Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation

Background Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation. Results We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems. Conclusions These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells.

Non-formal adult education coordinators as developers of educational activities and community interaction

The growing importance of communities and community interaction is witnessed by the growing interest in these areas: in the emphasis on community development and in the need to bring educational and social services closer to local communities, both at the level of the European Union and at the political level of each of its member countries. Analyzing the community interactions active involvement in community functions, concern and trust in its people, and a look into the future are emphasized. The choice of the research methodology was determined by the aim of the research – to reveal the functions of non-formal learning coordinators of adult learning in municipalities as those of the developers of learning and community developers through their work experience. The analysis of the data highlighted the role of coordinators as community activators and community developers, bringing together adult learning groups, involving young people, gymnasium students, and volunteers in the implementation of training, through local non-formal education providers.

Parkinson’s Disease and the Metal–Microbiome–Gut–Brain Axis: A Systems Toxicology Approach

Parkinson’s Disease (PD) is a neurodegenerative disease, leading to motor and non-motor complications. Autonomic alterations, including gastrointestinal symptoms, precede motor defects and act as early warning signs. Chronic exposure to dietary, environmental heavy metals impacts the gastrointestinal system and host-associated microbiome, eventually affecting the central nervous system. The correlation between dysbiosis and PD suggests a functional and bidirectional communication between the gut and the brain. The bioaccumulation of metals promotes stress mechanisms by increasing reactive oxygen species, likely altering the bidirectional gut–brain link. To better understand the differing molecular mechanisms underlying PD, integrative modeling approaches are necessary to connect multifactorial perturbations in this heterogeneous disorder. By exploring the effects of gut microbiota modulation on dietary heavy metal exposure in relation to PD onset, the modification of the host-associated microbiome to mitigate neurological stress may be a future treatment option against neurodegeneration through bioremediation. The progressive movement towards a systems toxicology framework for precision medicine can uncover molecular mechanisms underlying PD onset such as metal regulation and microbial community interactions by developing predictive models to better understand PD etiology to identify options for novel treatments and beyond. Several methodologies recently addressed the complexity of this interaction from different perspectives; however, to date, a comprehensive review of these approaches is still lacking. Therefore, our main aim through this manuscript is to fill this gap in the scientific literature by reviewing recently published papers to address the surrounding questions regarding the underlying molecular mechanisms between metals, microbiota, and the gut–brain-axis, as well as the regulation of this system to prevent neurodegeneration.

An Interplay between Viruses and Bacteria Associated with the White Sea Sponges Revealed by Metagenomics

Sponges are remarkable holobionts harboring extremely diverse microbial and viral communities. However, the interactions between the components within holobionts and between a holobiont and environment are largely unknown, especially for polar organisms. To investigate possible interactions within and between sponge-associated communities, we probed the microbiomes and viromes of cold-water sympatric sponges Isodictya palmata (n = 2), Halichondria panicea (n = 3), and Halichondria sitiens (n = 3) by 16S and shotgun metagenomics. We showed that the bacterial and viral communities associated with these White Sea sponges are species-specific and different from the surrounding water. Extensive mining of bacterial antiphage defense systems in the metagenomes revealed a variety of defense mechanisms. The abundance of defense systems was comparable in the metagenomes of the sponges and the surrounding water, thus distinguishing the White Sea sponges from those inhabiting the tropical seas. We developed a network-based approach for the combined analysis of CRISPR-spacers and protospacers. Using this approach, we showed that the virus–host interactions within the sponge-associated community are typically more abundant (three out of four interactions studied) than the inter-community interactions. Additionally, we detected the occurrence of viral exchanges between the communities. Our work provides the first insight into the metagenomics of the three cold-water sponge species from the White Sea and paves the way for a comprehensive analysis of the interactions between microbial communities and associated viruses.

Telepresence with Hologram Effect: Technological Ecosystem for Distance Education

One of the most significant challenges of telepresence distance education is to bring the professor and the students closer together in a synchronistic educational experience where the professor is perceived as anatomically proportionate. Telepresence, an educational technology ecosystem using holograms, offers a way to solve this technological challenge. Our mixed exploratory research investigating this methodology had two purposes: (1) propose the key elements to teach distance courses synchronously in an educational technology ecosystem, and (2) demonstrate the technological, didactic practices that result in positive student learning outcomes in several specified courses. This methodology included applying a student questionnaire to collect their perceptions of the educational experience. The scores and written comments from the questionnaire were analyzed using Grounded Theory. On a Likert scale from 1 to 5, the students scored their educational experience, attaining a mean of 4.05. The positive perception affirmed that they valued: (a) recreating the natural dynamics of face-to-face classes, where the students perceived their professors as being physically present in the classroom; (b) professors renowned in their disciplines; (c) professor–student and campus and intercampus learning community interactions, and, finally, (d) class design and content. The main conclusions of this research were that students positively perceived the “wow” effect of the technology, feeling comfort, amazement, interest, and engagement. In addition, we found that professors and keynote speakers with excellent pedagogical skills and experts in their disciplines were well appreciated. Key elements for the success of the experience were professor–student, campus, and intercampus interactions and the quality of the technological and communication infrastructure.

Older Adults’ Experiences in an Online Intervention for Managing Subjective Depressive Symptoms

Background Many older adults struggle with late-life depression, stress, and anxiety, especially when facing age-related transitions including retirement, relocation, and the death of a spouse. Given the consequences of depression among older adults, which include higher rates of suicide, timely interventions that help to manage depressive symptoms are essential. Objective The primary purpose of this study was to explore the perceived efficacy of an online program in improving subjective depressive feelings. Methods Older adult participants were recruited for semi-structured interviews (n = 24) in a web-based intervention that included interactive games and activities undergirded by a cognitive behavioral therapy (CBT) approach. Participants were asked to provide feedback about program features, including weekly module content, games, interactive activities and community interactions, and any perceived effects on their health behaviors and/or emotional well-being. Participants’ responses were analyzed using qualitative content analysis. Results Participants reported several gains, including developing the habit of forming ongoing, incremental goals, achieving wellness-related goals, and experiencing an overall positive shift in perspective. In addition, participants reported feeling greater gratitude, increased positivity, and improvement in mood. Featured games and activities helped to promote stress relief and entertainment, and mindfulness exercises were cited as the most helpful and/or enjoyable among participants. Participants expressed a preference for program content related to aging and aging-related transitions. Conclusions This study demonstrated feasibility of an interactive web-based intervention for older adults with subjective depressive feelings, while also providing important findings about users’ preferences for personalized, aging-related feedback.

The burden and dynamics of hospital-acquired SARS-CoV-2 in England

Hospital-based transmission played a dominant role in MERS-CoV and SARS-CoV epidemics but large-scale studies of its role in the SARS-CoV-2 pandemic are lacking. Such transmission risks spreading the virus to the most vulnerable individuals and can have wider-scale impacts through hospital-community interactions. Using data from acute hospitals in England we quantify within-hospital transmission, evaluate likely pathways of spread and factors associated with heightened transmission risk, and explore the wider dynamical consequences. We show that hospital transmission is likely to have been a major contributor to the burden of COVID-19 in England. We estimate that between June 2020 and March 2021 between 95,000 and 167,000 patients acquired SARS-CoV-2 in hospitals with nosocomially-infected patients likely to have been the main sources of transmission to other patients. Increased transmission to patients was associated with hospitals having fewer single rooms and lower heated volume per bed. Moreover, we show that reducing hospital transmission could substantially enhance the efficiency of punctuated lockdown measures in suppressing community transmission. These findings reveal the previously unrecognised scale of hospital transmission, have direct implications for targeting of hospital control measures, and highlight the need to design hospitals better-equipped to limit the transmission of future high consequence pathogens.

Exploring the Microbial Dynamics of Organic Matter Degradation and Humification during Co-Composting of Cow Manure and Bedding Material Waste

The present study investigated the effects of bedding material (BM) waste on physicochemical properties, organic matter (OM) degradation, microbial community structure and metabolic function during composting. The results showed that bedding material (CK-0, S1-40%, S2-25%) optimized the composting conditions for lignocellulose and OM biodegradation. The highest OM degradation and humic substance (HS) synthesis rates were observed in the 40% BM addition group. Firmicutes was more abundant in the bedding material addition groups, whereas Proteobacteria was more abundant in the group without bedding material. Functional prediction showed higher carbohydrate and amino acid metabolism in the BM groups than that in control group. Animal and plant pathogens were almost eliminated, and saprotrophs were the dominant fungal trophic modes after 40% BM addition composting. Cellulose, hemicellulose, and organic matter had strong associations with microbial communities, such as Lysinibacillus and Corynebacterium (bacteria), compared to the associations of Aspergillus, Candida, and Sordariomycetes (fungi) (p value < 0.05). Network analysis revealed closer microbial community interactions in 40% BM addition group than in other groups. These findings provide detailed information about the coupling of material conversion, of bacterial and fungal succession during composting, and that bedding materials waste can also be used as an effective compost amendment.

The Disrupted and Realigned Self: Exploring the Narratives of New Zealanders with Chronic Fatigue Syndrome/Myalgic Encephalomyelitis

<p>Chronic Fatigue Syndrome/Myalgic Encephalomyelitis (CFS/ME) causes pronounced, debilitating fatigue that is not alleviated by rest, along with muscle and joint weakness, pain, cognitive difficulties and can be worsened through mental and physical exertion. However, it is also without an aetiology, and there is little consensus amongst both medical and patient spheres as to what CFS/ME actually is. In this thesis I draw on interviews with people with CFS/ME and participant observation in a patient-led support group in order to explore the way in which CFS/ME shaped participants’ identities and narratives of the self. I argue that participants moved through two stages that I call ‘The Disrupted Self’ and ‘The Realigned Self’. Falling ill with CFS/ME rapidly disrupted participants’ understandings of the bodies, their position within their family and the community, interactions with doctors, and all the usual markers on which they had previously formed their self-identities. In this state, I argue that participants and those with whom they engaged viewed both CFS/ME and my participants as liminal, ‘betwixt and between’ (Turner 1969) social roles and contemporary New Zealand ideals of illness, the individual, and the ‘sick person’. As the initial disruption and confusion of falling ill subsided, however, my participants worked to develop a new secure self-identity, the ‘Realigned Self’. They move into a normalised long-term liminal state by prioritising their health, adjusting their expectations of their body, developing their own conception of the aetiology of CFS/ME and forming a positive narrative of their new lives. This identity work utilised wider cultural ideals about the active, responsibilised and authentic self; common to late modern contemporary life (Beck and Beck-Gernsheim 2001, Desjarlais 1994, Giddens 1991, Rose 1996). Yet this realignment was often not reflected in the views of my participants’ friends, families and doctors. This illustrates the diverse perspectives and different degrees of liminality that exist within experiences and narratives of CFS/ME and contested illnesses.</p>