Editorial: Rhizosphere Spatiotemporal Organisation

Formation of the rhizosphere, interface between living plant roots and soil, leads to changes in soil properties, nutrient and water distribution and biogeochemical cycling, and to a selection of unique populations of microorganisms and invertebrates. Dynamic feedback processes between the plant, the soil and the biota govern rhizosphere formation. The Frontiers Research Topic on “Rhizosphere Spatiotemporal Organization” presents contributions which aim to advance our understanding of rhizosphere processes. All of the six articles took the challenge to elaborate on the dynamic interactions and feedback processes in both spatial and temporal contexts

Electronic Structure of Dangling Bonds in Amorphous Silicon Studied via a Density-Matrix Functional Method

A structural model of hydrogenated amorphous silicon containing an isolated dangling bond is used to investigate the effects of electron interactions on the electronic level splittings, localization of charge and spin, and fluctuations in charge and spin. These properties are calculated with a recently developed density-matrix correlation-energy functional applied to a generalized Anderson Hamiltonian, consisting of tight-binding one-electron terms parametrizing hydrogenated amorphous silicon plus a local interaction term. The energy level splittings approach an asymptotic value for large values of the electron-interaction parameter U, and for physically relevant values of U are in the range 0.3-0.5 eV. The electron spin is highly localized on the central orbital of the dangling bond while the charge is spread over a larger region surrounding the dangling bond site. These results are consistent with known experimental data and previous density-functional calculations. The spin fluctuations are quite different from those obtained with unrestricted Hartree-Fock theory.Comment: 6 pages, 6 figures, 1 tabl

In Vitro Analysis of Immersed Human Tissues by Raman Microspectroscopy

Raman microspectroscopy is a powerful tool for the analysis of tissue sections, providing a molecular map of the investigated samples. Nevertheless, data pre-processing and, particularly, the removal of the broad background to the spectra remain problematic. Indeed, the physical origin of the background has not been satisfactorily determined. Using 785 nm as source in a confocal geometry, it is demonstrated for the example of the protein kappa-elastin that the background and resulting quality of the recorded spectrum are dependent on the morphology of the sample. Whereas a fine powder yields a dominant broad background, compressed pellets and solution-cast thin films produce, respectively, improved quality spectra and significantly reduced spectral background. As the chemical composition of the samples is identical, the background is ascribed to stray light due to diffuse scattering rather than an intrinsic photoluminescence. The recorded spectra from a tissue sample exhibit a large and spatially variable background, resulting in poorly defined spectral features. A significant reduction of the background signal as well as improvement of the spectral quality is achieved by immersion of the sample in water and measurement with an immersion objective. The significant improvement in signal to background is attributed to a reduction of the diffuse scattering due to a change in the effective morphology as a result of an improved index matching at the water/tissue interface compared to the air/tissue interface. Compared to sections measured in air, the background is reduced to that of the water, and pre-processing is reduced to the subtraction of the substrate and water signal and correction for the instrument response, both of which are highly reproducible. Data pre-processing is thus greatly simplified and the results significantly more reliable

Spin detection with a micromechanical trampoline: towards magnetic resonance microscopy harnessing cavity optomechanics

We explore the prospects and benefits of combining the techniques of cavity optomechanics with efforts to image spins using magnetic resonance force microscopy (MRFM). In particular, we focus on a common mechanical resonator used in cavity optomechanics&mdash;high-stress stoichiometric silicon nitride (Si3N4) membranes. We present experimental work with a 'trampoline' membrane resonator that has a quality factor above 106 and an order of magnitude lower mass than a comparable standard membrane resonators. Such high-stress resonators are on a trajectory to reach 0.1 force sensitivities at MHz frequencies by using techniques such as soft clamping and phononic-crystal control of acoustic radiation in combination with cryogenic cooling. We present a demonstration of force-detected electron spin resonance of an ensemble at room temperature using the trampoline resonators functionalized with a magnetic grain. We discuss prospects for combining such a resonator with an integrated Fabry&ndash;Perot cavity readout at cryogenic temperatures, and provide ideas for future impacts of membrane cavity optomechanical devices on MRFM of nuclear spins. </div

High-Pressure Amorphous Nitrogen

The phase diagram and stability limits of diatomic solid nitrogen have been explored in a wide pressure--temperature range by several optical spectroscopic techniques. A newly characterized narrow-gap semiconducting phase $\eta$ has been found to exist in a range of 80--270 GPa and 10--510 K. The vibrational and optical properties of the $\eta$ phase produced under these conditions indicate that it is largely amorphous and back transforms to a new molecular phase. The band gap of the $\eta$ phase is found to decrease with pressure indicating possible metallization by band overlap above 280 GPa.Comment: 5 pages, 4 figure

Soil methane sink capacity response to a long-term wildfire chronosequence in Northern Sweden

Boreal forests occupy nearly one fifth of the terrestrial land surface and are recognised as globally important regulators of carbon (C) cycling and greenhouse gas emissions. Carbon sequestration processes in these forests include assimilation of CO2 into biomass and subsequently into soil organic matter, and soil microbial oxidation of methane (CH4). In this study we explored how ecosystem retrogression, which drives vegetation change, regulates the important process of soil CH4 oxidation in boreal forests. We measured soil CH4 oxidation processes on a group of 30 forested islands in northern Sweden differing greatly in fire history, and collectively representing a retrogressive chronosequence, spanning 5000 years. Across these islands the build-up of soil organic matter was observed to increase with time since fire disturbance, with a significant correlation between greater humus depth and increased net soil CH4 oxidation rates. We suggest that this increase in net CH4 oxidation rates, in the absence of disturbance, results as deeper humus stores accumulate and provide niches for methanotrophs to thrive. By using this gradient we have discovered important regulatory controls on the stability of soil CH4 oxidation processes that could not have not been explored through shorter-term experiments. Our findings indicate that in the absence of human interventions such as fire suppression, and with increased wildfire frequency, the globally important boreal CH4 sink could be diminished

Hydrogen for synthetic fuels via nuclear energy

Fluctuations in availability and recent increases in price of petroleum have had profound effects on the national economy. As synthetic fuels, in particular, hydrogen, become increasingly attractive, nuclear energy has a role in developing such fuels. It is postulated that the nuclear radiation of the fission process itself can be utilized directly in fluid fueled devices or radiation and heat can be used in special purpose solid-fuel reactors. Both fusion and fission are considered in this light.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44905/1/10894_2005_Article_BF01063684.pd

Discovery and population genomics of structural variation in a songbird genus

Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping

The rise and fall of methanotrophy following a deepwater oil-well blowout

The blowout of the Macondo oil well in the Gulf of Mexico in April 2010 injected up to 500,000 tonnes of natural gas, mainly methane, into the deep sea1. Most of the methane released was thought to have been consumed by marine microbes between July and August 20102, 3. Here, we report spatially extensive measurements of methane concentrations and oxidation rates in the nine months following the spill. We show that although gas-rich deepwater plumes were a short-lived feature, water column concentrations of methane remained above background levels throughout the rest of the year. Rates of microbial methane oxidation peaked in the deepwater plumes in May and early June, coincident with a rapid rise in the abundance of known and new methane-oxidizing microbes. At this time, rates of methane oxidation reached up to 5,900 nmol l−1 d−1—the highest rates documented in the global pelagic ocean before the blowout4. Rates of methane oxidation fell to less than 50 nmol l−1 d−1 in late June, and continued to decline throughout the remainder of the year. We suggest the precipitous drop in methane consumption in late June, despite the persistence of methane in the water column, underscores the important role that physiological and environmental factors play in constraining the activity of methane-oxidizing bacteria in the Gulf of Mexico