Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

Microbial organisms inhabit virtually all environments and encompass a vast biological diversity. The pangenome concept aims to facilitate an understanding of diversity within defined phylogenetic groups. Hence, pangenomes are increasingly used to characterize the strain diversity of prokaryotic species. To understand the interdependence of pangenome features (such as the number of core and accessory genes) and to study the impact of environmental and phylogenetic constraints on the evolution of conspecific strains, we computed pangenomes for 155 phylogenetically diverse species (from ten phyla) using 7,000 high-quality genomes to each of which the respective habitats were assigned. Species habitat ubiquity was associated with several pangenome features. In particular, core-genome size was more important for ubiquity than accessory genome size. In general, environmental preferences had a stronger impact on pangenome evolution than phylogenetic inertia. Environmental preferences explained up to 49% of the variance for pangenome features, compared with 18% by phylogenetic inertia. This observation was robust when the dataset was extended to 10,100 species (59 phyla). The importance of environmental preferences was further accentuated by convergent evolution of pangenome features in a given habitat type across different phylogenetic clades. For example, the soil environment promotes expansion of pangenome size, while host-associated habitats lead to its reduction. Taken together, we explored the global principles of pangenome evolution, quantified the influence of habitat, and phylogenetic inertia on the evolution of pangenomes and identified criteria governing species ubiquity and habitat specificity

Regional and seasonal patterns of litterfall in tropical South America

The production of aboveground soft tissue represents an important share of total net primary production in tropical rain forests. Here we draw from a large number of published and unpublished datasets (n=81 sites) to assess the determinants of litterfall variation across South American tropical forests. We show that across old-growth tropical rainforests, litterfall averages 8.61±1.91 Mg ha−1 yr−1 (mean ± standard deviation, in dry mass units). Secondary forests have a lower annual litterfall than old-growth tropical forests with a mean of 8.01±3.41 Mg ha−1 yr−1. Annual litterfall shows no significant variation with total annual rainfall, either globally or within forest types. It does not vary consistently with soil type, except in the poorest soils (white sand soils), where litterfall is significantly lower than in other soil types (5.42±1.91 Mg ha−1 yr−1). We also study the determinants of litterfall seasonality, and find that it does not depend on annual rainfall or on soil type. However, litterfall seasonality is significantly positively correlated with rainfall seasonality. Finally, we assess how much carbon is stored in reproductive organs relative to photosynthetic organs. Mean leaf fall is 5.74±1.83 Mg ha−1 yr−1 (71% of total litterfall). Mean allocation into reproductive organs is 0.69±0.40 Mg ha−1 yr−1 (9% of total litterfall). The investment into reproductive organs divided by leaf litterfall increases with soil fertility, suggesting that on poor soils, the allocation to photosynthetic organs is prioritized over that to reproduction. Finally, we discuss the ecological and biogeochemical implications of these result

A historic jet-emission minimum reveals hidden spectral features in 3C 273

Aims. The aim of this work is to identify and study spectral features in the quasar 3C 273 usually blended by its strong jet emission. Method. A historic minimum in the sub-millimetre emission of 3C 273 triggered coordinated multi-wavelength observations in June 2004. X-ray observations from the INTEGRAL, XMM-Newton and RXTE satellites are complemented by ground-based optical, infrared, millimetre and radio observations. The overall spectrum is used to model the infrared and X-ray spectral components. Results. Three thermal dust emission components are identified in the infrared. The dust emission on scales from 1 pc to several kpc is comparable to that of other quasars, as expected by AGN unification schemes. The observed weakness of the X-ray emission supports the hypothesis of a synchrotron self-Compton origin for the jet component. There is a clear soft-excess and we find evidence for a very broad iron line which could be emitted in a disk around a Kerr black hole. Other signatures of a Seyfert-like X-ray component are not detected.Comment: 4 pages. Accepted for publication in A&A Letter

Calibration and performance of the photon sensor response of FACT -- The First G-APD Cherenkov telescope

The First G-APD Cherenkov Telescope (FACT) is the first in-operation test of the performance of silicon photo detectors in Cherenkov Astronomy. For more than two years it is operated on La Palma, Canary Islands (Spain), for the purpose of long-term monitoring of astrophysical sources. For this, the performance of the photo detectors is crucial and therefore has been studied in great detail. Special care has been taken for their temperature and voltage dependence implementing a correction method to keep their properties stable. Several measurements have been carried out to monitor the performance. The measurements and their results are shown, demonstrating the stability of the gain below the percent level. The resulting stability of the whole system is discussed, nicely demonstrating that silicon photo detectors are perfectly suited for the usage in Cherenkov telescopes, especially for long-term monitoring purpose

FACT -- Operation of the First G-APD Cherenkov Telescope

Since more than two years, the First G-APD Cherenkov Telescope (FACT) is operating successfully at the Canary Island of La Palma. Apart from its purpose to serve as a monitoring facility for the brightest TeV blazars, it was built as a major step to establish solid state photon counters as detectors in Cherenkov astronomy. The camera of the First G-APD Cherenkov Telesope comprises 1440 Geiger-mode avalanche photo diodes (G-APD aka. MPPC or SiPM) for photon detection. Since properties as the gain of G-APDs depend on temperature and the applied voltage, a real-time feedback system has been developed and implemented. To correct for the change introduced by temperature, several sensors have been placed close to the photon detectors. Their read out is used to calculate a corresponding voltage offset. In addition to temperature changes, changing current introduces a voltage drop in the supporting resistor network. To correct changes in the voltage drop introduced by varying photon flux from the night-sky background, the current is measured and the voltage drop calculated. To check the stability of the G-APD properties, dark count spectra with high statistics have been taken under different environmental conditions and been evaluated. The maximum data rate delivered by the camera is about 240 MB/s. The recorded data, which can exceed 1 TB in a moonless night, is compressed in real-time with a proprietary loss-less algorithm. The performance is better than gzip by almost a factor of two in compression ratio and speed. In total, two to three CPU cores are needed for data taking. In parallel, a quick-look analysis of the recently recorded data is executed on a second machine. Its result is publicly available within a few minutes after the data were taken. [...]Comment: 19th IEEE Real-Time Conference, Nara, Japan (2014

FACT -- the First Cherenkov Telescope using a G-APD Camera for TeV Gamma-ray Astronomy (HEAD 2010)

Geiger-mode Avalanche Photodiodes (G-APD) bear the potential to significantly improve the sensitivity of Imaging Air Cherenkov Telescopes (IACT). We are currently building the First G-APD Cherenkov Telescope (FACT) by refurbishing an old IACT with a mirror area of 9.5 square meters and construct a new, fine pixelized camera using novel G-APDs. The main goal is to evaluate the performance of a complete system by observing very high energy gamma-rays from the Crab Nebula. This is an important field test to check the feasibility of G-APD-based cameras to replace at some time the PMT-based cameras of planned future IACTs like AGIS and CTA. In this article, we present the basic design of such a camera as well as some important details to be taken into account.Comment: Poster shown at HEAD 2010, Big Island, Hawaii, March 1-4, 201

A novel camera type for very high energy gamma-ray astronomy based on Geiger-mode avalanche photodiodes

Geiger-mode avalanche photodiodes (G-APD) are promising new sensors for light detection in atmospheric Cherenkov telescopes. In this paper, the design and commissioning of a 36-pixel G-APD prototype camera is presented. The data acquisition is based on the Domino Ring Sampling (DRS2) chip. A sub-nanosecond time resolution has been achieved. Cosmic-ray induced air showers have been recorded using an imaging mirror setup, in a self-triggered mode. This is the first time that such measurements have been carried out with a complete G-APD camera.Comment: 9 pages with 11 figure

FACT -- The G-APD revolution in Cherenkov astronomy

Since two years, the FACT telescope is operating on the Canary Island of La Palma. Apart from its purpose to serve as a monitoring facility for the brightest TeV blazars, it was built as a major step to establish solid state photon counters as detectors in Cherenkov astronomy. The camera of the First G-APD Cherenkov Telesope comprises 1440 Geiger-mode avalanche photo diodes (G-APD), equipped with solid light guides to increase the effective light collection area of each sensor. Since no sense-line is available, a special challenge is to keep the applied voltage stable although the current drawn by the G-APD depends on the flux of night-sky background photons significantly varying with ambient light conditions. Methods have been developed to keep the temperature and voltage dependent response of the G-APDs stable during operation. As a cross-check, dark count spectra with high statistics have been taken under different environmental conditions. In this presentation, the project, the developed methods and the experience from two years of operation of the first G-APD based camera in Cherenkov astronomy under changing environmental conditions will be presented.Comment: Proceedings of the Nuclear Science Symposium and Medical Imaging Conference (IEEE-NSS/MIC), 201

High-resolution mapping of forest carbon stocks in the Colombian Amazon

High-resolution mapping of tropical forest carbon stocks can assist forest management and improve implementation of large-scale carbon retention and enhancement programs. Previous high-resolution approaches have relied on field plot and/or light detection and ranging (LiDAR) samples of aboveground carbon density, which are typically upscaled to larger geographic areas using stratification maps. Such efforts often rely on detailed vegetation maps to stratify the region for sampling, but existing tropical forest maps are often too coarse and field plots too sparse for high-resolution carbon assessments. We developed a top-down approach for high-resolution carbon mapping in a 16.5 million ha region (> 40%) of the Colombian Amazon – a remote landscape seldom documented. We report on three advances for large-scale carbon mapping: (i) employing a universal approach to airborne LiDAR-calibration with limited field data; (ii) quantifying environmental controls over carbon densities; and (iii) developing stratification- and regression-based approaches for scaling up to regions outside of LiDAR coverage. We found that carbon stocks are predicted by a combination of satellite-derived elevation, fractional canopy cover and terrain ruggedness, allowing upscaling of the LiDAR samples to the full 16.5 million ha region. LiDAR-derived carbon maps have 14% uncertainty at 1 ha resolution, and the regional map based on stratification has 28% uncertainty in any given hectare. High-resolution approaches with quantifiable pixel-scale uncertainties will provide the most confidence for monitoring changes in tropical forest carbon stocks. Improved confidence will allow resource managers and decision makers to more rapidly and effectively implement actions that better conserve and utilize forests in tropical regions

FACT - The First G-APD Cherenkov Telescope: Status and Results

The First G-APD Cherenkov telescope (FACT) is the first telescope using silicon photon detectors (G-APD aka. SiPM). It is built on the mount of the HEGRA CT3 telescope, still located at the Observatorio del Roque de los Muchachos, and it is successfully in operation since Oct. 2011. The use of Silicon devices promises a higher photon detection efficiency, more robustness and higher precision than photo-multiplier tubes. The FACT collaboration is investigating with which precision these devices can be operated on the long-term. Currently, the telescope is successfully operated from remote and robotic operation is under development. During the past months of operation, the foreseen monitoring program of the brightest known TeV blazars has been carried out, and first physics results have been obtained including a strong flare of Mrk501. An instantaneous flare alert system is already in a testing phase. This presentation will give an overview of the project and summarize its goals, status and first results