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Bacteria catalyze the formation and destruction of soil organic matter, but the bacterial dynamics in soil that govern carbon (C) cycling are not well understood. Life history strategies explain the complex dynamics of bacterial populations and activities based on trade-offs in energy allocation to growth, resource acquisition, and survival. Such trade-offs influence the fate of soil C, but their genomic basis remains poorly characterized. We used multisubstrate metagenomic DNA stable isotope probing to link genomic features of bacteria to their C acquisition and growth dynamics. We identify several genomic features associated with patterns of bacterial C acquisition and growth, notably genomic investment in resource acquisition and regulatory flexibility. Moreover, we identify genomic trade-offs defined by numbers of transcription factors, membrane transporters, and secreted products, which match predictions from life history theory. We further show that genomic investment in resource acquisition and regulatory flexibility can predict bacterial ecological strategies in soil. IMPORTANCE Soil microbes are major players in the global carbon cycle, yet we still have little understanding of how the carbon cycle operates in soil communities. A major limitation is that carbon metabolism lacks discrete functional genes that define carbon transformations. Instead, carbon transformations are governed by anabolic processes associated with growth, resource acquisition, and survival. We use metagenomic stable isotope probing to link genome information to microbial growth and carbon assimilation dynamics as they occur in soil. From these data, we identify genomic traits that can predict bacterial ecological strategies which define bacterial interactions with soil carbon.

Tracking the metabolic activity of whole soil communities can improve our understanding of the transformation and fate of carbon in soils. We used stable isotope metabolomics to trace 13C from nine labeled carbon sources into the water-soluble metabolite pool of an agricultural soil over time. Soil was amended with a mixture of all nine sources, with one source isotopically labeled in each treatment. We compared changes in the 13C enrichment of metabolites with respect to carbon source and time over a 48-day incubation and contrasted differences between soluble sources (glucose, xylose, amino acids, etc.) and insoluble sources (cellulose and palmitic acid). Whole soil metabolite profiles varied singularly by time, while the composition of 13C-labeled metabolites differed primarily by carbon source (R2 = 0.68) rather than time (R2 = 0.07), with source-specific differences persisting throughout incubations. The 13C labeling of metabolites from insoluble carbon sources occurred slower than that from soluble sources but yielded a higher average atom percent (atom%) 13C in metabolite markers of biomass (amino acids and nucleic acids). The 13C enrichment of metabolite markers of biomass stabilized between 5 and 15 atom% 13C by the end of incubations. Temporal patterns in the 13C enrichment of tricarboxylic acid cycle intermediates, nucleobases (uracil and thymine), and by-products of DNA salvage (allantoin) closely tracked microbial activity. Our results demonstrate that metabolite production in soils is driven by the carbon source supplied to the community and that the fate of carbon in metabolites do not generally converge over time as a result of ongoing microbial processing and recycling. IMPORTANCE Carbon metabolism in soil remains poorly described due to the inherent difficulty of obtaining information on the microbial metabolites produced by complex soil communities. Our study demonstrates the use of stable isotope probing (SIP) to study carbon metabolism in soil by tracking 13C from supplied carbon sources into metabolite pools and biomass. We show that differences in the metabolism of sources influence the fate of carbon in soils. Heterogeneity in 13C-labeled metabolite profiles corresponded with compositional differences in the metabolically active populations, providing a basis for how microbial community composition correlates with the quality of soil carbon. Our study demonstrates the application of SIP-metabolomics in studying soils and identifies several metabolite markers of growth, activity, and other aspects of microbial function.

Microorganisms have evolved various life-history strategies to survive fluctuating resource conditions in soils. However, it remains elusive how the life-history strategies of microorganisms influence their processing of organic carbon, which may affect microbial interactions and carbon cycling in soils. Here, we characterized the genomic traits, exometabolite profiles, and interactions of soil bacteria representing copiotrophic and oligotrophic strategists. Isolates were selected based on differences in ribosomal RNA operon (rrn) copy number, as a proxy for life-history strategies, with pairs of "high" and "low" rrn copy number isolates represented within the Micrococcales, Corynebacteriales, and Bacillales. We found that high rrn isolates consumed a greater diversity and amount of substrates than low rrn isolates in a defined growth medium containing common soil metabolites. We estimated overlap in substrate utilization profiles to predict the potential for resource competition and found that high rrn isolates tended to have a greater potential for competitive interactions. The predicted interactions positively correlated with the measured interactions that were dominated by negative interactions as determined through sequential growth experiments. This suggests that resource competition was a major force governing interactions among isolates, while cross-feeding of metabolic secretion likely contributed to the relatively rare positive interactions observed. By connecting bacterial life-history strategies, genomic features, and metabolism, our study advances the understanding of the links between bacterial community composition and the transformation of carbon in soils.

Purpose: This study examined the discriminative ability of acoustic indices of vocal hyperfunction combining smoothed cepstral peak prominence (CPPS) and relative fundamental frequency (RFF). Method: Demographic, CPPS, and RFF parameters were entered into logistic regression models trained on two 1:1 case-control groups: individuals with and without nonphonotraumatic vocal hyperfunction (NPVH; n = 360) and phonotraumatic vocal hyperfunction (PVH; n = 240). Equations from the final models were used to predict group membership in two independent test sets (n = 100 each). Results: Both CPPS and RFF parameters significantly improved model fits for NPVH and PVH after accounting for demographics. CPPS explained unique variance beyond RFF in both models. RFF explained unique variance beyond CPPS in the PVH model. Final models included CPPS and RFF offset parameters for both NPVH and PVH; RFF onset parameters were significant only in the PVH model. Area under the receiver operating characteristic curve analysis for the independent test sets revealed acceptable classification for NPVH (72%) and good classification for PVH (86%). Conclusions: A combination of CPPS and RFF parameters showed better discriminative ability than either measure alone for PVH. Clinical cutoff scores for acoustic indices of vocal hyperfunction are proposed for assessment and screening purposes.

Purpose: This study examined the discriminative ability of acoustic indices of vocal hyperfunction combining smoothed cepstral peak prominence (CPPS) and relative fundamental frequency (RFF). Method: Demographic, CPPS, and RFF parameters were entered into logistic regression models trained on two 1:1 case-control groups: individuals with and without nonphonotraumatic vocal hyperfunction (NPVH; n = 360) and phonotraumatic vocal hyperfunction (PVH; n = 240). Equations from the final models were used to predict group membership in two independent test sets (n = 100 each). Results: Both CPPS and RFF parameters significantly improved model fits for NPVH and PVH after accounting for demographics. CPPS explained unique variance beyond RFF in both models. RFF explained unique variance beyond CPPS in the PVH model. Final models included CPPS and RFF offset parameters for both NPVH and PVH; RFF onset parameters were significant only in the PVH model. Area under the receiver operating characteristic curve analysis for the independent test sets revealed acceptable classification for NPVH (72%) and good classification for PVH (86%). Conclusions: A combination of CPPS and RFF parameters showed better discriminative ability than either measure alone for PVH. Clinical cutoff scores for acoustic indices of vocal hyperfunction are proposed for assessment and screening purposes., Voice disorders affect as many as 30% of individuals at some point in their lives (Cohen, 2010) and may significantly impact an individual's ability to participate in social and work [...]

Purpose: This study retrospectively examined patient-reported symptoms, quality of life, and swallowing kinematics in individuals with presumed muscle tension dysphagia (MTDg). Method: Twenty-six individuals met the inclusion criteria. Data were gathered from patient-reported outcome measures (PROs), symptomology, clinician reports of palpation, and hyolaryngeal and hyoid movements measured on a 20-ml thin liquid bolus during videofluoroscopic swallowing studies. Results: All PROs were outside of typical limits, except for the Voice Handicap Index-10. Mean hyoid excursion was 1.52 cm (SD = 0.46, range: 0.76-2.43), and hyolaryngeal excursion was 0.77 cm (SD = 0.44, range: -0.42-1.68). A minority of participants (4%-19%) demonstrated atypical hyoid and/or hyolaryngeal excursion compared to the available normative reference value sets. Conclusions: Individuals demonstrated abnormalities in the clinical evaluation of the areas of palpation and reported perilaryngeal discomfort and symptoms of laryngeal hyperresponsiveness, with a negative impact on their quality of life across various PROs. Atypical hyoid and/or hyolaryngeal excursion during swallowing was rare when compared to available normative reference values. The clinical evaluation of MTDg may be enhanced by including components related to muscle tension and laryngeal hyperresponsiveness in order to differentiate MTDg from idiopathic functional dysphagia and lead the patient to the otolaryngology/speech-language pathology clinic for intervention and management. [ABSTRACT FROM AUTHOR]

Purpose: This study is a secondary analysis of existing data. The goal of the study was to construct an acoustic model of perceived overall severity of dysphonia in adductory laryngeal dystonia (AdLD). We predicted that acoustic measures (a) related to voice and pitch breaks and (b) related to vocal effort would form the primary elements of a model corresponding to auditory-perceptual ratings of overall severity of dysphonia. Method: Twenty inexperienced listeners evaluated the overall severity of dysphonia of speech stimuli from 19 individuals with AdLD. Acoustic features related to primary signs of AdLD (hyperadduction resulting in pitch and voice breaks) and to a potential secondary symptom of AdLD (vocal effort, measures of relative fundamental frequency) were computed from the speech stimuli. Multiple linear regression analysis was applied to construct an acoustic model of the overall severity of dysphonia. Results: The acoustic model included an acoustic feature related to pitch and voice breaks and three acoustic measures derived from relative fundamental frequency; it explained 84.9% of the variance in the auditory-perceptual ratings of overall severity of dysphonia in the speech samples. Conclusions: Auditory-perceptual ratings of overall severity of dysphonia in AdLD were related to acoustic features of primary signs (pitch and voice breaks, hyperadduction associated with laryngeal spasms) and were also related to acoustic features of vocal effort. This suggests that compensatory vocal effort may be a secondary symptom in AdLD. Future work to generalize this acoustic model to a larger, independent data set is necessary before clinical translation is warranted.

Microbial interactions driving key biogeochemical fluxes often occur within multispecies consortia that form spatially heterogeneous microenvironments. Here, we describe the "green berry" consortia of the Sippewissett salt marsh (Falmouth, MA, United States): millimeter-sized aggregates dominated by an uncultured, diazotrophic unicellular cyanobacterium of the order Chroococcales (termed GB-CYN1). We show that GB-CYN1 is closely related to Crocosphaera watsonii (UCYN-B) and "Candidatus Atelocyanobacterium thalassa" (UCYN-A), two groups of unicellular diazotrophic cyanobacteria that play an important role in marine primary production. Other green berry consortium members include pennate diatoms and putative heterotrophic bacteria from the Alphaproteobacteria and Bacteroidetes. Tight coupling was observed between photosynthetic oxygen production and heterotrophic respiration. When illuminated, the green berries became supersaturated with oxygen. From the metagenome, we observed that GB-CYN1 encodes photosystem II genes and thus has the metabolic potential for oxygen production unlike UCYN-A. In darkness, respiratory activity rapidly depleted oxygen creating anoxia within the aggregates. Metagenomic data revealed a suite of nitrogen fixation genes encoded by GB-CYN1, and nitrogenase activity was confirmed at the whole-aggregate level by acetylene reduction assays. Metagenome reads homologous to marker genes for denitrification were observed and suggest that heterotrophic denitrifiers might co-occur in the green berries, although the physiology and activity of facultative anaerobes in these aggregates remains uncharacterized. Nitrogen fixation in the surface ocean was long thought to be driven by filamentous cyanobacterial aggregates, though recent work has demonstrated the importance of unicellular diazotrophic cyanobacteria (UCYN) from the order Chroococcales. The green berries serve as a useful contrast to studies of open ocean UCYN and may provide a tractable model system to investigate microbial dynamics within phytoplankton aggregates, a phenomenon of global importance to the flux of particulate organic carbon and nitrogen in surface waters.

Purpose: This study is a secondary analysis of existing data. The goal of the study was to construct an acoustic model of perceived overall severity of dysphonia in adductory laryngeal dystonia (AdLD). We predicted that acoustic measures (a) related to voice and pitch breaks and (b) related to vocal effort would form the primary elements of a model corresponding to auditory-perceptual ratings of overall severity of dysphonia. Method: Twenty inexperienced listeners evaluated the overall severity of dysphonia of speech stimuli from 19 individuals with AdLD. Acoustic features related to primary signs of AdLD (hyperadduction resulting in pitch and voice breaks) and to a potential secondary symptom of AdLD (vocal effort, measures of relative fundamental frequency) were computed from the speech stimuli. Multiple linear regression analysis was applied to construct an acoustic model of the overall severity of dysphonia. Results: The acoustic model included an acoustic feature related to pitch and voice breaks and three acoustic measures derived from relative fundamental frequency; it explained 84.9% of the variance in the auditory-perceptual ratings of overall severity of dysphonia in the speech samples. Conclusions: Auditory-perceptual ratings of overall severity of dysphonia in AdLD were related to acoustic features of primary signs (pitch and voice breaks, hyperadduction associated with laryngeal spasms) and were also related to acoustic features of vocal effort. This suggests that compensatory vocal effort may be a secondary symptom in AdLD. Future work to generalize this acoustic model to a larger, independent data set is necessary before clinical translation is warranted., Laryngeal dystonia (LD), also known as spasmodic dysphonia, is a focal neurological dystonia that affects the laryngeal musculature (Blitzer et al., 2018). Individuals may have adductory LD (AdLD), abductory LD, [...]

Microbial metabolism is the engine that drives global biogeochemical cycles, yet many key transformations are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the 'pink berry' consortia of the Sippewissett Salt Marsh through an integrative study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PB-PSB1) and sulfate-reducing bacteria (PB-SRB1). Using metagenomic sequencing and (34) S-enriched sulfate stable isotope probing coupled with nanoSIMS, we demonstrate interspecies transfer of reduced sulfur metabolites from PB-SRB1 to PB-PSB1. The pink berries catalyse net sulfide oxidation and maintain internal sulfide concentrations of 0-500 μm. Sulfide within the berries, captured on silver wires and analysed using secondary ion mass spectrometer, increased in abundance towards the berry interior, while δ(34) S-sulfide decreased from 6‰ to -31‰ from the exterior to interior of the berry. These values correspond to sulfate-sulfide isotopic fractionations (15-53‰) consistent with either sulfate reduction or a mixture of reductive and oxidative metabolisms. Together this combined metagenomic and high-resolution isotopic analysis demonstrates active sulfur cycling at the microscale within well-structured macroscopic consortia consisting of sulfide-oxidizing anoxygenic phototrophs and sulfate-reducing bacteria.

Microbial metabolism is the engine that drives global biogeochemical cycles, yet many key transformations are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the 'pink berry' consortia of the Sippewissett Salt Marsh through an integrative study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PB-PSB1) and sulfate-reducing bacteria (PB-SRB1). Using metagenomic sequencing and (34) S-enriched sulfate stable isotope probing coupled with nanoSIMS, we demonstrate interspecies transfer of reduced sulfur metabolites from PB-SRB1 to PB-PSB1. The pink berries catalyse net sulfide oxidation and maintain internal sulfide concentrations of 0-500 μm. Sulfide within the berries, captured on silver wires and analysed using secondary ion mass spectrometer, increased in abundance towards the berry interior, while δ(34) S-sulfide decreased from 6‰ to -31‰ from the exterior to interior of the berry. These values correspond to sulfate-sulfide isotopic fractionations (15-53‰) consistent with either sulfate reduction or a mixture of reductive and oxidative metabolisms. Together this combined metagenomic and high-resolution isotopic analysis demonstrates active sulfur cycling at the microscale within well-structured macroscopic consortia consisting of sulfide-oxidizing anoxygenic phototrophs and sulfate-reducing bacteria.

Intertidal microbial mats are comprised of distinctly colored millimeter-thick layers whose communities organize in response to environmental gradients such as light availability, oxygen/sulfur concentrations, and redox potential. Here, slight changes in depth correspond to sharp niche boundaries. We explore the patterns of biodiversity along this depth gradient as it relates to functional groups of bacteria, as well as trait-encoding genes. We used molecular techniques to determine how the mat’s layers differed from one another with respect to taxonomic, phylogenetic, and trait diversity, and used these metrics to assess potential drivers of community assembly. We used a range of null models to compute the degree of phylogenetic and functional dispersion for each layer. The SSU-rRNA reads were dominated by Cyanobacteria and Chromatiales, but contained a high taxonomic diversity. The composition of each mat core was significantly different for developmental stage, year, and layer. Phylogenetic richness and evenness positively covaried with depth, and trait richness tended to decrease with depth. We found evidence for significant phylogenetic clustering for all bacteria below the surface layer, supporting the role of habitat filtering in the assembly of mat layers. However, this signal disappeared when the phylogenetic dispersion of particular functional groups, such as oxygenic phototrophs, was measured. Overall, trait diversity measured by orthologous genes was also lower than would be expected by chance, except for genes related to photosynthesis in the topmost layer. Additionally, we show how the choice of taxa pools, null models, spatial scale, and phylogenies can impact our ability to test hypotheses pertaining to community assembly. Our results demonstrate that given the appropriate physiochemical conditions, strong phylogenetic, and trait variation, as well as habitat filtering, can occur at the millimeter-scale.

Objective: The purpose of this study was to determine whether automated estimates of vocal creak would differentiate speakers with adductor laryngeal dystonia (AdLD) from speakers with muscle tension dysphonia (MTD) and speakers without voice disorders. Methods: Sixteen speakers with AdLD, sixteen speakers with MTD, and sixteen speakers without voice disorders were recorded in a quiet environment reading aloud a standard paragraph. An open‐source creak detector was used to calculate the percentage of creak (% creak) in each of the speaker's six recorded sentences. Results: A Kruskal‐Wallis one‐way analysis of variance revealed a statistically significant effect of group on the % creak with a large effect size. Pairwise Wilcoxon tests revealed a statistically significant difference in % creak between speakers with AdLD and controls as well as between speakers with AdLD and MTD. Receiver operating characteristic curve analyses indicated that % creak differentiated AdLD from both controls and speakers with MTD with high sensitivity and specificity (area under the curve statistics of 0.94 and 0.86, respectively). Conclusion: Percentage of creak as calculated by an automated creak detector may be useful as a quantitative indicator of AdLD, demonstrating the potential for use as a screening tool or to aid in a differential diagnosis. Level of Evidence: 3 Laryngoscope, 133:2687–2694, 2023 [ABSTRACT FROM AUTHOR]

Objectives/Hypothesis: Interaction with voice recognition systems, such as Siri™ and Alexa™, is an increasingly important part of everyday life. Patients with voice disorders may have difficulty with this technology, leading to frustration and reduction in quality of life. This study evaluates the ability of common voice recognition systems to transcribe dysphonic voices. Study Design: Retrospective evaluation of "Rainbow Passage" voice samples from patients with and without voice disorders. Methods: Participants with (n = 30) and without (n = 23) voice disorders were recorded reading the "Rainbow Passage". Recordings were played at standardized intensity and distance‐to‐dictation programs on Apple iPhone 6S™, Apple iPhone 11 Pro™, and Google Voice™. Word recognition scores were calculated as the proportion of correctly transcribed words. Word recognition scores were compared to auditory–perceptual and acoustic measures. Results: Mean word recognition scores for participants with and without voice disorders were, respectively, 68.6% and 91.9% for Apple iPhone 6S™ (P <.001), 71.2% and 93.7% for Apple iPhone 11 Pro™ (P <.001), and 68.7% and 93.8% for Google Voice™ (P <.001). There were strong, approximately linear associations between CAPE‐V ratings of overall severity of dysphonia and word recognition score, with correlation coefficients (R2) of 0.609 (iPhone 6S™), 0.670 (iPhone 11 Pro™), and 0.619 (Google Voice™). These relationships persisted when controlling for diagnosis, age, gender, fundamental frequency, and speech rate (P <.001 for all systems). Conclusion: Common voice recognition systems function well with nondysphonic voices but are poor at accurately transcribing dysphonic voices. There was a strong negative correlation with word recognition scores and perceptual voice evaluation. As our society increasingly interfaces with automated voice recognition technology, the needs of patients with voice disorders should be considered. Level of Evidence: 4 Laryngoscope, 131:1599–1607, 2021 [ABSTRACT FROM AUTHOR]

Literature has long provided evidence that laterality (i.e. side preference in brain and behaviour) is demonstrated amongst populations in a variety of parrot species (Rogers 1980). Conversely, laterality in Budgerigars, Melopsittacus undulatus, an Australian parrot, appears to be limited to individual level preferences (Rogers and Workman 1993; Schiffner and Srinivasan 2013). However, laterality investigations in Budgerigars have mainly been confined to studies in which behavioural measurements are dependent upon the experimental task employed, and have not examined the freely occurring expression of lateral preferences outside of an experimental condition. The present investigation yields conclusions from systematic behavioural observations on a colony of Budgerigars (N = 8) in which the occurrence of several different freely occurring behaviours are tracked. Significant individual level lateral preferences are obtained for several birds who evidenced left foot unipedal perching preferences and for one bird who evidenced a left foot scratching side preference. No significant individual level lateral preferences are obtained for preening side or stretching side, and no population level preferences are obtained for any of the observed behaviours. These results are consistent with previous conclusions suggesting the presence of individual level lateral preferences and the absence of population level lateral preferences in this species. [ABSTRACT FROM AUTHOR]