Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, ...metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.
•A full-scale bioreactor was operated to treat high ammonium levels in groundwater.•One distinct comammox Nitrospira was strongly correlated with ammonia oxidation rates.•Moderate increases in copper ...availability led to dominance of comammox Nitrospira.•High copper dosage ultimately shifted the major nitrifier to Nitrosomonadaceae AOB.
Microbial ammonia oxidation is the initial nitrification step used in biological nitrogen-removal during water treatment processes, and the discovery of complete ammonia-oxidizing (comammox) bacteria added a novel member to this functional group. It is important to identify and understand the predominant microorganisms responsible for ammonium removal in biotechnological process design and optimization. In this study, we used a full-scale bioreactor to treat ammonium in groundwater (9.3 ± 0.5 mg NH4+-N/L) and investigated the key ammonia-oxidizing prokaryotes present. The groundwater ammonium was stably and efficiently oxidized throughout ∼700 days of bioreactor operation. 16S rRNA gene amplicon sequencing of the bioreactor community showed a high abundance of Nitrospira (12.5–45.9%), with the dominant sequence variant (3.5–37.8%) most closely related to Candidatus Nitrospira nitrosa. Furthermore, analyses of amoA, the marker gene for ammonia oxidation, indicated the presence of two distinct comammox Nitrospira populations, however, the relative abundance of only one of these populations was strongly correlated to ammonia oxidation rates and was robustly expressed. After 380 days of operation copper wires were immersed into the reactor at 0.04–0.06 m2/m3 tank, which caused a gradual abundance increase of one discrete comammox Nitrospira population. However, further increase of the copper dosing (0.08 m2/m3 tank) inverted the most abundant ammonia-oxidizing population to Nitrosomonas sp. These results indicate that comammox Nitrospira were capable of efficient ammonium removal in groundwater without exogenous nutrients, but copper addition can stimulate comammox Nitrospira or lead to dominance of Nitrosomonas depending on dosage.
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The current paradigm, widely incorporated in soil biogeochemical models, is that microbial methanogenesis can only occur in anoxic habitats. In contrast, here we show clear geochemical and biological ...evidence for methane production in well-oxygenated soils of a freshwater wetland. A comparison of oxic to anoxic soils reveal up to ten times greater methane production and nine times more methanogenesis activity in oxygenated soils. Metagenomic and metatranscriptomic sequencing recover the first near-complete genomes for a novel methanogen species, and show acetoclastic production from this organism was the dominant methanogenesis pathway in oxygenated soils. This organism, Candidatus Methanothrix paradoxum, is prevalent across methane emitting ecosystems, suggesting a global significance. Moreover, in this wetland, we estimate that up to 80% of methane fluxes could be attributed to methanogenesis in oxygenated soils. Together, our findings challenge a widely held assumption about methanogenesis, with significant ramifications for global methane estimates and Earth system modeling.
Meningeal lymphatic vessels have been described in animal studies, but limited comparable data is available in human studies. Here we show dural lymphatic structures along the dural venous sinuses in ...dorsal regions and along cranial nerves in the ventral regions in the human brain. 3D T2-Fluid Attenuated Inversion Recovery magnetic resonance imaging relies on internal signals of protein rich lymphatic fluid rather than contrast media and is used in the present study to visualize the major human dural lymphatic structures. Moreover we detect direct connections between lymphatic fluid channels along the cranial nerves and vascular structures and the cervical lymph nodes. We also identify age-related cervical lymph node atrophy and thickening of lymphatics channels in both dorsal and ventral regions, findings which reflect the reduced lymphatic output of the aged brain.
The impressive locomotion and manipulation capabilities of spiders have led to a host of bioinspired robotic designs aiming to reproduce their functionalities; however, current actuation mechanisms ...are deficient in either speed, force output, displacement, or efficiency. Here—using inspiration from the hydraulic mechanism used in spider legs—soft‐actuated joints are developed that use electrostatic forces to locally pressurize a hydraulic fluid, and cause flexion of a segmented structure. The result is a lightweight, low‐profile articulating mechanism capable of fast operation, high forces, and large displacement; these devices are termed spider‐inspired electrohydraulic soft‐actuated (SES) joints. SES joints with rotation angles up to 70°, blocked torques up to 70 mN m, and specific torques up to 21 N m kg−1 are demonstrated. SES joints demonstrate high speed operation, with measured roll‐off frequencies up to 24 Hz and specific power as high as 230 W kg−1—similar to human muscle. The versatility of these devices is illustrated by combining SES joints to create a bidirectional joint, an artificial limb with independently addressable joints, and a compliant gripper. The lightweight, low‐profile design, and high performance of these devices, makes them well‐suited toward the development of articulating robotic systems that can rapidly maneuver.
Spider‐inspired electrohydraulic soft‐actuated (SES) joints provide compliant, electrohydraulic actuation for articulated robots. These joints exhibit fast actuation, high forces, and large displacements. This article characterizes the quasistatic and dynamic performance of SES joints experimentally and presents a model of their quasistatic behavior. The versatility of SES joints is demonstrated in a bidirectional joint, an artificial limb, and a compliant gripper.
To determine factors predicting if a radiologists... report of a .. stone... on ultrasound (US) was not actually a clinically significant stone, based on subsequent computed tomogram (CT). US often ...overestimates stone size and various pathologic entities are also hyperechoic;.ßthus, a subsequent CT without a clinically significant stone may represent unnecessary radiation exposure. A decision-tree and nomogram were developed to predict when stones are unlikely on subsequent CT.
Retrospective analysis of patients, of any age, receiving CT within 24.ßhours of a sonographic report documenting a single renal stone, during 2019...2020, in any phase of care, at one institution. Novel stone-likelihood-systems for US and CT (US-SLS, CT-SLS) were devised and validated to classify stones as clinically significant or insignificant, with CT as the gold standard. Binomial logistic regression predicting clinically significant stones was performed with sonographic and patient characteristics.
Eight hundred twenty patients had US followed by CT, 228 (27.8%) reported documented stones, 140 (17.1%) reported a single stone. Clinically significant stones were associated with larger stone size (P: .002), location (P: .002), hydronephrosis (P: .04), shadowing-artifact (P: .02) depth.ßto.ßstone (P: .008), and Body mass Index (BMI) (P: .01). US-SLS had higher sensitivity (95.4%) and negative-predictive-value (81.8%) compared to a multivariate model of significant variables.
US-SLS appears to exclude clinically irrelevant .. stones... better than established criteria including twinkle or shadow in this retrospective analysis. A diagnostic algorithm and nomogram are presented. US-SLS and the associated decision tree can assist providers in avoiding unnecessary radiation when clinically significant stones are unlikely.
Inland waters are increasingly recognized as critical sites of methane emissions to the atmosphere, but the biogeochemical reactions driving such fluxes are less well understood. The Prairie Pothole ...Region (PPR) of North America is one of the largest wetland complexes in the world, containing millions of small, shallow wetlands. The sediment pore waters of PPR wetlands contain some of the highest concentrations of dissolved organic carbon (DOC) and sulfur species ever recorded in terrestrial aquatic environments. Using a suite of geochemical and microbiological analyses, we measured the impact of sedimentary carbon and sulfur transformations in these wetlands on methane fluxes to the atmosphere. This research represents the first study of coupled geochemistry and microbiology within the PPR and demonstrates how the conversion of abundant labile DOC pools into methane results in some of the highest fluxes of this greenhouse gas to the atmosphere ever reported. Abundant DOC and sulfate additionally supported some of the highest sulfate reduction rates ever measured in terrestrial aquatic environments, which we infer to account for a large fraction of carbon mineralization in this system. Methane accumulations in zones of active sulfate reduction may be due to either the transport of free methane gas from deeper locations or the co‐occurrence of methanogenesis and sulfate reduction. If both respiratory processes are concurrent, any competitive inhibition of methanogenesis by sulfate‐reducing bacteria may be lessened by the presence of large labile DOC pools that yield noncompetitive substrates such as methanol. Our results reveal some of the underlying mechanisms that make PPR wetlands biogeochemical hotspots, which ultimately leads to their critical, but poorly recognized role in regional greenhouse gas emissions.
Wetland sediments recovered from the Prairie Pothole Region of North America host microbial communities catalyzing some of the highest sulfate reduction rates ever measured. Concurrently, these same sediments drive some of the highest methane fluxes to atmosphere ever measured. Together, these data indicate that the PPR may play an oversized role in carbon cycling and greenhouse gas fluxes to the atmosphere.
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