Chiral anomaly in Dirac semimetals due to dislocations

The dislocation in Dirac semimetal carries an emergent magnetic flux parallel to the dislocation axis. We show that due to the emergent magnetic field the dislocation accommodates a single fermion massless mode of the corresponding low-energy one-particle Hamiltonian. The mode is propagating along the dislocation with its spin directed parallel to the dislocation axis. In agreement with the chiral anomaly observed in Dirac semimetals, an external electric field results in the spectral flow of the one-particle Hamiltonian, in pumping of the fermionic quasiparticles out from the vacuum, and in creating a nonzero axial (chiral) charge in the vicinity of the dislocation.Comment: 21 pages, 3 figure

Accurate FTIR determination of boron concentration in CVD homoepitaxial diamond layers

The intensive development of technology for fabrication semiconducting CVD diamond layers poses an important task of developing a precise and non-destructive method for estimation the boron content in thin epitaxial layers. For bulk and uniformly doped diamond samples, the infrared optical spectroscopy successfully performs such a role. Here we propose a correct method to determine the boron concentration in CVD homoepitaxial diamond layers from FTIR spectra. The method is the natural advancement of the existing technique for bulk samples. The feature of the novel technique is the accurate accounting of passing radiation through a multilayered structure with different thicknesses of absorbing media for special absorbing mechanisms. For this situation, an expression for the effective optical density is obtained. We have demonstrated the benefit of the method for a set of samples with CVD homoepitaxial layers grown on various HPHT substrates with and without nitrogen impurity. The measured FTIR spectra were subdivided into relevant sections responsible for the specific absorption mechanisms, and the correct amplitudes of the boron absorption peaks were derived. The data obtained from FTIR spectra is thoroughly compared to the charge carrier concentration derived from electrical capacitance-voltage measurements.Comment: 18 pages, 7 figures, 1 tabl

Composition of Ni2+ cation solvation shell in NiCl2–methanol solution by multinuclear NMR

1H-, 2H- and 13C-NMR spectra have been used to test the Ni2+ solvation shell composition in the 1.1 molal methanol solution of NiCl2. It has been confirmed that Cl− anion takes part in the nearest environment of Ni2+ cation at all the temperatures investigated. Using 2H-NMR allowed us to detect for the first time OD-signal of methanol in the primary solvation shell of Ni2+ cation. Both 2H- and 13C-NMR spectra show that the composition of the cation solvation shell becomes more complicated at temperatures lower than 220 K

Accumulation of ambient phosphate into the periplasm of marine bacteria is proton motive force dependent

Bacteria acquire phosphate (Pi) by maintaining a periplasmic concentration below environmental levels. We recently described an extracellular Pi buffer which appears to counteract the gradient required for Pi diffusion. Here, we demonstrate that various treatments to outer membrane (OM) constituents do not affect the buffered Pi because bacteria accumulate Pi in the periplasm, from which it can be removed hypo-osmotically. The periplasmic Pi can be gradually imported into the cytoplasm by ATP-powered transport, however, the proton motive force (PMF) is not required to keep Pi in the periplasm. In contrast, the accumulation of Pi into the periplasm across the OM is PMF-dependent and can be enhanced by light energy. Because the conventional mechanism of Pi-specific transport cannot explain Pi accumulation in the periplasm we propose that periplasmic Pi anions pair with chemiosmotic cations of the PMF and millions of accumulated Pi pairs could influence the periplasmic osmolarity of marine bacteria

In situ associations between marine photosynthetic picoeukaryotes and potential parasites - a role for fungi?

Photosynthetic picoeukaryotes (PPEs) are important components of the marine picophytoplankton community playing a critical role in CO2 fixation but also as bacterivores, particularly in the oligotrophic gyres. Despite an increased interest in these organisms and an improved understanding of the genetic diversity of this group, we still know little of the environmental factors controlling the abundance of these organisms. Here, we investigated the quantitative importance of eukaryotic parasites in the free-living fraction as well as in associations with PPEs along a transect in the South Atlantic. Using tyramide signal amplification-fluorescence in situ hybridization (TSA-FISH), we provide quantitative evidence of the occurrence of free-living fungi in open ocean marine systems, while the Perkinsozoa and Syndiniales parasites were not abundant in these waters. Using flow cytometric cell sorting of different PPE populations followed by a dual-labelled TSA-FISH approach, we also demonstrate fungal associations, potentially parasitic, occurring with both pico-Prymnesiophyceae and pico-Chrysophyceae. These data highlight the necessity for further work investigating the specific role of marine fungi as parasites of phytoplankton to improve understanding of carbon flow in marine ecosystems

Diel rhythmicity in amino acid uptake by Prochlorococcus

The marine cyanobacterium Prochlorococcus, the most abundant phototrophic organism on Earth, numerically dominates the phytoplankton in nitrogen (N)-depleted oceanic gyres. Alongside inorganic N sources such as nitrite and ammonium, natural populations of this genus also acquire organic N, specifically amino acids. Here, we investigated using isotopic tracer and flow cytometric cell sorting techniques whether amino acid uptake by Prochlorococcus is subject to a diel rhythmicity, and if so, whether this was linked to a specific cell cycle stage. We observed, in contrast to diurnally similar methionine uptake rates by Synechococcus cells, obvious diurnal rhythms in methionine uptake by Prochlorococcus cells in the tropical Atlantic. These rhythms were confirmed using reproducible cyclostat experiments with a light synchronised axenic Prochlorococcus (PCC9511 strain) culture and 35S-methionine and 3H-leucine tracers. Cells acquired the tracers at lower rates around dawn and higher rates around dusk despite >104 times higher concentration of ammonium in the medium, presumably because amino acids can be directly incorporated into protein. Leucine uptake rates by cells in the S+G2 cell cycle stage were consistently 2.2 times higher than those of cells at the G1 stage. Furthermore, S+G2 cells up-regulated amino acid uptake 3.5 times from dawn to dusk to boost protein synthesis prior to cell division. Because Prochlorococcus populations can account from 13% at midday, and up to 42% at dusk, of total microbial uptake of methionine and probably of other amino acids in N-depleted oceanic waters, this genus exerts diurnally variable, strong competitive pressure on other bacterioplankton populations

Contribution of bacterial respiration to plankton respiration from 50˚N to 44˚S in the Atlantic Ocean

Marine bacteria play an important role in the global cycling of carbon and therefore in climate regulation. However, the paucity of direct measurements means that our understanding of the magnitude and variability of bacterial respiration in the ocean is poor. Estimations of respiration in the 0.2-0.8 µm size-fraction (considered as bacterial respiration), total plankton community respiration, and the contribution of bacterial respiration to total plankton community respiration were made along two latitudinal transects in the Atlantic Ocean (ca. 50 ºN – 44 ºS) during 2010 and 2011. Two different methodologies were used: determination of changes in dissolved O2 concentration after standard 24 h dark bottle incubations, and measurements of in vivo reduction of 2-(ρ-iodophenyl)-3- (ρ-nitrophenyl)-5phenyl tetrazolium salt (INT). There was an overall significant correlation (r = 0.44, p <0.0001, n = 90) between the rates of community respiration estimated by both methods. Depth-integrated community respiration varied as much as three-fold between regions. Maximum rates occurred in waters of the western European shelf and Patagonian shelf, and minimum rates in the North and South oligotrophic gyres. Depth-integrated bacterial respiration followed the same pattern as community respiration. There was a significantly higher cell-specific bacterial respiration in the northern subtropical gyre than in the southern subtropical gyre which suggests that bacterial carbon turnover is faster in the northern gyre. The relationships between plankton respiration and physicochemical and biological variables were different in different years. In general, INTT was correlated to both chlorophyll-a and bacterial abundance, while INT0.2-0.8 was only correlated with bacterial abundance. However, in 2010 INTT and INT0.2-0.8 were also correlated with temperature and primary production while in 2011 they were correlated with nitrate + nitrite concentration. The bacterial contribution to depth integrated community respiration was highly variable within provinces (4 - 77 %). Results from this study suggest that the proportion of total community respiration attributable to bacteria is similar between the 6 oceanographic regions studied

Resilience of SAR11 bacteria to rapid acidification in the high latitude open ocean

Ubiquitous SAR11 Alphaproteobacteria numerically dominate marine planktonic communities. Because they are excruciatingly difficult to cultivate, there is comparatively little known about their physiology and metabolic responses to long- and short- term environmental changes. As surface oceans take up anthropogenic, atmospheric CO2, the consequential process of ocean acidification could affect the global biogeochemical significance of SAR11. Shipping accidents or inadvertent release of chemicals from industrial plants can have strong short-term local effects on oceanic SAR11. This study investigated the effect of 2.5 fold acidification of seawater on the metabolism of SAR11 and other heterotrophic bacterioplankton along a natural temperature gradient crossing the North Atlantic Ocean, Norwegian and Greenland Seas. Uptake rates of the amino acid leucine by SAR11 cells as well as other bacterioplankton remained similar to controls despite an instant ∼50% increase in leucine bioavailability upon acidification. This high physiological resilience to acidification even without acclimation, suggests that open ocean dominant bacterioplankton are able to cope even with sudden and therefore more likely with long-term acidification effects