Molecular tools have revolutionized the exploration of biodiversity, especially in organisms for which traditional taxonomy is difficult, such as for microscopic animals (meiofauna). Environmental (eDNA) metabarcode surveys of DNA extracted from sediment samples are increasingly popular for surveying biodiversity. Most eDNA surveys use the nuclear gene-encoding smallsubunit rDNA gene (18S) as a marker; however, different markers and metrics used for delimiting species have not yet been evaluated against each other or against morphologically defined species (morphospecies). We assessed more than 12,000 meiofaunal sequences of 18S and of the main alternatively used marker [Cytochrome c oxidase subunit I (COI) mtDNA] belonging to 55 datasets covering three taxonomic ranks. Our results show that 18S reduced diversity estimates by a factor of 0.4 relative to morphospecies, whereas COI increased diversity estimates by a factor of 7.6. Moreover, estimates of species richness using COI were robust among three of four commonly used delimitation metrics, whereas estimates using 18S varied widely with the different metrics. We show that meiofaunal diversity has been greatly underestimated by 18S eDNA surveys and that the use of COI provides a better estimate of diversity. The suitability of COI is supported by cross-mating experiments in the literature and evolutionary analyses of discreteness in patterns of genetic variation. Furthermore its splitting of morphospecies is expected from documented levels of cryptic taxa in exemplar meiofauna. We recommend against using 18S as a marker for biodiversity surveys and suggest that use of COI for eDNA surveys could provide more accurate estimates of species richness in the future.DNA barcodes | species delimitation | microinvertebrates | environmental DNA

Insight into how environmental change determines the production and distribution of cyanobacterial toxins is necessary for risk assessment. Management guidelines currently focus on hepatotoxins (microcystins). Increasing attention is given to other classes, such as neurotoxins (e.g., anatoxin-a) and cytotoxins (e.g., cylindrospermopsin) due to their potency. Most studies examine the relationship between individual toxin variants and environmental factors, such as nutrients, temperature and light. In summer 2015, we collected samples across Europe to investigate the effect of nutrient and temperature gradients on the variability of toxin production at a continental scale. Direct and indirect effects of temperature were the main drivers of the spatial distribution in the toxins produced by the cyanobacterial community, the toxin concentrations and toxin quota. Generalized linear models showed that a Toxin Diversity Index (TDI) increased with latitude, while it decreased with water stability. Increases in TDI were explained through a significant increase in toxin variants such as MC-YR, anatoxin and cylindrospermopsin, accompanied by a decreasing presence of MC-LR. While global warming continues, the direct and indirect effects of increased lake temperatures will drive changes in the distribution of cyanobacterial toxins in Europe, potentially promoting selection of a few highly toxic species or strains.

Many inland waters exhibit complete or partial desiccation, or have vanished due to global change, exposing sediments to the atmosphere. Yet, data on carbon dioxide (CO 2) emissions from these sediments are too scarce to upscale emissions for global estimates or to understand their fundamental drivers. Here, we present the results of a global survey covering 196 dry inland waters across diverse ecosystem types and climate zones. We show that their CO 2 emissions share fundamental drivers and constitute a substantial fraction of the carbon cycled by inland waters. CO 2 emissions were consistent across ecosystem types and climate zones, with local characteristics explaining much of the variability. Accounting for such emissions increases global estimates of carbon emissions from inland waters by 6% (~0.12 Pg C y −1). Our results indicate that emissions from dry inland waters represent a significant and likely increasing component of the inland waters carbon cycle.

Ecological research is moving from a species-based to a functional-based approach to better understand the underlying principles that govern community dynamics. Studies of functional-based ecology, however, have been limited for zooplankton and particularly for rotifers. While rotifers show a variety of trophi types and coronal shapes, suggesting the importance of niche differentiation in their feeding strategy, relatively little is known of how this relates to rotifer dynamics. We used the guild ratio (GR 0 , a ratio of raptorial to microphagous species), an index based on a functional trait (i.e. feeding strategy), as a novel approach to rotifer dynamics. We extracted the seasonal GR 0 by using seasonal trend decomposition and investigated similarities between study sites (Lake Washington, USA and Lake Caldonazzo, Italy) and its relation to cladocerans by cross-correlation analysis. Our study indicated that (i) raptorial and microphagous rotifers showed alternating dominance, and that raptorial rotifers and cladocerans had a synchronous pattern, (ii) the seasonal pattern of the GR 0 was consistent across different sampling frequencies, and (iii) the GR 0 was similar in both lakes. We interpreted these patterns as the general strength of the GR 0 : discernment of species-environment relationships and robustness across sampling regimes. The limitations of the GR 0 (i.e. species identity is neglected, simplification of food preferences) can also be seen as its strong point: synthesis of multi-species patterns. In addition, the independence of GR 0 from species-level identification and its potential to make use of datasets with infrequent sampling intervals and low taxon resolution could further support its innovative aspect.

Summary Life at low temperature imposes many constraints linked to sustaining cellular functions. The cold‐adapted freshwater dinoflagellate Peridinium aciculiferum has overcome these barriers, often causing blooms in winter but forming resting cysts in spring. Little is known of the biochemical changes that accompany this temperature‐induced transformation from vegetative cells to resting cysts. We investigated how the profiles of lipids and mycosporine‐like amino acids (MAAs) vary with temperature in vegetative cells and resting cysts of P. aciculiferum. The freshwater dinoflagellate was grown at four temperatures (2.7–7.7 °C), simulating the seasonal changes from winter to spring that also induce the transition from cells to cysts. Biochemical profiles were established by liquid chromatography/mass spectrometry with the simultaneous detection of polar and non‐polar compounds. Data were analysed by non‐metric multidimensional scaling and ANOVA. Over 100 species of galactolipids, betaine lipids, phospholipids and triacylglycerols (TAGs) were found, and many were strong biomarkers for specific temperatures and life stage. Variations in galactolipids, betaine lipids and phospholipids were unidirectional, as shown by an overall decrease in the unsaturation index with temperature. In contrast, changes in TAGs were specific to life stages: short‐chain TAGs (cumulative acyl length of 44–52 carbon atoms) decreased in cysts with respect to vegetative cells, while long‐chain TAGs (54–62) showed the opposite pattern. The concentration of MAAs decreased with increasing temperature. Final cell yield, a measure of population fitness, also decreased with increasing temperature, confirming the psychrophilic status of P. aciculiferum. We report the first detailed biochemical profiles of vegetative cells and resting cysts for a dinoflagellate and show how small‐scale temperature variations alter the biochemical make‐up within and between life stages, thus contributing to our understanding of seasonal succession of species.

Information based on taxon-based indices is species-specific while information gained from function-based

Under‐ice dissolved oxygen (DO) metabolism and DO depletion are poorly understood, limiting our ability to predict how changing winter conditions will affect lake ecosystems. We analyzed under‐ice DO dynamics based on high‐frequency (HF) data at two depths (5 and 25 m) for three winters (January–March 2014, 2015, and 2016) in oligotrophic Lake Tovel (1178 m above sea level; maximum depth 39 m). Specifically, we assessed diel metabolic rates based on HF data of DO, temperature, and light for winter 2016 and seasonal DO depletion rates based on HF data of DO for all three winters. For 2016, calculations of metabolic rates were possible only for 34% and 3% of days at 5 and 25 m, respectively; these metabolic rates generally indicated net heterotrophy at both depths. Low success in modeling metabolic rates was attributed to low diel DO variability and anomalous diel DO patterns, probably linked to under‐ice physical processes. Seasonal DO patterns for the three winters showed increasing, decreasing, or stable DO trends at 5 m while at 25 m patterns always showed decreasing DO trends but with different rates. Our multiyear study permitted us to hypothesize that the observed intraannual and interannual differences in DO depletion can be attributed to variable snow cover determining the penetration of radiation and thus photosynthesis. This study brings new insights to DO dynamics in ice‐covered systems, highlights the challenges linked to under‐ice lake metabolism, and advocates for a modeling approach that includes physical processes.

Summary 1. The occurrence of unresolved complexes of cryptic species may hinder the identification of the main ecological drivers of biodiversity when different cryptic taxa have different ecological requirements. 2. We assessed factors influencing the occurrence of Synchaeta species (monogonont rotifers) in 17 waterbodies of the Trentino‐South Tyrol region in the Eastern Alps. To do so, we compared the results of using unresolved complexes of cryptic species, as is common practice in limnological studies based on morphological taxonomy, and having resolved cryptic complexes, made possible by DNA taxonomy. 3. To identify cryptic species, we used the generalised mixed Yule coalescent (GMYC) model. We investigated the relationship between the environment and the occurrence of Synchaeta spp. by multivariate ordination using two definitions of the units of diversity, namely (i) unresolved species complexes (morphospecies) and (ii) putative cryptic species (GMYC entities). Our expectation was that resolving complexes of cryptic species could provide more information than using morphospecies. 4. As expected, DNA taxonomy provided greater taxonomic resolution than morphological taxonomy. Further, environmental‐based multivariate ordination on cryptic species explained a significantly higher proportion of variance than that based on morphospecies. Occurrence of GMYC entities was related to total phosphorus (TP), whereas no relationship could be found between morphospecies and the environment. Moreover, different cryptic species within the same morphospecies showed different, and even opposite, preferences for TP. In addition, the wide geographical distribution of haplotypes and cryptic species indicated the absence of barriers to dispersal in Synchaeta.