A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

Taskomat & Taskolib: A Versatile, Programmable Sequencer for Process Automation

This contribution introduces the Taskolib library, a powerful framework for automating processes. Users can easily assemble sequences out of process steps, execute these sequences, and follow their progress. Individual steps are fully programmable in the lightweight Lua language. If desired, sequences can be enhanced with flow control via well-known constructs such as IF, WHILE, or TRY. The library is written in platform-independent C++17 and carries no dependency on any specific control system or communication framework. Instead, such dependencies are injected by client code; as an example, the integration with a DOOCS server and a graphical user interface is demonstrated

Two-Color Operation of FLASH2 Undulator

FLASH is the first soft X-ray FEL user facility, routinely providing brilliant photon beams for users since 2005. The second undulator branch of this facility, FLASH2, is gaptunable which allows to test and use advanced lasing concepts.In particular, we tested recently a two-color mode of operation based on the alternation of tunes of the undulator segments (every other segment is tuned to the second wavelength).This scheme is advantageous in comparison with a subsequent generation of two colors in two consecutive sections of the undulator line. First, source positions of the two FEL beams are close to each other which makes it easier to handle them. Second, the amplification is more efficientin this configuration since the segments with respectively"wrong" wavelength still act as bunchers. We developed methods for online intensity measurements of the two colors simultaneously that require a combination of two detectors.We present some examples of such measurements in the XUV and soft X-ray regimes

An X-ray gas monitor for free-electron lasers

A novel X-ray gas monitor (XGM) has been developed which allows the measurement of absolute photon pulse energy and photon beam position at all existing and upcoming free-electron lasers (FELs) over a broad spectral range covering vacuum ultraviolet (VUV), extreme ultraviolet (EUV) and soft and hard X-rays. The XGM covers a wide dynamic range from spontaneous undulator radiation to FEL radiation and provides a temporal resolution of better than 200 ns. The XGM consists of two X-ray gas-monitor detectors (XGMDs) and two huge-aperture open electron multipliers (HAMPs). The HAMP enhances the detection efficiency of the XGM for low-intensity radiation down to 10$^5$ photons per pulse and for FEL radiation in the hard X-ray spectral range, while the XGMD operates in higher-intensity regimes. The relative standard uncertainty for measurements of the absolute photon pulse energy is well below 10%, and down to 1% for measurements of relative pulse-to-pulse intensity on pulses with more than 10$^{10}$ photons per pulse. The accuracy of beam-position monitoring in the vertical and horizontal directions is of the order of 10 µm

Operation of X-ray gas monitors at the European XFEL

X-ray gas monitors (XGMs) are operated at the European XFEL for non-invasive single-shot pulse energy measurements and average beam position monitoring. They are used for tuning and maintaining the self-amplified spontaneous emission (SASE) operation and for sorting single-shot experimental data according to the pulse-resolved energy monitor data. The XGMs were developed at DESY based on the specific requirements for the European XFEL. In total, six XGM units are continuously in operation. Here, the main principle and experimental setup of an XGM are summarized, and the locations of the six XGMs at the facility are shown. Pulse energy measurements at 0.134 nm wavelength are presented, exceeding 1 mJ obtained with an absolute measurement uncertainty of 7–10%; correlations between different XGMs are shown, from which a SASE1 beamline transmission of 97% is deduced. Additionally, simultaneous position measurements close to the undulator and at the end of the tunnel are shown, along with the correlation of beam position data simultaneously acquired by an XGM and an imager

Pulse energy measurement at the SXR instrument

A gas monitor detector was implemented and characterized at the Soft X-rayResearch (SXR) instrument to measure the average, absolute and pulse-resolved photon flux of the LCLS beam in the energy range between 280 and2000 eV. The detector is placed after the monochromator and addresses theneed to provide reliable absolute pulse energy as well as pulse-resolvedmeasurements for the various experiments at this instrument. This detectorprovides a reliable non-invasive measurement for determining flux levels on thesamples in the downstream experimental chamber and for optimizing signallevels of secondary detectors and for the essential need of data normalization.The design, integration into the instrument and operation are described, andexamples of its performance are given

Two-Color Operation of a Soft X-ray FEL with Alternation of Undulator Tunes

FLASH is the first soft X-ray FEL user facility, routinely providing brilliant photon beams for users since 2005. The second undulator branch of this facility, FLASH2, is gap-tunable, which allows for testing and using advanced lasing concepts. In particular, we developed a two-color operation mode based on the alternatingly tuned undulator segments (every other segment is tuned to the second wavelength). This scheme is advantageous in comparison with a subsequent generation of two colors in two consecutive sections of the undulator line. First, source positions of the two FEL beams are close to each other which makes it easier to focus them on a sample. Second, the amplification is more efficient in this configuration since the segments with respectively “wrong” wavelength still act as bunchers. We studied operation of this scheme in the regime of small and large separation of tunes (up to a factor of two). We developed new methods for online intensity measurements of the two colors simultaneously that require a combination of two detectors. We also demonstrated our capabilities to measure spectral and temporal properties of two pulses with different wavelengths