basis we suggest that B is taken up in the Cu catalyst while N is not (by relative amounts), indicating element-specific feeding mechanisms including the bulk of the catalyst. We further show that oxygen intercalation readily occurs under as-grown h-BN during ambient air exposure, as is common in further processing, and that this negatively affects the stability of h-BN on the catalyst. For extended air exposure Cu oxidation is observed, and upon re-heating in vacuum an oxygen-mediated disintegration of the h-BN film via volatile boron oxides occurs. Importantly, this disintegration is catalyst mediated, i.e., occurs at the catalyst/h-BN interface and depends on the level of oxygen fed to this interface. In turn, however, deliberate feeding of oxygen during h-BN deposition can positively affect control over film morphology. We discuss the implications of these observations in the context of corrosion protection and relate them to challenges in process integration and heterostructure CVD.

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.