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Aim: Intensive studies since the beginning of the 21st century have provided vast amounts of knowledge about soil microbial diversity at local and global scales. However, microbial habitats have been poorly investigated at large scale. This study aims to characterize soil bacterial habitats across France for the first time by integrating the description of numerous environmental factors and human activities. Location: We focus on the large spatial scale of mainland France using the largest spatially explicit soil sampling set available across France (2,173 soils, area = 5.5 × 105 km2). Major taxa studied: Soil bacteria and archaea were studied by a high throughput sequencing approach targeting the V3‐V4 region of the 16Sribosomal ribonucleic acid (rRNA) gene directly amplified from soil DNA. Methods: We applied decision tree learning and geostatistical approaches combining the abundant data on soil microbes and large‐scale environmental description in order to conduct a comprehensive analysis of soil bacterial and archaeal communities. Results: We identified a complex mosaic of 16 distinct terrestrial habitats, based on soil type and management (pH, C : N ratio, land use). As for plants and animals, each habitat hosted generalist and specialist taxa and a specific interaction network directly or indirectly impacted by human activities. Main conclusions: In a context of global change, our results emphasize that the policies for biodiversity and habitat conservation should now integrate soil microorganisms conceptually and technically. [ABSTRACT FROM AUTHOR]

Preliminary studies of perdeuterated crystals of human transthyretin (TTR) have been carried out using the LADI-III and D19 diffractometers at the Institut Laue-Langevin in Grenoble. The results demonstrate the feasibility of a full crystallographic analysis to a resolution of 2.0 Å using Laue diffraction and also illustrate the potential of using monochromatic instruments such as D19 for higher resolution studies where larger crystals having smaller unit cells are available. This study will yield important information on hydrogen bonding, amino-acid protonation states and hydration in the protein. Such information will be of general interest for an understanding of the factors that stabilize/destabilize TTR and for the design of ligands that may be used to counter TTR amyloid fibrillogenesis. [ABSTRACT FROM AUTHOR]

Peatland testate amoebae (TA) are well-established bioindicators for depth to water table (DWT), but effects of hydrological changes on TA communities have never been tested experimentally. We tested this in a field experiment by placing Sphagnum carpets (15 cm diameter) collected in hummock, lawn and pool microsites (origin) at three local conditions (dry, moist and wet) using trenches dug in a peatland. One series of samples was seeded with microorganism extract from all microsites. TA community were analysed at T0: 8-2008, T1: 5-2009 and T2: 8-2009. We analysed the data using conditional inference trees, principal response curves (PRC) and DWT inferred from TA communities using a transfer function used for paleoecological reconstruction. Density declined from T0 to T1 and then increased sharply by T2. Species richness, Simpson diversity and Simpson evenness were lower at T2 than at T0 and T1. Seeded communities had higher species richness in pool samples at T0. Pool samples tended to have higher density, lower species richness, Simpson diversity and Simpson Evenness than hummock and/or lawn samples until T1. In the PRC, the effect of origin was significant at T0 and T1, but the effect faded away by T2. Seeding effect was strongest at T1 and lowest vanished by T2. Local condition effect was strong but not in line with the wetness gradient at T1 but started to reflect it by T2. Likewise, TA-inferred DWT started to match the experimental conditions by T2, but more so in hummock and lawn samples than in pool samples. This study confirmed that TA responds to hydrological changes over a 1-year period. However, sensitivity of TA to hydrological fluctuations, and thus the accuracy of inferred DWT changes, was habitat specific, pool TA communities being least responsive to environmental changes. Lawns and hummocks may be thus better suited than pools for paleoecological reconstructions. This, however, contrasts with the higher prediction error and species' tolerance for DWT with increasing dryness observed in transfer function models.

The ecology of peatland testate amoebae is well studied along broad gradient from very wet (pool) to dry (hummock) micro-sites where testate amoebae are often found to respond primarily to the depth to water table (DWT). Much less is known on their responses to finer-scale gradients, and nothing is known of their possible response to phenolic compounds, which play a key role in carbon storage in peatlands. We studied the vertical (0-3, 3-6, and 6-9 cm sampling depths) micro-distribution patterns of testate amoebae in the same microhabitat (Sphagnum fallax lawn) along a narrow ecological gradient between a poor fen with an almost flat and homogeneous Sphagnum carpet (fen) and a "young bog" (bog) with more marked micro-topography and mosaic of poor fen and bog vegetation. We analyzed the relationships between the testate amoeba data and three sets of variables (1) "chemical" (pH, Eh potential, and conductivity), (2) "physical" (water temperature, altitude, i.e., Sphagnum mat micro-topography, and DWT), and (3) phenolic compounds in/from Sphagnum (water-soluble and primarily bound phenolics) as well as the habitat (fen/bog) and the sampling depth. Testate amoeba Shannon H' diversity, equitability J of communities, and total density peaked in lower parts of Sphagnum, but the patterns differed between the fen and bog micro-sites. Redundancy analyses revealed that testate amoeba communities differed significantly in relation to Eh, conductivity, water temperature, altitude, water-soluble phenolics, habitat, and sampling depth, but not to DWT, pH, or primarily bound phenolics. The sensitivity of testate amoebae to weak environmental gradients makes them particularly good integrators of micro-environmental variations and has implications for their use in paleoecology and environmental monitoring. The correlation between testate amoeba communities and the concentration of water-soluble phenolic suggests direct (e.g., physiological) and/or indirect (e.g., through impact on prey organisms) effects on testate amoebae, which requires further research.

The first phase of the ESRF beamline ID23 to be constructed was ID23-1, a tunable MAD-capable beamline which opened to users in early 2004. The second phase of the beamline to be constructed is ID23-2, a monochromatic microfocus beamline dedicated to macromolecular crystallography experiments. Beamline ID23-2 makes use of well characterized optical elements: a single-bounce silicon (111) monochromator and two mirrors in Kirkpatrick-Baez geometry to focus the X-ray beam. A major design goal of the ID23-2 beamline is to provide a reliable, easy-to-use and routine microfocus beam. ID23-2 started operation in November 2005, as the first beamline dedicated to microfocus macromolecular crystallography. The beamline has taken the standard automated ESRF macromolecular crystallography environment (both hardware and software), allowing users of ID23-2 to be rapidly familiar with the microfocus environment. This paper describes the beamline design, the special considerations taken into account given the microfocus beam, and summarizes the results of the first years of the beamline operation.

The demand for access to macromolecular crystallography synchrotron beam time continues to increase. To meet this demand the ESRF has constructed a dual station beamline using a canted undulator system as the X-ray source. The first phase of the beamline to be constructed is ID23-1, a tunable MAD-capable station with a mini-focus X-ray beam. The beamline makes use of well characterized optical elements: a channel-cut monochromator with a high-precision toroidal mirror to focus the X-ray beam. The beamline has been conceived with the aim of providing high levels of automation to create an industrial-like environment for protein crystallography. A new software suite has been developed to permit reliable easy operation for the beamline users and beamline staff. High levels of diagnostics are built in to allow rapid trouble-shooting. These developments are now being exported to the ESRF macromolecular crystallography beamline complex and have been made in a modular fashion to facilitate transportability to other synchrotrons.