Impact of UV radiation on DOM transformation on molecular level using FT-ICR-MS and PARAFAC

Dissolved organic matter (DOM) is an omnipresent constituent of natural water bodies. Reuse and transformation of DOM compounds in the water column is driven by physicochemical and biological processes leading to the production of refractory DOM. Typically, breakdown of DOM chemical compounds into smaller or more condensed fragments is triggered by ultraviolet (UV) radiation. Here, we present a study on the photodegradation of DOM produced during an incubation experiment with a natural microbial community. At the end of the first incubation without UV irradiation, the samples from 3 mesocosms were filtered to remove microbes and particles and continuously exposed to UV radiation (280–365 nm). We investigated DOM in depth via monitoring of dissolved organic carbon (DOC) concentrations, DOM molecular characterization by Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) and excitation emission matrix spectroscopy (EEMS). Analysis of variance indicated no significant differences in the DOC concentration between treatments. Main peaks in the fluorescent DOM (FDOM) were photo-bleached by UV radiation, and an increase in the fluorescent intensity of selected peaks was observed on irradiated samples toward the end of the experiment. Parallel factor analysis (PARAFAC) indicated the presence of three main components in all treatments: C1 (Marine humic M), C2 (Bacterial produced humic C), C3 (Tyrosine), and an additional component in the dark incubation of mesocosm 3, C4 (Tryptophan). Despite an intensive filtration protocol through 0.7, 0.2 and 0.1 μm filters, low bacterial abundances were determined (<2.5 × 10−3 cells mL−1). We observed a direct correlation between structural indices and the intensity of PARAFAC components. Average double bond equivalent and aromaticity were strongly positively correlated with PARAFAC components C1 and C2 for one or more mesocosm. Moreover, FT-ICR-MS showed that under the tested conditions, the refractory character of the DOM assessed as the similarity to a deep ocean DOM reference did not increase on molecular level. Thus, mechanisms other than photochemical transformations of relatively recent DOM are likely necessary to facilitate long-term stability of DOM in the oceans

Absorption of Ultrashort Laser Pulses in Strongly Overdense Targets

We report on the first absorption experiments of sub-10 fs high-contrast Ti:Sa laser pulses incident on solid targets. The very good contrast of the laser pulse assures the formation of a very small pre-plasma and the pulse interacts with the matter close to solid density. Experimental results indicate that p-polarized laser pulses are absorbed up to 80 percent at 80 degrees incidence angle. The simulation results of PSC PIC code clearly confirm the observations and show that the collisionless absorption works efficiently in steep density profiles

Riverine mixing at the molecular scale - An ultrahigh-resolution mass spectrometry study on dissolved organic matter and selected metals in the Amazon confluence zone (Manaus, Brazil)

The Amazon delivers a fifth of the global continental runoff and riverine dissolved organic carbon (DOC) to the ocean. Intensified biogeochemical processes are expected at the junction of the Amazon's major blackwater tributary, the Rio Negro, and its parent, the Rio Solimbes, due to large gradients in pH, conductivity, DOC and particle load. Dissolved organic matter (DOM) plays a major role in aquatic biogeochemical processes which are poorly understood on the molecular level. To gain insights into the potential role of DOM in non-conservative processes, we assessed dynamics of Cu, Fe and DOM by ultrahigh resolution mass spectrometry in: (1) endmembers, (2) regional samples and (3) laboratory mixing experiments under presence/absence of natural particles (>0.2 p.m). The relative abundances of 3600 DOM molecular formulae were interpreted via multivariate statistics which revealed major dynamics in the DOM molecular composition. >40% of molecular formulae displayed conservative behavior even in the presence of natural particles, agreeing with bulk DOC behavior, but opposing the oftenpresumed non-conservative behavior of DOM. Another 16-27% of formulae fluctuated in FT-ICRMS signal intensity during mixing, but did not show consistent non-conservative behavior. Both rivers left a clear molecular imprint within the DOM of the Amazon, each being linked to >800 molecular formulae. Characteristic for the Rio Negro was a dominance of phenolics with a wide molecular mass range (centered at similar to 400 Da), and for the Rio Solimbes more saturated but lower-molecular mass compounds (centered at similar to 300 Da). Both Fe and Cu showed distinct non-conservative mixing patterns under particle presence. In the controlled mixing experiments including original particles at natural concentration, up to 0.5 ttg/L Cu was released from the particles into solution at 20-40% blackwater contribution. Our molecular analysis revealed distinct DOM compositional changes in polyphenol- and nitrogencontaining formulae paralleling this release, suggesting links to desorption of potential ligands and charge-induced effects at particle surfaces caused by pH and conductivity changes in the course of mixing. (C) 2019 Elsevier Ltd. All rights reserved

Linking optical and molecular signatures of dissolved organic matter in the Mediterranean Sea

Original research paperDissolved organic matter (DOM) plays a key role in global biogeochemical cycles and experiences changes in molecular composition as it undergoes processing. In the semi-closed basins of the oligotrophic Mediterranean Sea, these gradual molecular modifications can be observed in close proximity. In order to extend the spatial resolution of information on DOM molecular composition available from ultrahigh resolution mass spectrometry in this area, we relate this data to optical (fluorescence and absorption spectroscopy) measurements. Covariance between molecular formulae signal intensities and carbon-specific fluorescence intensities was examined by means of Spearman’s rank correlations. Fifty two per cent of the assigned molecular formulae were associated with at least one optical parameter, accounting for 70% of the total mass spectrum signal intensity. Furthermore, we obtained significant multiple linear regressions between optical and intensity-weighted molecular indices. The resulting regression equations were used to estimate molecular parameters such as the double bond equivalent, degradation state and occurrence of unsaturated aliphatic compounds from optical measurements. The statistical linkages between DOM molecular and optical properties illustrate that the simple, rapid and cost-efficient optical spectroscopic measurements provide valuable proxy information on the molecular composition of open ocean marine DOM.y the project HOTMIX (grant number CTM2011-30010-C02-MAR) and the project FERMIO (MINECO, CTM2014-57334-JIN), both co-financed with FEDER fundsVersión del editor2,92

Molecular characterization of dissolved organic matter linked to microbial (Bacteria and Archaea) diversity in the main water masses of the Eastern North Atlantic Ocean

The microbe-dissolved organic matter (DOM) interactions include microbial uptake and DOM reworking and release, affecting the composition of the heterogeneous DOM pool. In turns, this distinct DOM composition can select for microbial assemblages. We investigated the diversity of microbial (both Bacteria and Archaea) communities (combining Illumina tag sequencing of 16S rRNA gen -amplicon sequencing variants, ASVs- and metagenomics) and the chemodiversity of dissolved organic molecules (extracted by solid phase extraction and analyzed by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, FT-ICR-MS) in the Eastern North Atlantic Ocean off the Galician coast (43oN, 9o-15oW). Sampling ranged from 100 m to 5000 m, thereby encompassing a wide variety of water masses with contrasting origins and different aging. Applying diversity ecological metrics to both organic compounds and ASVs, we found that microbial diversity and richness were negatively correlated with DOM concentration and chemo-diversity. Besides, our results demonstrated the link between this trend and water mass aging, which enhances biosphere taxonomic diversity but reduces molecular variety. DOM diversity, decreasing along the water mass aging gradient, would likely reflect the persistence of the most refractory molecules, generated as by- product of the DOM degradation by microbes. In two PCoAs based on the metagenomic data, combined PCoA axis 1 and PCoA axis 2, explained the 80% and 20% of the microbial gene ́s structural variability among water masses. The oldest water masses, originated at high latitudes, such as NADW and LDW, were associated to higher abundance of genes involved in metabolism of aromatic compound. Intermediate waters such as ENACWst were related to sulphur/iron/phosphorous metabolism related genes. Surface waters were linked to genes involved in photosynthesis, autotrophy and cell division. Taken together, the observed increase of DOM homogenization along water mass aging was associated to differences in the functional diversity of microbial communities

Niche partitioning by photosynthetic plankton as a driver of CO2-fixation across the oligotrophic South Pacific Subtropical Ocean

Oligotrophic ocean gyre ecosystems may be expanding due to rising global temperatures [1-5]. Models predicting carbon flow through these changing ecosystems require accurate descriptions of phytoplankton communities and their metabolic activities [6]. We therefore measured distributions and activities of cyanobacteria and small photosynthetic eukaryotes throughout the euphotic zone on a zonal transect through the South Pacific Ocean, focusing on the ultraoligotrophic waters of the South Pacific Gyre (SPG). Bulk rates of CO2 fixation were low (0.1 mu mol Cl--(1) d(-1)) but pervasive throughout both the surface mixed-layer (upper 150 m), as well as the deep chlorophyll a maximum of the core SPG. Chloroplast 16S rRNA metabarcoding, and single-cell (CO2)-C-13 uptake experiments demonstrated niche differentiation among the small eukaryotes and picocyanobacteria. Prochlorococcus abundances, activity, and growth were more closely associated with the rims of the gyre. Small, fast-growing, photosynthetic eukaryotes, likely related to the Pelagophyceae, characterized the deep chlorophyll a maximum. In contrast, a slower growing population of photosynthetic eukaryotes, likely comprised of Dictyochophyceae and Chrysophyceae, dominated the mixed layer that contributed 65-88% of the areal CO2 fixation within the core SPG. Small photosynthetic eukaryotes may thus play an underappreciated role in CO2 fixation in the surface mixed-layer waters of ultraoligotrophic ecosystems

Probing bulk electron temperature via x-ray emission in a solid density plasma

Bulk electron temperatures are calculated for thin Cu targets irradiated by the petawatt class Vulcan laser, from the Kα yield obtained using highly oriented pyrolytic graphite crystals. Cu-Kα emission studies have been used to probe the bulk electron temperature. A 30–80 eV core temperature extends homogeneously over distances up to ten times the laser focal spot size. Energy shifting has been observed due to different ionization states produced for different temperatures in the plasma. Polarization dependencies of plasma temperature are observed through the production of x-rays in different targets. 2D PIC simulations were performed to measure the polarization dependency of bulk electron temperature, which supports our experimental results. This paper could be of importance in understanding the different behavior of laser coupling at different polarizations and their role in x-ray production

Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys

<p>Abstract</p> <p>Background</p> <p>Colobine monkeys constitute a diverse group of primates with major radiations in Africa and Asia. However, phylogenetic relationships among genera are under debate, and recent molecular studies with incomplete taxon-sampling revealed discordant gene trees. To solve the evolutionary history of colobine genera and to determine causes for possible gene tree incongruences, we combined presence/absence analysis of mobile elements with autosomal, X chromosomal, Y chromosomal and mitochondrial sequence data from all recognized colobine genera.</p> <p>Results</p> <p>Gene tree topologies and divergence age estimates derived from different markers were similar, but differed in placing <it>Piliocolobus/Procolobus </it>and langur genera among colobines. Although insufficient data, homoplasy and incomplete lineage sorting might all have contributed to the discordance among gene trees, hybridization is favored as the main cause of the observed discordance. We propose that African colobines are paraphyletic, but might later have experienced female introgression from <it>Piliocolobus</it>/<it>Procolobus </it>into <it>Colobus</it>. In the late Miocene, colobines invaded Eurasia and diversified into several lineages. Among Asian colobines, <it>Semnopithecus </it>diverged first, indicating langur paraphyly. However, unidirectional gene flow from <it>Semnopithecus </it>into <it>Trachypithecus </it>via male introgression followed by nuclear swamping might have occurred until the earliest Pleistocene.</p> <p>Conclusions</p> <p>Overall, our study provides the most comprehensive view on colobine evolution to date and emphasizes that analyses of various molecular markers, such as mobile elements and sequence data from multiple loci, are crucial to better understand evolutionary relationships and to trace hybridization events. Our results also suggest that sex-specific dispersal patterns, promoted by a respective social organization of the species involved, can result in different hybridization scenarios.</p

Character and environmental lability of cyanobacteria-derived dissolved organic matter

Autotrophic dissolved organic matter (DOM) is central to the carbon biogeochemistry of aquatic systems, and the full complexity of autotrophic DOM has not been extensively studied, particularly by high-resolution mass spectrometry (HRMS). Terrestrial DOM tends to dominate HRMS studies in freshwaters due to the propensity of such compounds to ionize by negative mode electrospray, and possibly also because ionizable DOM produced by autotrophy is decreased to low steady-state concentrations by heterotrophic bacteria. In this study, we investigated the character of DOM produced by the widespread cyanobacteriaMicrocystis aeruginosausing high-pressure liquid chromatography-electrospray ionization-high-resolution mass spectrometry.M. aeruginosaproduced thousands of detectable compounds in axenic culture. These compounds were chromatographically resolved and the majority were assigned to aliphatic formulas with a broad polarity range. We found that the DOM produced byM. aeruginosawas highly susceptible to removal by heterotrophic freshwater bacteria, supporting the hypothesis that this autotroph-derived organic material is highly labile and accordingly only seen at low concentrations in natural settings

Phylogenetic Relationships among the Colobine Monkeys Revisited: New Insights from Analyses of Complete mt Genomes and 44 Nuclear Non-Coding Markers

Background: Phylogenetic relationships among Asian and African colobine genera have been disputed and are not yet well established. In the present study, we revisit the contentious relationships within the Asian and African Colobinae by analyzing 44 nuclear non-coding genes (.23 kb) and mitochondrial (mt) genome sequences from 14 colobine and 4 noncolobine primates. Principal Findings: The combined nuclear gene and the mt genome as well as the combined nuclear and mt gene analyses yielded different phylogenetic relationships among colobine genera with the exception of a monophyletic ‘odd-nosed’ group consisting of Rhinopithecus, Pygathrix and Nasalis, and a monophyletic African group consisting of Colobus and Piliocolobus. The combined nuclear data analyses supported a sister-grouping between Semnopithecus and Trachypithecus, and between Presbytis and the odd-nosed monkey group, as well as a sister-taxon association of Pygathrix and Rhinopithecus within the odd-nosed monkey group. In contrast, mt genome data analyses revealed that Semnopithecus diverged earliest among the Asian colobines and that the odd-nosed monkey group is sister to a Presbytis and Trachypithecus clade, as well as a close association of Pygathrix with Nasalis. The relationships among these genera inferred from the analyses of combined nuclear and mt genes, however, varied with the tree-building methods used. Another remarkable finding of the present study is that all of our analyses rejected the recently proposed African colobine paraphyl