High frequency environmental DNA metabarcoding provides rapid and effective monitoring of fish community dynamics

Long‐term monitoring is critical to measure the response of biodiversity patterns and processes to human‐mediated environmental pressures. This is particularly pertinent in freshwaters, where recent estimates indicated a third of all fish species are threatened with extinction, making ongoing biomonitoring essential for conservation management. High frequency annual monitoring is critical for identifying temporal changes in fish community composition; however, traditional survey methods are typically less practical over such timeframes. While environmental (e)DNA measurement represents a potentially powerful tool for monitoring temporal community dynamics, studies are lacking. To address this deficit, we generated a high frequency time‐series dataset of entire fish communities using eDNA metabarcoding, to directly assess the repeatability and sensitivity of this method for detecting annual population trends. We targeted two differing environments (freshwater vs. intertidal) within the Thames catchment, UK, where detailed historical records from traditional monitoring were available for comparison. To test how robust eDNA data is for inferring the known community, we applied a hierarchical, nested design encompassing short and longer‐term variation in eDNA data. Our analyses showed that irrespective of environment, eDNA metabarcoding represented known seasonal shifts in fish communities, where increased relative read abundance of eDNA coincided with known migratory and spawning events, including those of the critically endangered native species Anguilla anguilla (European eel). eDNA species detections across a single year included over 75% of species recorded in a ca. 30‐year historical dataset, highlighting the power of eDNA for species detection. Our findings provide greater insight into the utility of eDNA metabarcoding for recovering temporal trends in fish communities from dynamic freshwater systems and insight into the potential best sampling strategy for future eDNA surveys

Physical and biological controls on fine sediment transport and storage in rivers

Excess fine sediment, comprising particles <2 mm in diameter, is a major cause of ecological degradation in rivers. The erosion of fine sediment from terrestrial or aquatic sources, its delivery to the river, and its storage and transport in the fluvial environment are controlled by a complex interplay of physical, biological and anthropogenic factors. Whilst the physical controls exerted on fine sediment dynamics are relatively well-documented, the role of biological processes and their interactions with hydraulic and physico-chemical phenomena has been largely overlooked. The activities of biota, from primary producers to predators, exert strong controls on fine sediment deposition, infiltration and resuspension. For example, extracellular polymeric substances (EPS) associated with biofilms increase deposition and decrease resuspension. In lower energy rivers, aquatic macrophyte growth and senescence are intimately linked to sediment retention and loss, whereas riparian trees are dominant ecosystem engineers in high energy systems. Fish and invertebrates also have profound effects on fine sediment dynamics through activities that drive both particle deposition and erosion depending on species composition and abiotic conditions. The functional traits of species present will determine not only these biotic effects but also the responses of river ecosystems to excess fine sediment. We discuss which traits are involved and put them into context with spatial processes that occur throughout the river network. Whilst strides towards better understanding of the impacts of excess fine sediment have been made, further progress to identify the most effective management approaches is urgently required through close communication between authorities and scientists

Fluid-phase endocytosis and lysosomal degradation of bovine lactoferrin in lung cells

The iron-binding protein lactoferrin and the cell-penetrating peptides derived from its sequence utilise endocytosis to enter different cell types. The full-length protein has been extensively investigated as a potential therapeutic against a range of pathogenic bacteria, fungi, and viruses, including SARS-CoV-2. As a respiratory antiviral agent, several activity mechanisms have been demonstrated for lactoferrin, at the extracellular and plasma membrane levels, but as a protein that enters cells it may also have intracellular antiviral activity. Characterisation of lactoferrin&rsquo;s binding, endocytic traffic to lysosomes, or recycling endosomes for exocytosis is lacking, especially in lung cell models. Here, we use confocal microscopy, flow cytometry, and degradation assays to evaluate binding, internalisation, endocytic trafficking, and the intracellular fate of bovine lactoferrin in human lung A549 cells. In comparative studies with endocytic probes transferrin and dextran, we show that lactoferrin binds to negative charges on the cell surface and actively enters cells via fluid-phase endocytosis, in a receptor-independent manner. Once inside the cell, we show that it is trafficked to lysosomes where it undergoes degradation within two hours. These findings provide opportunities for investigating both lactoferrin and derived cell-penetrating peptides activities of targeting intracellular pathogens

Trait-based ecology at large scales: Assessing functional trait correlations, phylogenetic constraints and spatial variability using open data

The growing use of functional traits in ecological research has brought new insights into biodiversity responses to global environmental change. However, further progress depends on overcoming three major challenges involving (a) statistical correlations between traits, (b) phylogenetic constraints on the combination of traits possessed by any single species, and (c) spatial effects on trait structure and trait–environment relationships. Here, we introduce a new framework for quantifying trait correlations, phylogenetic constraints and spatial variability at large scales by combining openly available species’ trait, occurrence and phylogenetic data with gridded, high‐resolution environmental layers and computational modelling. Our approach is suitable for use among a wide range of taxonomic groups inhabiting terrestrial, marine and freshwater habitats. We demonstrate its application using freshwater macroinvertebrate data from 35 countries in Europe. We identified a subset of available macroinvertebrate traits, corresponding to a life‐history model with axes of resistance, resilience and resource use, as relatively unaffected by correlations and phylogenetic constraints. Trait structure responded more consistently to environmental variation than taxonomic structure, regardless of location. A re‐analysis of existing data on macroinvertebrate communities of European alpine streams supported this conclusion, and demonstrated that occurrence‐based functional diversity indices are highly sensitive to the traits included in their calculation. Overall, our findings suggest that the search for quantitative trait–environment relationships using single traits or simple combinations of multiple traits is unlikely to be productive. Instead, there is a need to embrace the value of conceptual frameworks linking community responses to environmental change via traits which correspond to the axes of life‐history models. Through a novel integration of tools and databases, our flexible framework can address this need

Do agri-environment schemes result in improved water quality?

Welsh Government. Grant Number: 183/2007/0

Responses of benthic invertebrates to chemical recovery from acidification

Prosjektleder: Heleen de WitThe report provides an assessment of biological recovery from acidification in freshwater environments in Europe. The report consists of two parts, a regional data analysis based on an international dataset of biological and water chemical records, and a collection of national contributions on monitoring and assessment of biological recovery in different countries. The regional analysis showed that 47% of all included rivers (21 sites, for the period 1994-2018) and 35% percent of all lakes (34 sites, for the period 2000 to 2018) showed significant increases in species richness. Correlations between species diversity and water chemical components (ANC, pH, SO4) were found, supporting that the biological responses were related to chemical recovery. Additionally, the composition of functional traits in rivers underwent significant changes over time. Both parts of the report demonstrate ongoing biological recovery from acidification in European acid-sensitive freshwater environments.Norwegian Ministry of Climate and Environment, United Nations Economic Commission for Europe (UNECE)publishedVersio

UK Upland Waters Monitoring Network data interpretation 1988-2019

This report is the latest in a series of occasional interpretive reports to Defra, extending back to 1993, that have documented trends in the chemistry and biota of UK Upland Waters Monitoring (UWMN) sites

Freshwater invertebrate responses to fine sediment stress: a multi-continent perspective

Excessive fine sediment (particles <2 mm) deposition in freshwater systems is a pervasive stressor worldwide. However, understanding of ecological response to excess fine sediment in river systems at the global scale is limited. Here, we aim to address whether there is a consistent response to increasing levels of deposited fine sediment by freshwater invertebrates across multiple geographic regions (Australia, Brazil, New Zealand, and the UK). Results indicate ecological responses are not globally consistent and are instead dependent on both the region and the facet of invertebrate diversity considered, i.e., taxonomic or functional trait structure. Invertebrate communities of Australia were most sensitive to deposited fine sediment, with the greatest rate of change in communities occurring when fine sediment cover was low (below 25% of the reach). Communities in the UK displayed greater tolerance with most compositional change occurring between 30-60% cover. In both New Zealand and Brazil, which included the most heavily sedimented sampled streams, the communities were more tolerant or demonstrated ambiguous responses, likely due to historic environmental filtering of invertebrate communities. We conclude that ecological responses to fine sediment are not generalisable globally and are dependent on landscape filters with regional context and historic land management playing important roles