Kinetic Monte Carlo simulations of oscillatory shape evolution for electromigration-driven islands

The shape evolution of two-dimensional islands under electromigration-driven periphery diffusion is studied by kinetic Monte Carlo (KMC) simulations and continuum theory. The energetics of the KMC model is adapted to the Cu(100) surface, and the continuum model is matched to the KMC model by a suitably parametrized choice of the orientation-dependent step stiffness and step atom mobility. At 700 K shape oscillations predicted by continuum theory are quantitatively verified by the KMC simulations, while at 500 K qualitative differences between the two modeling approaches are found.Comment: 7 pages, 6 figure

Seasonal variation in denitrification and dissimilatory nitrate reduction to ammonia process rates and corresponding key functional genes along an estuarine nitrate gradient

This research investigated spatial-temporal variation in benthic bacterial community structure, rates of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) processes and abundances of corresponding genes and transcripts at three sites—the estuary-head, mid-estuary and the estuary mouth (EM) along the nitrate gradient of the Colne estuary over an annual cycle. Denitrification rates declined down the estuary, while DNRA rates were higher at the estuary head and middle than the EM. In four out of the six 2-monthly time-points, rates of DNRA were greater than denitrification at each site. Abundance of gene markers for nitrate-reduction (nitrate reductase narG and napA), denitrification (nitrite reductase nirS) and DNRA (DNRA nitrite reductase nrfA) declined along the estuary with significant relationships between denitrification and nirS abundance, and DNRA and nrfA abundance. Spatially, rates of denitrification, DNRA and corresponding functional gene abundances decreased along the estuary. However, temporal correlations between rate processes and functional gene and transcript abundances were not observed

<i>amoA</i> Gene Abundances and Nitrification Potential Rates Suggest that Benthic Ammonia-Oxidizing Bacteria and Not Archaea Dominate N Cycling in the Colne Estuary, United Kingdom

ABSTRACT Nitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase ( amoA ) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw] −1 day −1 in June, increasing to 37.4 μmol N gdw −1 day −1 in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw −1 day −1 in June, increasing to 11.7 μmol N gdw −1 day −1 in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOB amoA gene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally. Nitrosomonas spp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOA amoA gene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possibly Nitrosomonas spp.) were of major significance in nitrification. </jats:p

Mineralization and nitrification: Archaea dominate ammonia-oxidising communities in grassland soils

In grasslands, N mineralization and nitrification are important processes and are controlled by several factors, including the in situ microbial community composition. Nitrification involves ammonia oxidising archaea (AOA) and bacteria (AOB) and although AOA and AOB co-exist in soils, they respond differently to environmental characteristics and there is evidence of AOA/AOB niche differentiation. Here, we investigated temporal variation in N mineralization and nitrification rates, together with bacterial, archaeal and ammonia-oxidiser communities in grassland soils, on different geologies: clay, Greensand and Chalk. Across geologies, N mineralization and nitrification rates were slower in the autumn than the rest of the year. Turnover times for soil ammonium pools were <24 h, whilst several days for nitrate. In clay soils, bacterial, archaeal, AOA, and AOB communities were clearly distinct from those in Chalk and Greensand soils. Spatially and temporally, AOA were more abundant than AOB. Notably, Nitrososphaera were predominant, comprising 37.4% of archaeal communities, with the vast majority of AOA found in Chalk and Greensand soils. AOA abundance positively correlated with nitrate concentration, whereas AOB abundance correlated with ammonium and nitrite concentrations, suggesting that these N compounds may be potential drivers for AOA/AOB niche differentiation in these grassland soils

Nitrate Reduction Functional Genes and Nitrate Reduction Potentials Persist in Deeper Estuarine Sediments. Why?

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are processes occurring simultaneously under oxygen-limited or anaerobic conditions, where both compete for nitrate and organic carbon. Despite their ecological importance, there has been little investigation of how denitrification and DNRA potentials and related functional genes vary vertically with sediment depth. Nitrate reduction potentials measured in sediment depth profiles along the Colne estuary were in the upper range of nitrate reduction rates reported from other sediments and showed the existence of strong decreasing trends both with increasing depth and along the estuary. Denitrification potential decreased along the estuary, decreasing more rapidly with depth towards the estuary mouth. In contrast, DNRA potential increased along the estuary. Significant decreases in copy numbers of 16S rRNA and nitrate reducing genes were observed along the estuary and from surface to deeper sediments. Both metabolic potentials and functional genes persisted at sediment depths where porewater nitrate was absent. Transport of nitrate by bioturbation, based on macrofauna distributions, could only account for the upper 10 cm depth of sediment. A several fold higher combined freeze-lysable KCl-extractable nitrate pool compared to porewater nitrate was detected. We hypothesised that his could be attributed to intracellular nitrate pools from nitrate accumulating microorganisms like Thioploca or Beggiatoa. However, pyrosequencing analysis did not detect any such organisms, leaving other bacteria, microbenthic algae, or foraminiferans which have also been shown to accumulate nitrate, as possible candidates. The importance and bioavailability of a KCl-extractable nitrate sediment pool remains to be tested. The significant variation in the vertical pattern and abundance of the various nitrate reducing genes phylotypes reasonably suggests differences in their activity throughout the sediment column. This raises interesting questions as to what the alternative metabolic roles for the various nitrate reductases could be, analogous to the alternative metabolic roles found for nitrite reductases

Denitrifier Still Has the Important Role in Nitrate Reduction to N2 Although It is Not the Predominant Population in the Estuarine Bacterial Community of Nitrate Reducing Bacteria

Denitrification and nitrate-ammonification are the responsible processes for nitrate removal in the estuaries. Temperature, nitrate and organic carbon availability are key factors controlling a rate of the nitrate reduction processes. This mixed cultures chemostat study investigates the competition ability and their nitrate reduction end-products of the bacteria isolated from an estuary at different temperatures. This study will help us to understand the seasonal nitrate reduction processes in an estuary. The experiments showed that a nitrate-ammonifier was the predominant process in the steady-state chemostat at high temperature. While a facultative denitrifier-nitrate ammonifier was the predominant process at low temperature. However, the main end products of nitrate reduction at high temperature were up to 61% N2 indicating a denitrifier still had an important role in the end products of nitrate reduction in the estuary. The data also showed that a nitrite respiring bacterium reduced nitrite to N2, that responsible for approximately 6-9% of total N2 produced in the culture. This study confirmed that nitrate ammonifiers out-compete denitrifiers at high temperature, however, denitrifiers still had an important role in end products of nitrate reduction

Sources of nitrogen used for denitrification and nitrous oxide formation in sediments of the hypernutrified Colne, the nutrified Humber, and the oligotrophic Conwy estuaries, United Kingdom

Rates of denitrification and nitrous oxide (N2O) formation, and the sources of N-2 and N2O, were examined by the isotope-pairing technique in three U.K. estuaries (Colne, Humber, Conwy), which ranged from extremely nutrified to oligotrophic. Nitrous oxide concentrations were supersaturated throughout the year with annual averages of 603% in the Colne, 158% in the Humber, and 133% in the Conwy, indicating that the estuaries were sources of atmospheric N2O. Denitrification and N2O formation were from benthic processes, and not from water-column processes. Generally, both denitrification and N2O formation decreased down the estuary as nitrate concentrations lowered. The proportion of N-2 and N2O derived from nitrate in the overlying water column (Dw) also decreased with nitrate concentration, while that from benthic coupled nitrification-denitrification (D-n) increased. Scaled to the total estuary area, in the hypemutrified Colne, water-column nitrate was the main source of N-2 and N2O; in the moderately nutrified Humber, D-w and D-n contributed approximately equally, while in the oligotrophic Conwy, coupled nitrification-denitrification (D-n) was the main source of N-2 and N2O. For the first time, the formation of N2O from either the nitrification or denitrification steps of D-n was also determined. In the Colne, that from the nitrification step predominated at the top of the estuary but decreased down the estuary, while in the Humber that from denitrification dominated at the top and decreased down the estuary. In the oligotrophic Conwy, there were approximately equal contribution