20 years of bibliometric data illustrates a lack of concordance between journal impact factor and fungal species discovery in systematic mycology.

Journal impact factors were devised to qualify and compare university library holdings but are frequently repurposed for use in ranking applications, research papers, and even individual applicants in mycology and beyond. The widely held assumption that mycological studies published in journals with high impact factors add more to systematic mycology than studies published in journals without high impact factors nevertheless lacks evidential underpinning. The present study uses the species hypothesis system of the UNITE database for molecular identification of fungi and other eukaryotes to trace the publication history and impact factor of sequences uncovering new fungal species hypotheses.

Emerging contaminants: A One Health perspective.

Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention.

How, not if, is the question mycologists should be asking about DNA-based typification.

Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings challenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be.

Phenotypic and transcriptomic acclimation of the green microalga Raphidocelis subcapitata to high environmental levels of the herbicide diflufenican.

Herbicide pollution poses a worldwide threat to plants and freshwater ecosystems. However, the understanding of how organisms develop tolerance to these chemicals and the associated trade-off expenses are largely unknown. This study aims to investigate the physiological and transcriptional mechanisms underlying the acclimation of the green microalgal model species Raphidocelis subcapitata (Selenastraceae) towards the herbicide diflufenican, and the fitness costs associated with tolerance development.

The curse of the uncultured fungus.

The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as "uncultured fungus". These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 "uncultured fungus" sequences that represent truly unidentifiable fungal taxa - and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition.

Tolerance Patterns in Stream Biofilms Link Complex Chemical Pollution to Ecological Impacts.

Preventing and remedying fresh waters from chemical pollution is a fundamental societal and scientific challenge. With other nonchemical stressors potentially co-occurring, assessing the ecological consequences of reducing chemical loads in the environment is arduous. In this case study, we comparatively assessed the community structure, functions, and tolerance of stream biofilms to micropollutant mixtures extracted from deployed passive samplers at wastewater treatment plant effluents.

Triclosan changes community composition and selects for specific bacterial taxa in marine periphyton biofilms in low nanomolar concentrations.

The antibacterial agent Triclosan (TCS) is a ubiquitous environmental contaminant due to its widespread use. Sensitivity to TCS varies substantially among eu- and pro-karyotic species and its risk for the marine environment remains to be better elucidated. In particular, the effects that TCS causes on marine microbial communities are largely unknown.

Copper Affects Composition and Functioning of Microbial Communities in Marine Biofilms at Environmentally Relevant Concentrations.

Copper (Cu) pollution in coastal areas is a worldwide threat for aquatic communities. This study aims to demonstrate the usefulness of the DNA metabarcoding analysis in order to describe the ecotoxicological effect of Cu at environmental concentrations on marine periphyton. Additionally, the study investigates if Cu-induced changes in community structure co-occurs with changes in community functioning (i.

Fluvial biofilms exposed to desiccation and pharmaceutical pollution: New insights using metabolomics.

In many arid and semi-arid systems, biological communities in river ecosystems are submitted to flow interruption and desiccation, as well as to the impact of urban wastewaters. In this work, we studied (using a LC-LTQ-Orbitrap) the metabolomic response of biofilm communities exposed to both hydrological and chemical stressors. Fluvial biofilms were exposed to a mixture of 9 pharmaceuticals at a total concentration of 5000ng/L (mimicking concentrations and compounds found in polluted aquatic environments) and/or to seven days of desiccation, under laboratory conditions.

Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing.

High-throughput DNA sequencing technologies are increasingly used for the metagenomic characterisation of microbial biodiversity. However, basic issues, such as the choice of an appropriate DNA extraction method, are still not resolved for non-model microbial communities. This study evaluates four commonly used DNA extraction methods for marine periphyton biofilms in terms of DNA yield, efficiency, purity, integrity and resulting 16S rRNA bacterial diversity.

Cumulative Stressors Trigger Increased Vulnerability of Diatom Communities to Additional Disturbances.

Chronic, non-lethal stressors occurring gradually (in space or time) can result in cumulative impacts that are more dramatic than higher intensities or occasional critical levels of any single one of these stressors. The negative effects of the chronic stressors trigger lasting impacts that may grow in intensity and become problematic over time and/or to higher trophic levels. In rivers, aquatic organisms experience this type of cumulative stress along the up- to downstream gradient in natural and anthropogenic contaminants generally observed in inhabited watersheds.

Pollution-induced community tolerance to non-steroidal anti-inflammatory drugs (NSAIDs) in fluvial biofilm communities affected by WWTP effluents.

We assessed the tolerance acquired by stream biofilms to two non-steroidal anti-inflammatory-drugs (NSAIDs), ibuprofen and diclofenac. Biofilms came from a stream system receiving the effluent of a wastewater treatment plant (WWTP). The response of biofilms from a non-polluted site (upstream the WWTP) was compared to that of others downstream with relevant and decreasing levels of NSAIDs.

Effects of flow intermittency and pharmaceutical exposure on the structure and metabolism of stream biofilms.

Increasing concentrations of pharmaceutical compounds occur in many rivers, but their environmental risk remains poorly studied in stream biofilms. Flow intermittency shapes the structure and functions of ecosystems, and may enhance their sensitivity to toxicants. This study evaluates the effects of a long-term exposure of biofilm communities to a mixture of pharmaceutical compounds at environmental concentrations on biofilm bioaccumulation capacity, the structure and metabolic processes of algae and bacteria communities, and how their potential effects were enhanced or not by the occurrence of flow intermittency.

Experimental evaluation of the contribution of acidic pH and Fe concentration to the structure, function and tolerance to metals (Cu and Zn) exposure in fluvial biofilms.

An indoor channel system was colonised with fluvial biofilms to study the chronic effects of high Fe and SO4(2-) concentrations and acidic pH, the water chemistry in the surrounding streams of Aljustrel mining area (Alentejo, Portugal), and their contribution to community (in)tolerance to metal toxicity by short-term experiments with Cu and Zn. Biofilms were subjected to four different treatments during 8 weeks: high Fe and SO4(2-) concentrations (1 mg Fe l(-1)+ 700 mg SO4(2-) l(-1)) and acidic pH, high Fe and SO4(2-) at alkaline pH; lower Fe and SO4(2-) at acidic pH: and lower Fe and SO4(2-) concentrations at alkaline pH as negative control. During chronic exposure, acidic pH affected growth negatively, based on low values of algal biomass and the autotrophic index, high values of the antioxidant enzyme activities and low diversity diatom communities, dominated by acidophilic species (Pinnularia aljustrelica) in acidic treatments, being the effects more marked with high Fe and SO4(2-).

Antioxidant enzyme activities in biofilms as biomarker of Zn pollution in a natural system: an active bio-monitoring study.

This study aimed to explore the use of antioxidant enzyme activities (AEA) and biofilm metal accumulation capacity in natural communities as effect-based indicator of metal exposure in fluvial systems. To achieve these objectives, an active biomonitoring using fluvial biofilm communities was performed during 5 weeks. Biofilm was colonized over artificial substrata in a non-polluted site.

Seasonal changes in antioxidant enzyme activities of freshwater biofilms in a metal polluted Mediterranean stream.

While seasonal variations in fluvial communities have been extensively investigated, effects of seasonality on community responses to environmental and/or chemical stress are poorly documented. The aim of this study was to describe antioxidant enzyme activity (AEA) variability in fluvial biofilms over an annual cycle, under multi-stress scenarios due to environmental variability (e.g.

Light History Influences the Response of Fluvial Biofilms to Zn Exposure.

Fluvial biofilms are subject to multistress situations in natural ecosystems, such as the co-occurrence of light intensity changes and metal toxicity. However, studies simultaneously addressing both factors are rare. This study evaluated in microcosm conditions the relationship between short-term light intensity changes and Zn toxicity on fluvial biofilms with long-term photoacclimation to different light conditions.

Antioxidant enzyme activities as biomarkers of Zn pollution in fluvial biofilms.

The potential of the antioxidant enzyme catalase (CAT) and ascorbate peroxidase (APX) as molecular biomarkers of Zn toxicity in freshwater biofilms has been explored in this study jointly with other classical functional and structural endpoints (photosynthetic parameters, algal group composition and bioaccumulation). Biofilms were colonized in an indoor microcosm system for 5 weeks and then exposed to Zn for 5 weeks. To evaluate Zn effects, biofilms were sampled 5 and 3 days before exposure, just before exposure (time 0), and after 6h, 1, 3, 7, 21 and 35 days of metal exposure.

In situ spatio-temporal changes in pollution-induced community tolerance to zinc in autotrophic and heterotrophic biofilm communities.

Pollution-induced community tolerance (PICT) uses increased tolerance in populations at contaminated sites as an indicator of contaminant effects. However, given the broad structural and functional complexity that characterizes biological communities, the acquisition of PICT could vary with (i) target community, (ii) intensity of toxicant exposure, (iii) the species succession stage, and (iv) the physicochemical characteristics of the studied site. To assess the spatio-temporal changes of zinc-induced tolerance in fluvial biofilm communities, we conducted an in situ study in Osor River (North-East Catalonia, Spain), which has zinc contamination.

Catalase in fluvial biofilms: a comparison between different extraction methods and example of application in a metal-polluted river.

Antioxidant enzymes are involved in important processes of cell detoxification during oxidative stress and have, therefore, been used as biomarkers in algae. Nevertheless, their limited use in fluvial biofilms may be due to the complexity of such communities. Here, a comparison between different extraction methods was performed to obtain a reliable method for catalase extraction from fluvial biofilms.