The origin and recycling of sedimented biogenic debris in a subalphine eutrophic lake (Lake Bled, Slovenia)

The areal distribution of organic C contents, ¹³C values, total N and P and biogenic Si contents in surficial sediments were used to study the distribution, origin and diagenetic transformations of sedimented biogenic debris in the eutrophic subalpine Lake Bled (Slovenia), which for most of the yearhas an anoxic hypolimnion. The influence of an allochthonous input, restricted to the western basin, was clearly traced by higher organic C and total N and P contents, higher ¹³C values, and higher sedimentation rate in comparison to the eastern basin. The low ¹³C values of sedimentary organic matter in the major part of the lake, lower than the ¹³C values of different types of organic matter, suggest that this sedimentary organic matter is most probably the product of a microbial community and not a residue of primary production.The temporal variation of benthic diffusive fluxes of NH₄, Si and PO₄, derived from modelling the pore water profiles, was related to sedimentation of phytoplanktonic blooms, while the PO₄ fluxes were also dependent on changing redox conditions at the sediment-water interface in the period of the winter-spring overtum. The removal of PO₄ in pore waters is probably due to the adsorption of phosphate and precipitation of apatite and vivianite. The budget of C, N and P at the sediment-water interface revealed a high recycling efficiency (>70%), also confirmed by the rather uniform (or only slightly decreasing) vertical profiles of organic C, total N and P in sediment cores and C/N and C/P ratios. The percentage of biogenic Si recycling is low (<10%), suggesting its removal in sediments.     

MolMod – an open access database of force fields for molecular simulations of fluids

The MolMod database is presented, which is openly accessible at http://molmod.boltzmann-zuse.de and contains intermolecular force fields for over 150 pure fluids at present. It was developed and is maintained by the Boltzmann-Zuse Society for Computational Molecular Engineering (BZS). The set of molecular models in the MolMod database provides a coherent framework for molecular simulations of fluids. The molecular models in the MolMod database consist of Lennard-Jones interaction sites, point charges, and point dipoles and quadrupoles, which can be equivalently represented by multiple point charges. The force fields can be exported as input files for the simulation programmes ms2 and ls1 mardyn, GROMACS, and LAMMPS. To characterise the semantics associated with the numerical database content, a force field nomenclature is introduced that can also be used in other contexts in materials modelling at the atomistic and mesoscopic levels. The models of the pure substances that are included in the database were generally optimised such as to yield good representations of experimental data of the vapour–liquid equilibrium with a focus on the vapour pressure and the saturated liquid density. In many cases, the models also yield good predictions of caloric, transport, and interfacial properties of the pure fluids. For all models, references to the original works in which they were developed are provided. The models can be used straightforwardly for predictions of properties of fluid mixtures using established combination rules. Input errors are a major source of errors in simulations. The MolMod database contributes to reducing such errors.     

Sources of Lipids in Anoxic Lacustrine Sediments Using Stable Carbon Isotopes

The origin of organic matter in recent anoxic sediments of the alpine Lake Bled (NW Slovenia) was determined by analyzing the carbon isotope composition of lipid biomarkers, i.e. alkanes, alcohols, sterols and fatty acids, busing compound specific, carbon isotope analysis. The results indicate that, although biomarker analysis indicated mostly plankton and terrestrial sources for lipids, an important part of sedimentary lipids, especially sterols, are autochthonous, of anaerobic microbial (methanotrophic) origin. Marked differences were observed in δ¹³C values of lipid biomarkers in settling particles collected 2 m above the bottom, and in δ¹³C values determined in surface sediment. These results indicate that even some compounds found in both particulate organic matter and sediments are the same in terms of chemical structures, their sources can be different and thus, isotopic composition should be used as a complementary tool for source identification.     

Sources and fluxes of particulate organic matter in shallow coastal waters characterized by summer macroaggregate formation

The origin and temporal variation in composition of sedimented particulate organic matter (POM) in the Gulf of Trieste (northern Adriatic) was studied over the year with special reference to the composition and sedimentation of macroaggregates in summer of 1991 using sediment traps.Suspended and sedimented POM, comprising a minor part of the largely inorganic total particulate matter, was prevalently of marine origin and composed mostly of humic substances followed by carbohydrates and proteins. Seasonal variations of particulate proteins and carbohydrates were correlated with variations of phytoplankton biomass. New production, occurring in late spring as a consequence of massive riverine inputs of N, Si and P nutrients in the surface layer of the Gulf, produced high particulate carbohydrate and protein concentrations. Subsequent depletion of introduced nutrients caused the decrease of particulate protein concentration but not that of particulate carbohydrate. The prolonged plankton biosynthesis of carbohydrates successively produced marine snow and later macroaggregates. The macroaggregates were characterized by ¹³C value of –19.9. and their carbohydrates were mostly composed of glucose followed in decreasing order by mannose, fructose, galactose, arabinose, ribose, xylose and fucose, suggesting a prevalent origin from phytoplankton structural heteropolysaccharides. Sedimentation of particulate organic constituents in the summertime, characterized by the massive presence of macroaggregates in the surface layer above the pycnocline, was the highest at a depth of 10 m at the end of this phenomenon, about six weeks after its first appearance. Sedimented macroaggregates were clearly traced by a characteristic ¹³C signal and higher carbohydrate concentrations. The monosaccharide composition was influenced by selective degradation in the water column. Sedimented POM in the bottom layer was, on the other hand, more affected by sediment resuspension. The mean yearly decrease of particulate protein-C and carbohydrate-C by 40–50% in the water column between the depths of 10 and 20 m indicates the preferential utilization of these constituents by microorganisms. The decrease of particulate humic-C is probably more the result of the export of particulate matter from the Gulf. This study also indicates that the macroaggregate formation has little impact on the annual C and N budget in such coastal areas.     

Orthobaric Densities from Simulations of the Liquid Vapour Interface

Molecular dynamics studies of the liquid vapour interface of a Lennard-Jones fluid performed on a CYBER 205 are reported for kT/ε = 0.70, 0.85, and 1.10. The main emphasis is on the orthobaric fluid densities: their dependence on different cut-off radii and long range corrections as well as their comparison with the coexisting densities from bulk fluid simulations. As previously reported bubble densities from bulk simulations differ by about 3 per cent at kT/ε = 1.10, phase equilibrium was redetermined there with the NpT + test particle method. Concerning the bubble densities from the interface simulations, increase of the cut-off radius and use of long range corrections shift them up rather close to the “bulk” values. The dew densities from the interface simulations which for the usual cut-off radius of 2.5 [sgrave] are mostly too high by a factor of 3 are decreased dramatically by accounting for the long range part of the potential. For a cut-off radius of 5 [sgrave] and long range corrections they agree with the “bulk” values within the accuracy of the latters which, however, is estimated to be only by about 20 per cent. Some characteristic density profiles are also shown.     

Pelagic organic matter in the Adriatic Sea in relation to winter hydrographic conditions

The spatial distribution of chlorophyll a (Chla), paniculateorganic carbon (POC) and nitrogen (PON), net zoopiankton ash-freedry weight (AFDW), dry weight (DW) and carbon and nitrogen content,in parallel with primary production, was studied during a jointYugoslav cruise in January 1980. The results were interpretedin relation to hydrographic properties, with special emphasison the relationship between pelagic parameters. Spatial distributionof POC, PON and net zoopiankton AFDW and C and N contents showedsimilarities over the major part of the Adriatic, while Chlaand POC showed dissimilarities since higher Chla values wererestricted to the northwestern part of the Adriatic, separatedfrom the rest of the Adriatic by a pronounced thermal frontextending south of the Istrian peninsula. High POC was foundin the centre of the south Adriatic gyre and in the Jabuka Pit,the latter filled with cold water originating from the arealocated south of the thermal front. The areas of high POC werecharacterized by a higher POC recycling time than in other Adriaticregions. High Chla, POC, PON and net zooplankton AFDW and Cand N contents in parallel with increased primary productionwere found in the southwestern part of the Adriatic off Puglia(Italy) affected by a continuous terrigenous supply of nutrients.The observed spatial distribution pattern of pelagic organicmatter suggests that this distribution is mostly influencedby hydrographic conditions and that the assumption of permanentproductivity zones in the Adriatic is not applicable to thewinter situation.     

Profiling grapevine trunk pathogens <Emphasis Type="Italic">in planta</Emphasis>: a case for community-targeted DNA metabarcoding

Background

DNA metabarcoding, commonly used in exploratory microbial ecology studies, is a promising method for the simultaneous in planta-detection of multiple pathogens associated with disease complexes, such as the grapevine trunk diseases. Profiling of pathogen communities associated with grapevine trunk diseases is particularly challenging, due to the presence within an individual wood lesion of multiple co-infecting trunk pathogens and other wood-colonizing fungi, which span a broad range of taxa in the fungal kingdom. As such, we designed metabarcoding primers, using as template the ribosomal internal transcribed spacer of grapevine trunk-associated ascomycete fungi (GTAA) and compared them to two universal primer widely used in microbial ecology.

Results

We first performed in silico simulations and then tested the primers by high-throughput amplicon sequencing of (i) multiple combinations of mock communities, (ii) time-course experiments with controlled inoculations, and (iii) diseased field samples from vineyards under natural levels of infection. All analyses showed that GTAA had greater affinity and sensitivity, compared to those of the universal primers. Importantly, with GTAA, profiling of mock communities and comparisons with shotgun-sequencing metagenomics of field samples gave an accurate representation of genera of important trunk pathogens, namely Phaeomoniella, Phaeoacremonium, and Eutypa, the abundances of which were over- or under-estimated with universal primers.

Conclusions

Overall, our findings not only demonstrate that DNA metabarcoding gives qualitatively and quantitatively accurate results when applied to grapevine trunk diseases, but also that primer customization and testing are crucial to ensure the validity of DNA metabarcoding results.

     

Anoxic degradation of biogenic debris in sediments of eutrophic subalpine Lake Bled (Slovenia)

Anoxic degradation of sedimentary biogenic debris using closed sediment incubation experiments was studied in eutrophic subalpine Lake Bled (NW Slovenia) which, for most of the year, has an anoxic hypolimnion. Production rates of dissolved inorganic carbon (DIC), NH₄ ⁺, PO₄ ^3- and dissolved Si, and reduction rates of SO₄ ^2- were measured and anoxic mineralization rates were modelled using G-model. The depth profiles indicated major mineralization of biogenic debris and SO₄ ^2- reduction near the sediment surface. A comparison between depth integrated anoxic mineralization rates and diffusive benthic fluxes of DIC, NH₄ ⁺ and PO₄ ^3- showed that the anoxic incubation experiments provide a good estimate of N degradation of biogenic debris. The contributions of SO₄ ^2- reduction and acetate fermentation in NH₄ ⁺ production are about 30 and 70%, respectively. The DIC production accounted for only 15% of DIC benthic flux, indicating that methanogenesis and oxidation of methane provides 80% of this flux. Only about 30% of PO₄ ^3- was released because phosphate precipitated in the closed incubation experiments. The depth integrated production of Si accounts for 70–80% of Si benthic fluxes indicating intense dissolution of biogenic Si in the surficial lake sediment.