Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors.

BACKGROUND: The phylum Chloroflexi is highly abundant in a wide variety of wastewater treatment bioreactors. It has been suggested that they play relevant roles in these ecosystems, particularly in degrading carbon compounds and on structuring flocs or granules. Nevertheless, their function is not yet well understood as most species have not been isolated in axenic cultures. Here we used a metagenomic approach to investigate Chloroflexi diversity and their metabolic potential in three environmentally different bioreactors: a methanogenic full-scale reactor, a full-scale activated sludge reactor and a lab scale anammox reactor. RESULTS: Differential coverage binning approach was used to assemble the genomes of 17 new Chloroflexi species, two of which are proposed as new Candidatus genus. In addition, we recovered the first representative genome belonging to the genus 'Ca. Villigracilis'. Even though samples analyzed were collected from bioreactors operating under different environmental conditions, the assembled genomes share several metabolic features: anaerobic metabolism, fermentative pathways and several genes coding for hydrolytic enzymes. Interestingly, genome analysis from the anammox reactor indicated a putative role of Chloroflexi in nitrogen conversion. Genes related to adhesiveness and exopolysaccharides production were also detected. Complementing sequencing analysis, filamentous morphology was detected by Fluorescent in situ hybridization. CONCLUSION: Our results suggest that Chloroflexi participate in organic matter degradation, nitrogen removal and biofilm aggregation, playing different roles according to the environmental conditions.

Putative metabolism of Ca. Accumulibacter via the utilization of glucose.

Ca. Accumulibacter was the predominant microorganism (relative FISH bio-abundance of 67 ± 5%) in a lab-scale sequential batch reactor that accomplished enhanced biological phosphorus removal (EBPR) while using glucose and acetate as the carbon sources (1:1 COD-based ratio). Both organic compounds were completely anaerobically consumed. The reactor's performance in terms of P/C ratio, phosphorous release and uptake, and overall kinetic and stoichiometric parameters were on the high end of the reported spectrum for EBPR systems (100:9.3 net mg phosphate removal per mg COD consumed when using glucose and acetate in a 1:1 ratio). The batch tests showed that, to the best of our knowledge, this is the first time a reactor enriched with Ca. Accumulibacter can putatively utilize glucose as the sole carbon source to biologically remove phosphate (COD:P (mg/mg) removal ratio of 100:6.3 when using only glucose). Thus, this research proposes that Ca. Accumulibacter directly anaerobically stored the fed glucose primarily as glycogen by utilizing the ATP provided via the hydrolysis of poly-P and secondarily as PHA by balancing its ATP utilization (glycogen generation) and formation (PHA storage). Alternative hypotheses are also discussed. The reported findings could challenge the conventional theories of glucose assimilation by Ca. Accumulibacter, and can be of significance for the biological removal of phosphorus from wastewaters with high contents of fermentable compounds or low VFAs.

A combined microbial and biogeochemical dataset from high-latitude ecosystems with respect to methane cycle.

High latitudes are experiencing intense ecosystem changes with climate warming. The underlying methane (CH4) cycling dynamics remain unresolved, despite its crucial climatic feedback. Atmospheric CH4 emissions are heterogeneous, resulting from local geochemical drivers, global climatic factors, and microbial production/consumption balance. Holistic studies are mandatory to capture CH4 cycling complexity. Here, we report a large set of integrated microbial and biogeochemical data from 387 samples, using a concerted sampling strategy and experimental protocols. The study followed international standards to ensure inter-comparisons of data amongst three high-latitude regions: Alaska, Siberia, and Patagonia. The dataset encompasses different representative environmental features (e.g. lake, wetland, tundra, forest soil) of these high-latitude sites and their respective heterogeneity (e.g. characteristic microtopographic patterns). The data included physicochemical parameters, greenhouse gas concentrations and emissions, organic matter characterization, trace elements and nutrients, isotopes, microbial quantification and composition. This dataset addresses the need for a robust physicochemical framework to conduct and contextualize future research on the interactions between climate change, biogeochemical cycles and microbial communities at high-latitudes.

Ubiquity and Diversity of Cold Adapted Denitrifying Bacteria Isolated From Diverse Antarctic Ecosystems.

Nitrogen cycle has been poorly investigated in Antarctic ecosystems. In particular, how extreme conditions of low temperature, dryness, and high radiation select the microorganisms involved in the cycle is not yet understood. Denitrification is an important step in the nitrogen cycle in which nitrate is reduced stepwise to the gases NO, N2O, and N2. Denitrification is carried out by a wide group of microorganisms spread in the phylogenetic tree. The aim of this work was to isolate and characterize denitrifying bacteria present in different cold environments from Antarctica. Bacterial isolates were obtained from lake, meltwater, sea, glacier ice, ornithogenic soil, and penguin feces samples from King George Island, Fildes peninsula in the Antarctic. Samples were taken during the deicing season in five sampling campaigns. From all the samples we were able to isolate denitrifying strains. A total of 199 bacterial isolates with the capacity to grow in anaerobic mineral media reducing nitrate at 4°C were obtained. The characterization of the isolates by 16S rRNA gene sequence analysis showed a high predominance of the genus Pseudomonas, followed by Janthinobacterium, Flavobacterium, Psychrobacter, and Yersinia. Other minor genera detected were Cryobacterium, Iodobacter, Kaistella, and Carnobacterium. The capacity to denitrify was not previously described for most of the bacteria related to our isolates and in many of them denitrifying genes were not present suggesting the presence of new genes in this extreme environment. Our work demonstrates the ubiquity of denitrification in the Maritime Antarctica and gives important information linking denitrification at cold temperature with taxa in an unequivocal way.

Use of real-time multimodal sensory feedback home program improved backward stride and retention for people with Parkinson Disease: A pilot study.

INTRODUCTION: Parkinson disease (PD) impairs sensory integration, contributes to motor dysfunction, loss of gait automaticity, and increased fall risk. Employing multimodal sensory feedback (MMSF) has the potential to improve proprioceptive integration and gait safety while reducing exercise burden especially for backward gait. METHODS: This single-blinded, randomized controlled pilot study used a home program with or without real-time visual, proprioceptive, and auditory feedback with stepping exercises which progressed in speed and distance. Both groups completed a six-week intervention followed by 6 weeks without exercise to assess long-term retention. Six additional weeks of exercises were completed to assess recovery of potential losses after the washout session.Eleven people with PD exercised with real-time MMSF and 7 exercised without MMSF. Outcome measures included backward stride length, velocity, cadence, and double support time. The Dual Timed Up and Go measured automaticity. Self-perceived improvements in gait, activities of daily living, participation, and quality of life were registered by a questionnaire. RESULTS: Analysis was by repeated measures ANOVA. Using MMSF significantly improved backward stride length at 12 and 18 weeks, p = .007, η2 = 0.239. Both groups improved in all outcome measures after the initial 6-week exercise program, supporting efficacy of stepping exercises. The MMSF + ex group's significant improvements after a 6-week washout supported automaticity development. Questionnaire items received higher agreement percentages from MMSF + ex participants. CONCLUSION: Using real-time MMSF in a home program for pwPD provided significant and lasting improvements in backward stride, and potentially decreased fall risk and exercise burden compared to the same program without MMSF.

ID2 controls differentiation of enteroendocrine cells in mouse small intestine.

AIMS: The mammalian gut is the largest endocrine organ. Dozens of hormones secreted by enteroendocrine cells regulate a variety of physiological functions of the gut but also of the pancreas and brain. Here, we examined the role of the helix-loop-helix transcription factor ID2 during the differentiation of intestinal stem cells along the enteroendocrine lineage. METHODS: To assess the functions of ID2 in the adult mouse small intestine, we used single-cell RNA sequencing, genetically modified mice, and organoid assays. RESULTS: We found that in the adult intestinal epithelium Id2 is predominantly expressed in enterochromaffin and peptidergic enteroendocrine cells. Consistently, the loss of Id2 leads to the reduction of Chromogranin A-positive enteroendocrine cells. In contrast, the numbers of tuft cells are increased in Id2 mutant small intestine. Moreover, ablation of Id2 elevates the numbers of Serotonin+ enterochromaffin cells and Ghrelin+ X-cells in the posterior part of the small intestine. Finally, ID2 acts downstream of BMP signalling during the differentiation of Glucagon-like peptide-1+ L-cells and Cholecystokinin+ I-cells towards Neurotensin+ PYY+ N-cells. CONCLUSION: ID2 plays an important role in cell fate decisions in the adult small intestine. First, ID2 is essential for establishing a differentiation gradient for enterochromaffin and X-cells along the anterior-posterior axis of the gut. Next, ID2 is necessary for the differentiation of N-cells thus ensuring a differentiation gradient along the crypt-villi axis. Finally, ID2 suppresses the commitment of secretory intestinal epithelial progenitors towards tuft cell lineage and thus controls host immune response to commensal and parasitic microbiota.

Towards centralized biogas plants: Co-digestion of sewage sludge and pig manure maintains process performance and active microbiome diversity.

The aim of this study is to assess the performance of anaerobic digestion against co-digestion systems during the start-up stages based on key process parameters and biological indicators. Two parallel experiments treating sewage sludge alone or co-digested with low concentration of pig manure (8% vol., 2-3% in COD basis) were carried out in two lab-scale CSTR at mesophilic conditions. Same inoculant and organic loading rate sequences were applied for two consecutive runs of 79 and 90 days. According to the removal efficiencies achieved, no significant differences were encountered amongst mono-digestion and co-digestion. This observation was reinforced with the analysis of the total/active microbiome, sequencing 16S rRNA genes and transcripts. The addition of a co-substrate at low concentration had a negligible effect on the total/active microbial communities; they evolved following the same pattern. This might be an advantage in order to upgrade existing wastewater treatment plants to become centralized biogas facilities.

Database Mining to Unravel the Ecology of the Phylum Chloroflexi in Methanogenic Full Scale Bioreactors.

Although microbial communities of anaerobic bioreactors have been extensively studied using DNA-based tools, there are still several knowledge gaps regarding the microbiology of the process, in particular integration of all generated data is still limited. One understudied core phylum within anaerobic bioreactors is the phylum Chloroflexi, despite being one of the most abundant groups in anaerobic reactors. In order to address the abundance, diversity and phylogeny of this group in full-scale methanogenic reactors globally distributed, a compilation of 16S ribosomal RNA gene sequence data from 62 full-scale methanogenic reactors studied worldwide, fed either with wastewater treatment anaerobic reactors (WTARs) or solid-waste treatment anaerobic reactors (STARs), was performed. One of the barriers to overcome was comparing data generated using different primer sets and different sequencing platforms. The sequence analysis revealed that the average abundance of Chloroflexi in WTARs was higher than in STARs. Four genera belonging to the Anaerolineae class dominated both WTARs and STARs but the core populations were different. According to the phylogenetic analysis, most of the sequences formed clusters with no cultured representatives. The Anaerolineae class was more abundant in reactors with granular biomass than in reactors with disperse biomass supporting the hypothesis that Anaerolineae play an important role in granule formation and structure due to their filamentous morphology. Cross-study comparisons can be fruitfully used to understand the complexity of the anaerobic digestion process. However, more efforts are needed to standardize protocols and report metadata information.

A correlation study of social network usage among health care students.

BACKGROUND: Due to anecdotal concerns about adequacy of health professions students' communication skills, health professions faculty at a private university formed an interprofessional research team. The study was designed to explore whether the use of social networking services (SNS) influenced health care students' written and oral communication skills. METHOD: One hundred thirty-two students participated in the study. Communication skills were assessed by using assignments from a health care ethics course required of all students. Use of SNS was measured with an information technology questionnaire. RESULTS: Contrary to expected findings, this exploratory correlation study found no meaningful relationship between the frequency of SNS usage and oral and written communication skills in health professions students. CONCLUSIONS: Future studies of SNS would benefit from a younger and more homogeneous study population to assess the use of SNS for learning versus leisure.

Platform tilt perturbation as an intervention for people with chronic vestibular dysfunction.

BACKGROUND AND PURPOSE: Training to improve responses to perturbations may be beneficial for individuals with unilateral vestibular dysfunction. We evaluated the effects of an incrementally increasing surface tilt perturbation intervention for individuals with chronic vestibular pathology on gait, activities of daily living, and dizziness. METHODS: Participants (n = 29) were randomly assigned to 1 of 3 groups. The first group received random surface tilt perturbations of increasing angles and speed, half of the trials with vision-occluding goggles, 3 times weekly for 3 weeks (P group). The second group received tilt perturbation intervention (as above) plus a home program of vestibular rehabilitation exercises (P+EX group). The third group performed only the vestibular rehabilitation exercises (EX group). Outcome measures included temporospatial gait measures, Dynamic Gait Index (DGI), Dizziness Handicap Inventory (DHI), Patient Specific Functional Scale (PSFS), and a Perceived Outcomes Scale (POS). RESULTS: The P and P+EX groups showed greater improvement on the PSFS and the POS compared to the EX group. DGI scores indicated decreased fall risk in 8 of 9 individuals who participated in P or P+EX training and who initially scored below the 19-point cutoff score. Both the P and P+EX groups showed significant within-group changes on some gait characteristics, DGI, DHI, PSFS, and POS measures. The EX group showed within-group change only on the DHI. DISCUSSION AND CONCLUSION: Surface tilt perturbation training appears to be more effective for improving abilities at the activities and participation levels than vestibular exercises alone. In addition, tilt perturbation training reduced fall risk as measured by the DGI.

Colour appearance and compensation in the near periphery.

The spectral sensitivity of the visual system varies markedly between the fovea and surrounding periphery owing in part to the rapid fall in macular pigment density with eccentricity. We examined how colour appearance changes between the fovea and near periphery (8 degrees) by measuring achromatic loci and the loci of unique and binary hues. Chosen colours remained much more similar at the two locations than predicted by the change in spectral sensitivity. Compensation for white may reflect long-term gain changes within the cones that equate sensitivity for the local average stimulus in the fovea and periphery. However, adjusting only to the average stimulus cannot correct for all of the effects of a spectral sensitivity change, and predicts differences in colour percepts between the fovea and periphery that were not observed. The similarities in hue percepts at 0 and 8 degrees thus suggest that additional processes help compensate colour appearance to maintain constancy in the near periphery. We model the results of previous studies to show that similar adjustments are implied by age-related changes in lens pigment, and to show that these adjustments are consistent with previous measurements of peripheral colour appearance based on hue cancellation.

Ocular fixation, vestibular dysfunction, and visual motion hypersensitivity.

BACKGROUND: A subgroup of individuals with vestibular dysfunction and visual motion hypersensitivity (VMH) become dizzy and imbalanced in response to movement of the visual environment. The purpose of this study was to investigate ocular fixational stability during gaze on a target, with and without visual background movement. Binocular vision functions were also examined as possible contributory factors to the dizziness and imbalance. METHODS: Twenty-four individuals with VMH, 20 with vestibular disorders without VMH and 20 healthy subjects were tested. Assignment to the experimental group was by symptoms of VMH. Outcome measures included electro-oculogram recordings of horizontal fixation and blink. Four clinical binocular vision functions were also tested. The Dizziness Handicap Inventory was used to assess the level of dizziness. CONCLUSION: Subjects with VMH made significantly more refixational eye movements and had higher levels of dizziness than those in the other 2 diagnostic groups. There were abnormalities of binocular function in both the VMH and vestibular dysfunction groups compared with the control group. Individuals with VMH were unable to maintain stable gaze and inhibit eye movements to background motion. The large number of subjects with diagnosis of fluctuating vestibular function in the VMH group compared with the vestibular dysfunction group may indicate that VMH is a maladaptation of the system.