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•A relation between groundwater temperature and quality is established.•Soil and groundwater are warming in the studied area.•Warming is associated with changes in groundwater ...quality.
Climate change and urbanization are currently leading to a warming of the subsurface worldwide with yet unforeseen consequences for groundwater quality. The temperature-sensitivity of chemical and biological processes suggests that small temperature changes driven by current warming should have a detectable effect on the ecology of aquifers and the composition of groundwater itself, but field observations covering temperatures that are environmentally relevant are sparse. The analysis of a large data set provides field-scale evidence that, within the naturally occurring temperature range between 5 and 20 °C, temperature affects the quality of groundwater. A difference in temperature of +1 K is linked to a 4% decline in oxygen saturation and a pH drop of 0.02 due to the accumulation of carbon dioxide. Further, warmer groundwater shows signs of enhanced mineral weathering and higher concentrations of drinking water-relevant elements such as manganese. The observed trends in groundwater quality are consistent with a temperature-associated intensification of microbial metabolic rates and enhanced organic matter mineralization at warmer temperatures either within the aquifers or in the overlying soils. A times series analysis reveals that soil and groundwater temperatures in the studied area have been increasing at a rate of 0.1–0.4 K per decade -comparable to recent global warming- driving subtle, but distinct changes in groundwater pH and oxygen concentrations. The results confirm, that certain but central aspects of groundwater quality (pH, O2, pCO2, Mn, DOC) change due to warming, which may increase the costs for purification when drinking water is produced from groundwater resources and may turn some aquifers uninhabitable for groundwater biota.
Fourier Transform Ion Cyclotron Resonance mass spectra (FT-ICR-MS) of natural organic matter are complex and consist of several thousands of peaks. The corresponding mass to charge ratios (m/z) and ...signal intensities result from analytes and noise. The most commonly applied way of distinguishing between analyte and noise is a fixed signal-to-noise ratio below which a detected peak is considered noise. However, this procedure is problematic and can yield ambiguous results. For example, random noise peaks can occur slightly above the signal-to-noise threshold (false positives), while peaks of low abundance analytes may occasionally fall below the fixed threshold (false negatives). Thus, cumulative results from repeated measurements of the same sample contain more peaks than a single measurement. False positive and false negative signals are difficult to distinguish, which affects the reproducibility between replicates of a sample. To target this issue, we tested the feasibility of a method detection limit (MDL) for the analysis of natural organic matter to identify peaks that can reliably be distinguished from noise by estimating the uncertainty of the noise. We performed 556 replicate analyses of a dissolved organic matter sample from the deep North Pacific on a 15 T FT-ICR-MS; each of these replicate runs consisted of 500 cumulated broadband scans. To unambiguously identify analyte peaks in the mass spectra, the sample was also run at time-consuming high-sensitivity settings. The resulting data set was used to establish and thoroughly test a MDL. The new method is easy to establish with software help, does only require the additional analysis of replicate blanks (low time increase), and can implement all steps of sample preparation. Especially when analysis time does not allow for replicate runs, major merits of the MDL are reliable removal of false positive (noise) peaks and better reproducibility, while the risk of losing analytes with low signal intensities (false negative) is comparatively low. When replicate analyses are feasible, the removal of all singly detected peaks is further recommended, as these have the highest probability of being noise peaks. We suggest that the here proposed detection limit should become routine in FT-ICR-MS data processing.
Reactive iron and organic carbon are intimately associated in soils and sediments. However, to date, the organic compounds involved are uncharacterized on the molecular level. At redox interfaces in ...peatlands, where the biogeochemical cycles of iron and dissolved organic matter (DOM) are coupled, this issue can readily be studied. We found that precipitation of iron hydroxides at the oxic surface layer of two rewetted fens removed a large fraction of DOM via coagulation. On aeration of anoxic fen pore waters, >90% of dissolved iron and 27 ± 7% (mean ± SD) of dissolved organic carbon were rapidly (within 24 h) removed. Using ultra-high-resolution MS, we show that vascular plant-derived aromatic and pyrogenic compounds were preferentially retained, whereas the majority of carboxyl-rich aliphatic acids remained in solution. We propose that redox interfaces, which are ubiquitous in marine and terrestrial settings, are selective yet intermediate barriers that limit the flux of land-derived DOM to oceanic waters.
Increasing number of application of ultrahigh-resolution mass spectrometry (UHR-MS) to natural organic matter (NOM) characterization requires an efficient and accurate formula assignment from a ...number of mass data. Herein, we newly developed two automated batch codes (namely TRFu and FuJHA) and assessed their formula assignment accuracy together with frequently used open access algorithms (i.e., Formularity and WHOI). Overall assignment accuracy for 8719 NOM-like emerging chemicals with known molecular formulae (mass range from 68 Da to 1000 Da) was highest (94%) for TRFu. Further, TRFu showed up to 99.1% formula assignment ratio for a total 76,880 UHR-MS peaks from 35 types of NOM (e.g., aquatic, soil/sediment, biochar). Therefore, as a reliable and practically feasible tool, the automated batch TRFu (freely available at ChemRxiv, https://doi.org/10.26434/chemrxiv.9917399) can precisely characterize UHR-MS spectra of various NOM and could be extended to non-target screening of NOM-like emerging chemicals in natural and engineered environments.
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•Two automated batch codes were newly developed for natural organic matter (NOM).•For the first time, the formula assignment was compared for different NOM types.•The TRFu code provided high assignment accuracy (94%) for NOM-like chemicals.•The TRFu code can be useful for non-target screening of NOM-like chemicals.•The freely available TRFu code provides a useful tool for NOM research community.
Electrical impedance tomography (EIT) is used on the thorax to measure impedance changes due to the presence of air and blood in the lung. This experimental study was performed to investigate the ...effect of posture on cardiac and respiratory related impedance changes.
EIT measurements were performed on 14 healthy subjects in left-, right lateral, prone, supine and upright positions. Simultaneously, tidal volume was recorded with an ultrasonic flowmeter. For image reconstruction, the classic Sheffield back-projection and three variants of the modern GREIT algorithm were applied with two different reference frames. Amplitudes of cardiac- and respiratory impedance changes were extracted and compared between the positions.
We found significant differences in both cardiac and respiratory amplitudes between postures. Especially, supine and upright positions showed dramatic changes in amplitude. These differences between postures were unaffected by the change of reference frames in all reconstruction methods except of the classic Sheffield back projection. Possible sources that explain the observed posture dependency are discussed.
Researchers and clinicians need to be aware of this phenomenon when comparing EIT amplitudes in different body positions.
Summary
Cultivation via classical agar plate (CAP) approaches is widely used to study microbial communities, but they are time‐consuming. An alternative approach is the application of single‐cell ...dispensing (SCD), which allows high‐throughput, label‐free sorting of microscopic particles. We aimed to develop a new anaerobic SCD workflow to cultivate human gut bacteria and compared it with CAP using faecal communities on three rich culture media. We found that the SCD approach significantly decreased the experimental time to obtain pure cultures from 17 ± 4 to 5 ± 0 days, while the isolate diversity and relative abundance coverage were comparable for both approaches. We further tested the total captured fraction by sequencing the sorted bacteria directly after growth as bulk biomass from 2400 dispensed single cells without downstream identification of individual strains. In this approach, the cultured fraction increased from 35.2% to 52.2% for SCD, highlighting the potential for deeper cultivation projects from single samples. SCD‐based cultivation also captured species not detected by sequencing (16 ± 5 per sample, including seven novel taxa). From this work, 82 human gut bacterial species across five phyla (Actinobacteriota, Bacteroidota, Desulfobacterota, Firmicutes and Proteobacteria) and 24 families were obtained, including the first cultured member of 11 novel genera and 10 novel species that were fully characterized taxonomically.
Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria ...from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called 'Pig intestinal bacterial collection' (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.
Apnoeic oxygenation has experienced a resurgence in interest in critical care and perioperative medicine. However, its effect on cerebral oxygenation and factors influencing it, have not yet been ...investigated in detail. By using near-infrared spectroscopy, we intended to provide further evidence for the safety of apnoeic oxygenation and to increase our understanding of the association between cerebral perfusion, haemodynamic, respiratory and demographic factors. In this secondary analysis of a prospective randomized controlled noninferiority trial, we recruited 125 patients, who underwent surgery under general anaesthesia with neuromuscular blockade. Arterial blood samples were taken every 2 min for a total of 15 min under apnoeic oxygenation with 100% oxygen. Near-infrared spectroscopy and cardiac output were continuously measured. Statistical analysis was performed using uni- and multivariable statistics. Ninety-one complete data sets were analysed. In six patients the SpO
fell below 92% (predefined study termination criterion). The significant average increase of cerebral oxygenation was 0.5%/min and 2.1 mmHg/min for the arterial pressure of carbon dioxide (paCO2). The median cardiac output increased significantly from 5.0 l/min (IQR 4.5-6.0) to 6.5 l/min (IQR 5.7-7.5). The most significant effect on cerebral oxygenation was exhibited by the variable paCO2 and non-specific patient factors, followed by cardiac output and paO2. Apnoeic oxygenation proves to have a high safety profile while significantly increasing cerebral oxygenation, paCO2 and cardiac output. In reverse, NIRS might act as a reliable clinical surrogate of paCO2 and cardiac output during stable arterial oxygenation.
The study of microbial communities is hampered by the large fraction of still unknown bacteria. However, many of these species have been isolated, yet lack a validly published name or description. ...The validation of names for novel bacteria requires that the uniqueness of those taxa is demonstrated and their properties are described. The accepted format for this is the protologue, which can be time-consuming to create. Hence, many research fields in microbiology and biotechnology will greatly benefit from new approaches that reduce the workload and harmonise the generation of protologues.We have developed Protologger, a bioinformatic tool that automatically generates all the necessary readouts for writing a detailed protologue. By producing multiple taxonomic outputs, functional features and ecological analysis using the 16S rRNA gene and genome sequences from a single species, the time needed to gather the information for describing novel taxa is substantially reduced. The usefulness of Protologger was demonstrated by using three published isolate collections to describe 34 novel taxa, encompassing 17 novel species and 17 novel genera, including the automatic generation of ecologically and functionally relevant names. We also highlight the need to utilise multiple taxonomic delineation methods, as while inconsistencies between each method occur, a combined approach provides robust placement. Protologger is open source; all scripts and datasets are available, along with a webserver at www.protologger.de.
The zoonotic pathogen Wohlfahrtiimonas chitiniclastica can cause several diseases in humans, including sepsis and bacteremia. Although the pathogenesis is not fully understood, the bacterium is ...thought to enter traumatic skin lesions via fly larvae, resulting in severe myiasis and/or wound contamination. Infections are typically associated with, but not limited to, infestation of an open wound by fly larvae, poor sanitary conditions, cardiovascular disease, substance abuse, and osteomyelitis. W. chitiniclastica is generally sensitive to a broad spectrum of antibiotics with the exception of fosfomycin. However, increasing drug resistance has been observed and its development should be monitored with caution. In this review, we summarize the currently available knowledge and evaluate it from both a clinical and a genomic perspective.
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