Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide.

The sources and sinks of nitrous oxide, as control emissions to the atmosphere, are generally poorly constrained for most environmental systems. Initial depth-resolved analysis of nitrous oxide flux from observation wells and the proximal surface within a nitrate contaminated aquifer system revealed high subsurface production but little escape from the surface. To better understand the environmental controls of production and emission at this site, we used a combination of isotopic, geochemical, and molecular analyses to show that chemodenitrification and bacterial denitrification are major sources of nitrous oxide in this subsurface, where low DO, low pH, and high nitrate are correlated with significant nitrous oxide production. Depth-resolved metagenomes showed that consumption of nitrous oxide near the surface was correlated with an enrichment of Clade II nitrous oxide reducers, consistent with a growing appreciation of their importance in controlling release of nitrous oxide to the atmosphere. Our work also provides evidence for the reduction of nitrous oxide at a pH of 4, well below the generally accepted limit of pH 5.

Enhanced Photon-Phonon Interaction in WSe2 Acoustic Nanocavities.

Acoustic nanocavities (ANCs) with resonance frequencies much above 1 GHz are prospective to be exploited in sensors and quantum operating devices. Nowadays, acoustic nanocavities fabricated from van der Waals (vdW) nanolayers allow them to exhibit resonance frequencies of the breathing acoustic mode up to f ∼ 1 THz and quality factors up to Q ∼ 103. For such high acoustic frequencies, electrical methods fail, and optical techniques are used for the generation and detection of coherent phonons. Here, we study experimentally acoustic nanocavities fabricated from WSe2 layers with thicknesses from 8 up to 130 nm deposited onto silica colloidal crystals. The substrate provides a strong mechanical support for the layers while keeping their acoustic properties the same as in membranes. We concentrate on experimental and theoretical studies of the amplitude of the optically measured acoustic signal from the breathing mode, which is the most important characteristic for acousto-optical devices. We probe the acoustic signal optically with a single wavelength in the vicinity of the exciton resonance and measure the relative changes in the reflectivity induced by coherent phonons up to 3 × 10-4 for f ∼ 100 GHz. We reveal the enhancement of photon-phonon interaction for a wide range of acoustic frequencies and show high sensitivity of the signal amplitude to the photoelastic constants governed by the deformation potential and dielectric function for photon energies near the exciton resonance. We also reveal a resonance in the photoelastic response (we call it photoelastic resonance) in the nanolayers with thickness close to the Bragg condition. The estimates show the capability of acoustic nanocavities with an exciton resonance for operations with high-frequency single phonons at an elevated temperature.

Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut.

Clostridioides difficile colonizes up to 30-40% of community-dwelling adults without causing disease. C. difficile infections (CDIs) are the leading cause of antibiotic-associated diarrhea in the U.S. and typically develop in individuals following disruption of the gut microbiota due to antibiotic or chemotherapy treatments. Further treatment of CDI with antibiotics is not always effective and can lead to antibiotic resistance and recurrent infections (rCDI). The most effective treatment for rCDI is the reestablishment of an intact microbiota via fecal microbiota transplants (FMTs). However, the success of FMTs has been difficult to generalize because the microbial interactions that prevent engraftment and facilitate the successful clearance of C. difficile are still only partially understood. Here we show how microbial community-scale metabolic models (MCMMs) accurately predicted known instances of C. difficile colonization susceptibility or resistance in vitro and in vivo. MCMMs provide detailed mechanistic insights into the ecological interactions that govern C. difficile engraftment, like cross-feeding or competition involving metabolites like succinate, trehalose, and ornithine, which differ from person to person. Indeed, three distinct C. difficile metabolic niches emerge from our MCMMs, two associated with positive growth rates and one that represents non-growth, which are consistently observed across 15,204 individuals from five independent cohorts. Finally, we show how MCMMs can predict personalized engraftment and C. difficile growth suppression for a probiotic cocktail (VE303) designed to replace FMTs for the treatment rCDI. Overall, this powerful modeling approach predicts personalized C. difficile engraftment risk and can be leveraged to assess probiotic treatment efficacy. MCMMs could be extended to understand the mechanistic underpinnings of personalized engraftment of other opportunistic bacterial pathogens, beneficial probiotic organisms, or more complex microbial consortia.

Island biogeography theory and the gut: why taller people tend to harbor more diverse gut microbiomes.

Prior work has shown a positive scaling relationship between vertebrate body size and gut microbiome alpha-diversity. This observation mirrors commonly observed species area relationships (SAR) in many other ecosystems. Here, we show a similar scaling relationship between human height and gut microbiome alpha-diversity across two large, independent cohorts, controlling for a wide range of relevant covariates, such as body mass index, age, sex, and bowel movement frequency. Island Biogeography Theory (IBT), which predicts that larger islands tend to harbor greater species diversity through neutral demographic processes, provides a simple mechanism for these positive SARs. Using an individual-based model of IBT adapted to the gut, we demonstrate that increasing the length of a flow-through ecosystem is associated with increased species diversity. We delve into the possible clinical implications of these SARs in the American Gut Cohort. Consistent with prior observations that lower alpha-diversity is a risk factor for Clostridioides difficile infection (CDI), we found that individuals who reported a history of CDI were shorter than those who did not and that this relationship appeared to be mediated by alpha-diversity. We also observed that vegetable consumption mitigated this risk increase, also by mediation through alpha-diversity. In summary, we find that body size and gut microbiome diversity show a robust positive association, that this macroecological scaling relationship is related to CDI risk, and that greater vegetable intake can mitigate this effect.

Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification.

Competition between nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) for resources in anoxic environments is generally thought to be governed largely by thermodynamics. It is now recognized that intermediates of nitrogen and sulfur cycling (e.g., hydrogen sulfide, nitrite, etc.) can also directly impact NRB and SRB activities in freshwater, wastewater, and sediment and therefore may play important roles in competitive interactions. Here, through comparative transcriptomic and metabolomic analyses, we have uncovered mechanisms of hydrogen sulfide- and cysteine-mediated inhibition of nitrate respiratory growth for the NRB Intrasporangium calvum C5. Specifically, the systems analysis predicted that cysteine and hydrogen sulfide inhibit growth of I. calvum C5 by disrupting distinct steps across multiple pathways, including branched-chain amino acid (BCAA) biosynthesis, utilization of specific carbon sources, and cofactor metabolism. We have validated these predictions by demonstrating that complementation with BCAAs and specific carbon sources relieves the growth inhibitory effects of cysteine and hydrogen sulfide. We discuss how these mechanistic insights give new context to the interplay and stratification of NRB and SRB in diverse environments.IMPORTANCE Nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) colonize diverse anoxic environments, including soil subsurface, groundwater, and wastewater. NRB and SRB compete for resources, and their interplay has major implications on the global cycling of nitrogen and sulfur species, with undesirable outcomes in some contexts. For instance, the removal of reactive nitrogen species by NRB is desirable for wastewater treatment, but in agricultural soils, NRB can drive the conversion of nitrates from fertilizers into nitrous oxide, a potent greenhouse gas. Similarly, the hydrogen sulfide produced by SRB can help sequester and immobilize toxic heavy metals but is undesirable in oil wells where competition between SRB and NRB has been exploited to suppress hydrogen sulfide production. By characterizing how reduced sulfur compounds inhibit growth and activity of NRB, we have gained systems-level and mechanistic insight into the interplay of these two important groups of organisms and drivers of their stratification in diverse environments.

Selective carbon sources influence the end products of microbial nitrate respiration.

Respiratory and catabolic genes are differentially distributed across microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content, and function.

Use and abuse of correlation analyses in microbial ecology.

Correlation analyses are often included in bioinformatic pipelines as methods for inferring taxon-taxon interactions. In this perspective, we highlight the pitfalls of inferring interactions from covariance and suggest methods, study design considerations, and additional data types for improving high-throughput interaction inferences. We conclude that correlation, even when augmented by other data types, almost never provides reliable information on direct biotic interactions in real-world ecosystems. These bioinformatically inferred associations are useful for reducing the number of potential hypotheses that we might test, but will never preclude the necessity for experimental validation.

Deciphering microbial interactions in synthetic human gut microbiome communities.

The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history-dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human-associated intestinal species and illuminated design principles of microbial communities.

Vision of the body improves inter-hemispheric integration of tactile-motor responses.

Sensory input from and motor output to the two sides of the body needs to be continuously integrated between the two cerebral hemispheres. This integration can be measured through its cost in terms of processing speed. In simple detection tasks, reaction times (RTs) are faster when stimuli are presented to the side of the body ipsilateral to the body part used to respond. This advantage - the contralateral-ipsilateral difference (also known as the crossed-uncrossed difference: CUD) - is thought to reflect inter-hemispheric interactions needed for sensorimotor information to be integrated between the two hemispheres. Several studies have shown that non-informative vision of the body enhances performance in tactile tasks. However, it is unknown whether the CUD can be similarly affected by vision. Here, we investigated whether the CUD is modulated by vision of the body (i.e., the stimulated hand) by presenting tactile stimuli unpredictably on the middle fingers when one hand was visible (i.e., either the right or left hand). Participants detected the stimulus and responded as fast as possible using either their left or right foot. Consistent with previous results, a clear CUD (5.8ms) was apparent on the unseen hand. Critically, however, no such effect was found on the hand that was visible (-2.2ms). Thus, when touch is delivered to a seen hand, the usual cost in processing speed of responding with a contralateral effector is eliminated. This result suggests that vision of the body improves the interhemispheric integration of tactile-motor responses.

Young Children's Letter-Sound Knowledge.

PURPOSE: This study compares three essential skills in early literacy: letter-sound recognition, letter-sound recall, and letter reproduction. Previous research comparing these aspects of letter-sound knowledge is limited. METHOD: Eighty-three normally developing children between the ages of 4:11 (years:months) and 6:4 were asked to recognize (i.e., point to the appropriate letter when the letter's sound is given), recall (i.e., say the letter's sound), and reproduce (i.e., write the letter when the letter's sound is given) 32 letter sounds. RESULTS: The children performed better in letter-sound recognition than in letter-sound recall, and better in letter-sound recall than in letter reproduction. Girls performed no differently from boys. Younger children performed as well as older children. Socioeconomic status had significant influence on the level of development for all tasks. CLINICAL IMPLICATIONS: Clinicians and educators need to be aware of the different aspects of letter-sound knowledge development and how it can be assessed so that intervention can follow the normal developmental sequence of acquisition.