Archaeal diversity in deep-sea sediments estimated by means of different Terminal-Restriction Fragment Length Polymorphisms (T-RFLP) protocols

Despite the increasing recognition of the quantitative importance of Archaea in all marine systems, the protocols for a rapid estimate of Archaeal diversity patterns in deep-sea sediments have been only poorly tested yet. We collected sediment samples from 11 deep-sea sites covering a wide latitudinal range (from 79°N to 36°N, at depths comprised from 469 to 5500 m) and compared the performance of two different primer sets (ARCH21f/ARCH958r and ARCH109f/ARCH 915r) and three restriction enzymes (AluI, Rsa I and HaeIII) for the fingerprinting analysis (T-RFLP) of Archaeal diversity. In silico and experimental analyses consistently indicated that different combinations of primer sets and restriction enzymes can result in different values of benthic Archaeal ribotype richness and different Archaeal assemblage compositions. The use of the ARCH109f/ARCH 915r primer set in combination with AluI provided the best results (a number ribotypes up to 4-folds higher than other combinations), suggesting that this primer set should be used in future studies dealing with the analysis of the patterns of Archaeal diversity in deep-sea sediments. Multivariate, multiple regression analysis revealed that, whatever the T-RFLP protocol utilized, latitude and temperature explained most of the variance in benthic Archaeal ribotype richness, while water depth had a negligible role

Mechanisms of goethite dissolution in the presence of desferrioxamine B and Suwannee River fulvic acid at pH 6.5

Siderophores are Fe3+ specific low MW chelating ligands secreted by microorganisms in response to Fe stress. Low MW organic acids such as oxalate have been shown to enhance siderophore mediated dissolution of Fe3+ oxides. However, the effect of fulvic acid presence on siderophore function remains unknown. We used batch dissolution experiments to investigate Fe release from goethite in the goethite-fulvic acid desferrioxamine B (goethite-SRFA-DFOB) ternary system. Experiments were conducted at pH 6.5 while varying reagent addition sequence. FTIR and UV-Vis spectroscopy were employed to characterise the Fe-DFOB, Fe-SRFA and DFOB–SRFA complexes. Iron released from goethite in the presence of SRFA alone was below detection limit. In the presence of both SRFA and DFOB, dissolved Fe increased with reaction time, presence of the DFOB-SRFA complex, and where SRFA was introduced prior to DFOB. FTIR data show that in the ternary system, Fe3+ is complexed primarily to oxygen of the DFOB hydroxamate group, whilst the carboxylate C=O of SRFA forms an electrostatic association with the terminal NH3+ of DFOB. We propose that SRFA sorbed to goethite lowers the net positive charge of the oxide surface, thus facilitating adsorption of cationic DFOB and subsequent Fe3+ chelation and release. Furthermore, the sorbed SRFA weakens Fe-O bonds at the goethite surface, increasing the population of kinetically labile Fe. This work demonstrates the positive, though indirect role of SRFA in increasing the bioavailability of Fe3+

Summer CO2 evasion from streams and rivers in the Kolyma River basin, north-east Siberia

Inland water systems are generally supersaturated in carbon dioxide (CO2) and are increasingly recognized as playing an important role in the global carbon cycle. The Arctic may be particularly important in this respect, given the abundance of inland waters and carbon contained in Arctic soils; however, a lack of trace gas measurements from small streams in the Arctic currently limits this understanding.We investigated the spatial variability of CO2 evasion during the summer low-flow period from streams and rivers in the northern portion of the Kolyma River basin in north-eastern Siberia. To this end, partial pressure of carbon dioxide (pCO2) and gas exchange velocities (k) were measured at a diverse set of streams and rivers to calculate CO2 evasion fluxes. We combined these CO2 evasion estimates with satellite remote sensing and geographic information system techniques to calculate total areal CO2 emissions. Our results show that small streams are substantial sources of atmospheric CO2 owing to high pCO2 and k, despite being a small portion of total inland water surface area. In contrast, large rivers were generally near equilibrium with atmospheric CO2. Extrapolating our findings across the Panteleikha-Ambolikha sub-watersheds demonstrated that small streams play a major role in CO2 evasion, accounting for 86% of the total summer CO2 emissions from inland waters within these two sub-watersheds. Further expansion of these regional CO2 emission estimates across time and space will be critical to accurately quantify and understand the role of Arctic streams and rivers in the global carbon budget

Untersuchung zur Diversität und Funktion benthischer Mikroalgen und Protozoen im Nahrungsnetz mariner und limnischer Sedimente

This thesis aimed at achieving a deeper understanding of the dynamics and structure of microbenthic communities with a focus on protists. The most important discovery concerning protozoa in recent years is the fact that they play a much more important role in for example carbon and energy flow in nature than previously believed. In this thesis several studies were presented which focus on the seasonal dynamics and the spatial distribution of components of the small benthic community in marine and freshwater environments in temperate and arctic climates and which aim at establishing a generalised model of relationships and controlling factors in small benthic food webs. Samples of the upper 3 mm of the surface of soft sediment were collected in coastal freshwater and marine sites in Germany, USA and North East Greenland. The abundance and biomass of bacteria, cyanobacteria, diatoms and nanoflagellates (phototrophic and heterotrophic) were enumerated by means of epifluorescence microscopy. Ciliate species and meiofauna were enumerated with the help of light microscopy after QPS (quantitative protagol staining). Environmental data, such as temperature, salinity, sediment water content, grain size distribution, total and organic carbon- and nitrogen content as well as chlorophyll-a values were determined in order to study their influence on the community structures and total biomass. The investigation of a habitat in a mudflat in Dorum (Germany) revealed that the benthic microbial food web varied with the season with a primacy of bottom-up control during winter and spring, an increasing influence of top-down forces mainly by meiofauna grazing towards summer, decreasing again towards autumn, accompanied by a recovery of microphytobenthos.Investigations of soft sediment communities in different climate and geographic positions of freshwater and marine sites in Germany, North America (USA; Pennsylvania, New Jersey) and in North East Greenland were carried out. The results revealed considerable differences in the biomass of the small benthic components as well as in ciliate species composition and richness. The study of the ciliate species composition also exhibited a high variability of feeding types between the investigated sites, but the herbivorous feeding type seemed to be dominant in all sediments. Differences in total microbenthic biomass, abundance and ciliate species richness could not be attributed to the differences measured in carbon content, salinity or climatic parameters. The amount of chlorophyll-a was the only factor influencing the small benthic biomass. The sources of chlorophyll-a remained unclear. The hypothesis of Manini et al. (2003) stating that the composition of available carbon has a strong influence on the structure and biomass of microbial communities in shallow sediments seemed to hold true for the investigated sites. In a series of laboratory experiments the influence of the absence of all macrograzers as well as the presence of a single common abundant small macrograzer such as Hydrobia ulvae, Corophium sp. as well as Chironomid larvae and polychaets on the components of the microbenthic communities in sediments from all study sites were investigated. The structuring influence of Arenicola marina on components of the small food web was investigated in a long term field experiment on the island of Sylt. The results of the laboratory experiments and those of the field study revealed that the small macrofauna tended to have positive stimulating effects on the microbial community by bioengineering, rather than negative ones by grazing. The exclusion of Arenicola marina in a long term experiment revealed the fact that the role of this grazer was adopted by other grazers.The results of this thesis and literature data led to the conclusion that in small communities of soft sediments the trophic levels are blurred and most species rather feed opportunistically on what is most available. The dominance of the omnivourous feeding type, detritus feeding, stimulating bioengineering effects and feed back mechanisms compose a highly networked food web. The fundamental attributes of microbes such as large absolute population sizes, short generation times and high dispersal capabilities, form a system with rapid changes in species composition.The outcome of this thesis verified the model of Fretwell (1977) for benthic microbial food webs in coastal regions, predicting that top-down forces form the trophic structure, but the bottom-up attributes of the ecosystems, such as nutrients availability, temperature and light, determine the fundament of the community as total biomass, abundance and production

Exploiting Mapped Files for Parallel I/O

Harnessing the full I/O capabilities of a large-scale multiprocessor is difficult and requires a great deal of cooperation between the application programmer, the compiler and the operating (/file) system. Hence, the parallel I/O interface used by the application to communicate with the system is crucial in achieving good performance. We present a set of properties we believe that a good I/O interface should have and consider current parallel I/O interfaces from the perspective of these properties. We describe the advantages and disadvantages of mapped-file I/O and argue that if properly implemented it can be a good basis for a parallel I/O interface that can fulfill the suggested properties. To demonstrate that such an implementation is feasible, we describe methodology used in our previous work on the Hurricane operating system and in our current work on the Tornado operating system to implement mapped files. 1 Introduction Harnessing the full I/O capabilities of a large-scale share..

The Importance of Performance-Oriented Flexibility in System Software for Large-Scale Shared-Memory Multiprocessors

arallel applications, and from scientific applications to transactional data base systems. These applications have very different requirements with respect to the requests they make, the resources they use, and their performance objective, such as response time or throughput. This is in sharp contrast to operating systems for workstations, which have been reasonably successful optimizing for a workload consisting of "typical" Unix applications. Second, the system software for large-scale multiprocessors must be flexible in order to meet the specific requirements of different large-scale parallel programs. These applications often require application-specific policies, and even minor deviations in the expected behavior of a service can severely degrade their performance. For example, an I/O intensive application may require that data be distributed across disks to match the way it intends to access the data and that a specific prefetching policy be used; minor deviations may cause unex