The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered.

UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.

The impact of the COVID-19 pandemic on people experiencing homelessness: a qualitative interview study in the UK.

BACKGROUND: People experiencing homelessness faced unique challenges during the COVID-19 pandemic, including changes to accommodation availability, societal restrictions impacting access to essentials like food, and services moving to remote access. There is a paucity of in-depth qualitative research exploring how the pandemic affected this population, which this research aims to address. METHODS: 33 semi-structured qualitative interviews (22 with people who experienced homelessness during the pandemic and 11 with homelessness sector service providers) were done in the UK between April 26, 2021, and Jan, 25, 2022. Ethical approval was granted by the University College London research ethics committee (Project ID: 14895/005) and all participants provided informed consent. Interviews were audio-recorded, transcribed, and analysed using reflexive thematic analysis utilising NVivo software. Four interviews were coded by two researchers for consistency of codes. FINDINGS: In our sample of people experiencing homelessness, 11 (50%) were female, 13 (59%) White British, all were aged between 24 and 59 years, and all had lived in hostels or hotels, with friends or family, or on the streets during the pandemic. Providers interviewed worked for varied services, including support charities, housing, and addiction services. Four key themes were identified: understanding of and adherence to COVID guidelines; changes to accommodation and experiences of "Everyone In" (a government initiative in which people sleeping on the street or in accommodation where it was difficult to self-isolate were provided emergency accommodation); living through a pandemic while navigating homelessness; and, adaptations to service provision for people experiencing homelessness. INTERPRETATION: Policy makers and public health communicators must learn from people experiencing homelessness to maximise effectiveness of future public health strategies. Housing providers and support services should recognise the implications of imposing a scarcity of choice on people who need accommodation during a public health emergency. The loss of usual support was destabilising for people experiencing homelessness, triggering a need to adopt survival tactics which negatively influence their health. Although this research was limited by the possibility that views expressed might differ from those unwilling or unable to participate, it does highlight successes and difficulties in supporting people experiencing homelessness during the COVID-19 pandemic and informs planning for similar public health events. FUNDING: Nuffield Foundation, Wellcome Trust.

Mpox knowledge, behaviours and barriers to public health measures among gay, bisexual and other men who have sex with men in the UK: a qualitative study to inform public health guidance and messaging.

BACKGROUND: The 2022-23 mpox epidemic is the first-time sustained community transmission had been reported in countries without epidemiological links to endemic areas. During that period, the outbreak almost exclusively affected sexual networks of gay, bisexual, or other men who have sex with men (GBMSM) and people living with HIV. In efforts to control transmission, multiple public health measures were implemented, including vaccination, contact tracing and isolation. This study examines knowledge, attitudes, and perceptions of mpox among a sample of GBMSM during the 2022-23 outbreak in the UK, including facilitators for and barriers to the uptake of public health measures. METHODS: Interviews were conducted with 44 GBMSM between May and December 2022. Data were analysed using reflexive thematic analysis. Positive and negative comments pertaining to public health measures were collated in a modified version of a 'table of changes' to inform optimisations to public health messages and guidance. RESULTS: Most interviewees were well informed about mpox transmission mechanisms and were either willing to or currently adhering to public health measures, despite low perceptions of mpox severity. Measures that aligned with existing sexual health practices and norms were considered most acceptable. Connections to GBMSM networks and social media channels were found to increase exposure to sexual health information and norms influencing protective behaviours. Those excluded or marginalized from these networks found some measures challenging to perform or adhere to. Although social media was a key mode of information sharing, there were preferences for timely information from official sources to dispel exaggerated or misleading information. CONCLUSIONS: There are differential needs, preferences, and experiences of GBMSM that limit the acceptability of some mitigation and prevention measures. Future public health interventions and campaigns should be co-designed in consultation with key groups and communities to ensure greater acceptability and credibility in different contexts and communities.

Disturbance alters the forest soil microbiome.

Billions of microorganisms perform critical below-ground functions in all terrestrial ecosystems. While largely invisible to the naked eye, they support all higher lifeforms, form symbiotic relationships with ~90% of terrestrial plant species, stabilize soils, and facilitate biogeochemical cycles. Global increases in the frequency of disturbances are driving major changes in the structure and function of forests. However, despite their functional significance, the disturbance responses of forest microbial communities are poorly understood. Here, we explore the influence of disturbance on the soil microbiome (archaea, fungi and bacteria) of some of the world's tallest and most carbon-dense forests, the Mountain Ash forests of south-eastern Australia. From 80 sites, we identified 23,277 and 19,056 microbial operational taxonomic units from the 0-10 cm and 20-30 cm depths of soil respectively. From this extensive data set, we found the diversity and composition of these often cryptic communities has been altered by human and natural disturbance events. For instance, the diversity of ectomycorrhizal fungi declined with clearcut logging, the diversity of archaea declined with salvage logging, and bacterial diversity and overall microbial diversity declined with the number of fires. Moreover, we identified key associations between edaphic (soil properties), environmental (slope, elevation) and spatial variables and the composition of all microbial communities. Specifically, we found that soil pH, manganese, magnesium, phosphorus, iron and nitrate were associated with the composition of all microbial communities. In a period of widespread degradation of global forest ecosystems, our findings provide an important and timely insight into the disturbance responses of soil microbial communities, which may influence key ecological functions.

Direct and indirect disturbance impacts in forests.

Human and natural disturbances are key drivers of change in forest ecosystems. Yet, the direct and indirect mechanisms which underpin these changes remain poorly understood at the ecosystem level. Here, using structural equation modelling across a 150+ year chronosequence, we disentangle the direct and indirect effects of major disturbances in a temperate forest ecosystem. We show that wildfires, logging and post-fire (salvage) logging can affect plant and microbial communities and abiotic soil properties both directly and indirectly through plant-soil-microbial interactions. We quantified 68 direct and indirect disturbance effects across these components, with the majority resulting in ecosystem-wide adverse effects. Indirect disturbance effects accounted for 43% of total disturbance effects, with some amplifying or partially mitigating direct disturbance effects. Overall, human disturbances were associated with more negative effects than natural disturbances. Our analyses provide novel insights into the multifaceted dynamics of forest disturbances and the mechanisms which underpin their relative impacts.

Naming names: the first women taxonomists in mycology.

The transition from amateur to professional in natural history is generally regarded as having taken place in the nineteenth century, but landmark events such as the 1917 appointment of mycologist Johanna Westerdijk (1883-1961) as the first female professor in the Netherlands indicate that the pattern of change for women was more varied and delayed than for men. We investigate this transition in mycology, and identify only 43 women in the Western World who published scientific mycological literature pre-1900, of whom twelve published new fungal taxa. By charting the emergence of these women over time, and comparing the output of self-taught amateurs and university graduates, we establish the key role of access to higher education in female participation in mycology. Using a suite of strategies, six of the self-taught amateurs managed to overcome their educational disadvantages and name names - Catharina Dörrien (the first to name a fungal taxon), Marie-Anne Libert, Mary Elizabeth Banning, Élise-Caroline Bommer, Mariette Rousseau, and Annie Lorrain Smith. By 1900, the professional era for women in mycology was underway, and increasing numbers published new taxa. Parity with male colleagues in recognition and promotion, however, remains an ongoing issue.

Biophysical characterization and structural determination of the potent cytotoxic Psathyrella asperospora lectin.

A lectin with strong cytotoxic effect on human colon cancer HT29 and monkey kidney VERO cells was recently identified from the Australian indigenous mushroom Psathyrella asperospora and named PAL. We herein present its biochemical and structural analysis using a multidisciplinary approach. Glycan arrays revealed binding preference towards N-acetylglucosamine (GlcNAc) and, to a lesser extent, towards sialic acid (Neu5Ac). Submicromolar and millimolar affinity was measured by surface plasmon resonance for GlcNAc and NeuAc, respectively. The structure of PAL was resolved by X-ray crystallography, elucidating both the protein's amino acid sequence as well as the molecular basis rationalizing its binding specificity. Proteins 2017; 85:969-975. © 2016 Wiley Periodicals, Inc.

Mushroom lectins: specificity, structure and bioactivity relevant to human disease.

Lectins are non-immunoglobulin proteins that bind diverse sugar structures with a high degree of selectivity. Lectins play crucial role in various biological processes such as cellular signaling, scavenging of glycoproteins from the circulatory system, cell-cell interactions in the immune system, differentiation and protein targeting to cellular compartments, as well as in host defence mechanisms, inflammation, and cancer. Among all the sources of lectins, plants have been most extensively studied. However, more recently fungal lectins have attracted considerable attention due to their antitumor, antiproliferative and immunomodulatory activities. Given that only 10% of mushroom species are known and have been taxonomically classified, mushrooms represent an enormous unexplored source of potentially useful and novel lectins. In this review we provide an up-to-date summary on the biochemical, molecular and structural properties of mushroom lectins, as well as their versatile applications specifically focusing on mushroom lectin bioactivity.

Concordance of seven gene genealogies compared to phenotypic data reveals multiple cryptic species in Australian dermocyboid Cortinarius (Agaricales).

This study aims to delimit species of Australian dermocyboid fungi (Cortinarius, Agaricales) using genealogical concordance on well-characterised phenotypic species and to assess the utility of seven loci for DNA barcoding Australian Cortinarius taxa. Eighty-six collections of dermocyboid Cortinarius were sampled from across southern Australia. Phenotypic species were first recognised by performing clustering analyses on a comprehensive phenotypic dataset including morphological, colour and pigment data. Then phylogenetic species were delimited from the concordance of seven locus genealogies (ITS, nLSU, gpd, mcm7, rpb1, rpb2 and tef1). Seventeen phenotypic species were recognised while the concordance of gene genealogies recovered 35 phylogenetic species. All loci except for LSU recovered most phylogenetic species, although only rpb1 correctly identified all phylogenetic species. The ITS region is confirmed as an effective barcode for Cortinarius and a standard pairwise distance threshold of 2.0% is proposed to DNA barcode Australian Cortinarius taxa. Australian dermocyboid fungi belong in separate clades to the boreal clade Dermocybe, mostly in the clade Splendidi. This study provides a solid foundation for future ecological, taxonomic and systematic research on one of the most diverse genera of mushrooms worldwide.

G2/M cell cycle arrest by an N-acetyl-D-glucosamine specific lectin from Psathyrella asperospora.

A new N-acetyl-D-glucosamine (GlcNAc) specific lectin was identified and purified from the fruiting body of the Australian indigenous mushroom Psathyrella asperospora. The functional lectin, named PAL, showed hemagglutination activity against neuraminidase treated rabbit and human blood types A, B and O, and exhibited high binding specificity towards GlcNAc, as well as mucin and fetuin, but not against asialofetuin. PAL purified to homogeneity by a combination of ammonium sulfate precipitation, chitin affinity chromatography and size exclusion chromatography, was monomeric with a molecular mass of 41.8 kDa, was stable at temperatures up to 55 °C and between pH 6-10, and did not require divalent cations for optimal activity. De novo sequencing of PAL using LC-MS/MS, identified 10 tryptic peptides that revealed substantial sequence similarity to the GlcNAc recognizing lectins from Psathyrella velutina (PVL) and Agrocybe aegerita (AAL-II) in both the carbohydrate binding and calcium binding sites. Significantly, PAL was also found to exert a potent anti-proliferative effect on HT29 cells (IC50 0.48 µM) that was approximately 3-fold greater than that observed on VERO cells; a difference found to be due to the differential expression of cell surface GlcNAc on HT29 and VERO cells. Further characterization of this activity using propidium iodine staining revealed that PAL induced cell cycle arrest at G2/M phase in a manner dependent on its ability to bind GlcNAc.

On the trail of a critically endangered fungus: A world-first application of wildlife detection dogs to fungal conservation.

Plant and animal conservation have benefited from the assistance of wildlife detection dogs (WDDs) since 1890, but their application to fungal conservation has not been trialed. In a world-first, we tested the effectiveness of WDDs and human surveyors when searching for experimentally outplanted fungi in natural habitat. We focused on a critically endangered fungus from Australia, Hypocreopsis amplectens, and showed that a WDD outperformed a human surveyor: our WDD detected a greater proportion of targets, had a faster time to first discovery, and had fewer false negatives. Our study highlights the tremendous potential for WDDs to enhance fungal conservation by demonstrating their utility in one of the most challenging fungal systems: a rare species with low population densities and low volatility. Our findings suggest that the application of WDDs to fungal conservation should enhance continuing efforts to document and conserve an understudied kingdom that is threatened by habitat loss and climate change.

Multigene sequence data reveal morphologically cryptic phylogenetic species within the genus Laccaria in southern Australia.

Laccaria (Hydnangiaceae, Agaricales, Basidiomycota) is one of the more intensively studied ectomycorrhizal genera; however, species boundaries within Laccaria and the closely related Hydnangium and Podohydnangium in Australia have not yet been examined with molecular sequence data. Based on morphological characters, eight native species of Laccaria are currently recognized in Australia, as well as three Hydnangium species and the monotypic Podohydnangium australe. Sequences of the internal transcribed spacer region of nuclear rDNA (ITS), RNA polymerase beta subunit II (rpb2) and translation elongation factor 1 alpha (tef-1α) were generated from 77 collections of Laccaria, Hydnangium and Podohydnangium from Australia. Ten phylogenetic species and a further 11 potential species (represented by singletons) of Laccaria in Australia are delimited from sequence analyses. Most of the morphological species contained cryptic phylogenetic species, but these species were always nested entirely within a given morphological species, although not always as sister taxa. The rpb2 locus performed best as a species barcode with pairwise and patristic distance measures. The ITS sequence region returned the least resolved gene tree of the three regions examined and was the least useful as a barcode region. Based on the phylogenetic topology, there appears to have been multiple gains and/or losses of the ectomycorrhizal association of some species with the myrtle beech, Nothofagus cunninghamii as well as of sequestrate basidiocarps and two-spored basidia.

Fungal taxonomy: current status and research agendas for the interdisciplinary and globalisation era.

Fungal taxonomy is a fundamental discipline that aims to recognise all fungi and their kinships. Approximately 5% of a practical estimate of 2.2-3.8 million species globally are currently known, and consequently the Fungal Tree of Life (FTOL) is very incompletely reconstructed. With the advances of new technologies, mycology is marching into the interdisciplinary and globalisation era. To make fungal taxonomy relevant, innovative sampling methods and phylogenomics analyses should be performed to reconstruct a much more comprehensive FTOL. In association with this densely sampled FTOL, multiomics will reveal what drives fungal species diversification and how fungal traits evolve to adapt to various environments, while metagenomics will facilitate the understanding and protection of the ecological functions of fungi. A coordinated approach to pursuing these research agendas that includes conceiving of and costing a mission to describe all the fungi on the planet will unlock potential of fungi to support sustainable development of our society.

Financial adversity and subsequent health and wellbeing during the COVID-19 pandemic in the UK: A qualitative interview study.

Aims: There are concerns that the economic impacts of the COVID-19 pandemic, including employment inactivity and job loss, will have consequences for the UK population's health and wellbeing. However, there is limited qualitative research into how financial adversity contributes to poor health outcomes in this context. This study aimed to explore forms of financial adversity experienced during the pandemic and their subsequent impacts for health and wellbeing. Methods: Qualitative semi-structured interviews with 20 people who experienced a form of financial adversity during the pandemic and six service providers employed in social welfare support services. Data were analysed using reflexive thematic analysis. Results: Two main sources of financial adversity were identified: reductions in household incomes and increased living costs which engendered emotional and physical burdens. Coping strategies included increased financial borrowing, support from informal and formal networks and cutting back on energy use, food and non-essential items. Conclusion: Our study highlighted exposure to multiple financial adversities because of the pandemic and how these experiences led to poor mental and physical health. The findings underline the importance of measures attending to the immediate needs of individuals, including accessible, co-located financial and psychological services, as well as broader measures that seek to reduce social and economic inequalities.

Understanding changes to perceived socioeconomic and psychosocial adversities during COVID-19 for UK freelance cultural workers.

There is a dearth of qualitative research exploring how freelancers working in the cultural industries have been affected during COVID-19. In particular, there is a lack of research exploring how socioeconomic and psychosocial adversities may have changed or evolved, and how these changes have been perceived and subjectively experienced by freelance cultural workers. This study builds on qualitative interviews carried out in July-November 2020 (n = 20) by exploring findings from follow-up interviews conducted in May-July 2021 (n = 16). It presents an inequality of experiences connected to a range of socioeconomic and psychosocial factors, showing how some freelancers experienced small changes (e.g. to the kind of work carried out), with others experiencing major changes (e.g. leaving the sector completely). It concludes with a call for highly bespoke financial and psychological support, as well as a need to rethink what cultural value is for this workforce in the "new normal", considering changing valuing processes.

A comparison of the accuracy of mushroom identification applications using digital photographs.

OBJECTIVE: To compare the accuracy of three popular mushroom identification software applications in identifying mushrooms involved in exposures reported to the Victorian Poisons Information Centre and Royal Botanic Gardens Victoria. BACKGROUND: Over the past 10 years, an increasing number of software applications have been developed for use on smart phones and tablet devices to identify mushrooms. We have observed an increase in poisonings after incorrect identification of poisonous species as edible, using these applications. DESIGN: We compared the accuracy of three iPhone™ and Android™ mushroom identification applications: Picture Mushroom (Next Vision Limited©), Mushroom Identificator (Pierre Semedard©), and iNaturalist (iNaturalist, California Academy of Sciences©). Each app was tested independently by three researchers using digital photographs of 78 specimens sent to the Victorian Poisons Information Centre and Royal Botanic Gardens Victoria over a two-year period, 2020-2021. Mushroom identification was confirmed by an expert mycologist. For each app, individual and combined results were compared. RESULTS: Picture Mushroom was the most accurate of the three apps and correctly identified 49% (95% CI [0-100]) of specimens, compared with Mushroom Identificator (35% [15-56]) and iNaturalist (35% [0-76]). Picture Mushroom correctly identified 44% of poisonous mushrooms [0-95], compared with Mushroom Identificator (30% [1-58]) and iNaturalist (40% [0-84), but Mushroom Identificator identified more specimens of Amanita phalloides correctly (67%), compared to Picture Mushroom (60%) and iNaturalist (27%). Amanita phalloides was falsely identified, twice by Picture Mushroom and once by iNaturalist. CONCLUSIONS: Mushroom identification applications may be useful future tools to assist clinical toxicologists and the general public in the accurate identification of mushrooms species but, at present, are not reliable enough to exclude exposure to potentially poisonous mushrooms when used alone.

Did mpox knowledge, attitudes and beliefs affect intended behaviour in the general population and men who are gay, bisexual and who have sex with men? An online cross-sectional survey in the UK.

OBJECTIVES: To investigate rates of mpox beliefs, knowledge and intended behaviours in the general population and in gay, bisexual or other men who have sex with men (GBMSM), and factors associated with intended behaviours. To test the impact of motivational messages (vs a factual control) on intended behaviours. DESIGN: Cross-sectional online survey including a nested randomised controlled trial. SETTING: Data collected from 5 September 2022 to 6 October 2022. PARTICIPANTS: Participants were aged 18 years or over and lived in the UK (general population). In addition, GBMSM were male, and gay, bisexual or had sex with men. The general population sample was recruited through a market research company. GBMSM were recruited through a market research company, the dating app Grindr and targeted adverts on Meta (Facebook and Instagram). MAIN OUTCOME MEASURES: Intention to self-isolate, seek medical help, stop all sexual contact, share details of recent sexual contacts and accept vaccination. RESULTS: Sociodemographic characteristics differed by sample. There was no effect of very brief motivational messaging on behavioural intentions. Respondents from Grindr and Meta were more likely to intend to seek help immediately, completely stop sexual behaviour and be vaccinated or intend to be vaccinated, but being less likely to intend to self-isolate (ps<0.001). In the general population sample, intending to carry out protective behaviours was generally associated with being female, older, having less financial hardship, greater worry, higher perceived risk to others and higher perceived susceptibility to and severity of mpox (ps<0.001). There were fewer associations with behaviours in the Grindr sample, possibly due to reduced power. CONCLUSIONS: GBMSM were more likely to intend to enact protective behaviours, except for self-isolation. This may reflect targeted public health efforts and engagement with this group. Associations with socioeconomic factors suggest that providing financial support may encourage people to engage with protective behaviours.

The Agile Co-production and Evaluation framework for developing public health interventions, messaging and guidance.

A lesson identified from the COVID-19 pandemic is that we need to extend existing best practice for intervention development. In particular, we need to integrate (a) state-of-the-art methods of rapidly coproducing public health interventions and messaging to support all population groups to protect themselves and their communities with (b) methods of rapidly evaluating co-produced interventions to determine which are acceptable and effective. This paper describes the Agile Co-production and Evaluation (ACE) framework, which is intended to provide a focus for investigating new ways of rapidly developing effective interventions and messaging by combining co-production methods with large-scale testing and/or real-world evaluation. We briefly review some of the participatory, qualitative and quantitative methods that could potentially be combined and propose a research agenda to further develop, refine and validate packages of methods in a variety of public health contexts to determine which combinations are feasible, cost-effective and achieve the goal of improving health and reducing health inequalities.

A qualitative study exploring the impact of the COVID-19 pandemic on People Who Inject Drugs (PWID) and drug service provision in the UK: PWID and service provider perspectives.

BACKGROUND: People Who Inject Drugs (PWID) are subject to distinct socio-structural inequalities that can expose them to high risks of COVID-19 transmission and related health and social complications. In response to COVID-19 mitigation strategies, these vulnerabilities are being experienced in the context of adapted drug treatment service provision, including reduced in-person support and increased regulatory flexibility in opioid substitution therapy (OST) guidelines. This study aimed to explore the longer-term impact of the pandemic on the health and wellbeing of PWID in the UK, including provider and client experiences of treatment changes. METHODS: Interviews were conducted with 19 PWID and 17 drug treatment providers between May and September 2021, recruited from drug and homelessness charities providing treatment services and healthcare in the UK. Data were analysed using reflexive thematic analysis. RESULTS: Most participants expressed ongoing fears of COVID-19 transmission, although socio-structural inequalities limited the contexts in which physical distancing could be practised. In addition, virus mitigation strategies altered the risk environment for PWID, resulting in ongoing physical (e.g. changing drug use patterns, including transitions to crack cocaine, benzodiazepine and pregabalin use) and socio-economic harms (e.g. limited opportunities for sex work engagement and income generation). Finally, whilst clients reported some favourable experiences from service adaptations prompted by COVID-19, including increased regulatory flexibility in OST guidelines, there was continued scepticism and caution among providers toward sustaining any treatment changes beyond the pandemic period. CONCLUSIONS: Whilst our findings emphasize the importance of accessible harm reduction measures attending to changing indices of drug-related harm during this period, there is a need for additional structural supports to ensure pre-existing disparities and harms impacting PWID are not exacerbated further by the conditions of the pandemic. In addition, any sustained policy and service delivery adaptations prompted by COVID-19 will require further attention if they are to be acceptable to both service users and providers.