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RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We report a large-scale set of predictions by 18 groups for 23 RNA-Puzzles: 4 RNA elements, 2 Aptamers, 4 Viral elements, 5 Ribozymes and 8 Riboswitches. We describe automatic assessment protocols for comparisons between prediction and experiment. Our analyses reveal some critical steps to be overcome to achieve good accuracy in modeling RNA structures: identification of helix-forming pairs and of non-Watson-Crick modules, correct coaxial stacking between helices and avoidance of entanglements. Three of the top four modeling groups in this round also ranked among the top four in the CASP15 contest.

Human-induced salinization increasingly threatens inland waters; yet we know little about the multifaceted response of lake communities to salt contamination. By conducting a coordinated mesocosm experiment of lake salinization across 16 sites in North America and Europe, we quantified the response of zooplankton abundance and (taxonomic and functional) community structure to a broad gradient of environmentally relevant chloride concentrations, ranging from 4 to ca. 1400 mg Cl− L−1. We found that crustaceans were distinctly more sensitive to elevated chloride than rotifers; yet, rotifers did not show compensatory abundance increases in response to crustacean declines. For crustaceans, our among-site comparisons indicate: (1) highly consistent decreases in abundance and taxon richness with salinity; (2) widespread chloride sensitivity across major taxonomic groups (Cladocera, Cyclopoida, and Calanoida); and (3) weaker loss of functional than taxonomic diversity. Overall, our study demonstrates that aggregate properties of zooplankton communities can be adversely affected at chloride concentrations relevant to anthropogenic salinization in lakes.

Human-induced salinization caused by the use of road deicing salts, agricultural practices, mining operations, and climate change is a major threat to the biodiversity and functioning of freshwater ecosystems. Yet, it is unclear if freshwater ecosystems are protected from salinization by current water quality guidelines. Leveraging an experimental network of land-based and in-lake mesocosms across North America and Europe, we tested how salinization-indicated as elevated chloride (Cl-) concentration-will affect lake food webs and if two of the lowest Cl- thresholds found globally are sufficient to protect these food webs. Our results indicated that salinization will cause substantial zooplankton mortality at the lowest Cl- thresholds established in Canada (120 mg Cl-/L) and the United States (230 mg Cl-/L) and throughout Europe where Cl- thresholds are generally higher. For instance, at 73% of our study sites, Cl- concentrations that caused a ≥50% reduction in cladoceran abundance were at or below Cl- thresholds in Canada, in the United States, and throughout Europe. Similar trends occurred for copepod and rotifer zooplankton. The loss of zooplankton triggered a cascading effect causing an increase in phytoplankton biomass at 47% of study sites. Such changes in lake food webs could alter nutrient cycling and water clarity and trigger declines in fish production. Current Cl- thresholds across North America and Europe clearly do not adequately protect lake food webs. Water quality guidelines should be developed where they do not exist, and there is an urgent need to reassess existing guidelines to protect lake ecosystems from human-induced salinization.

Freshwater salinization is an increasing threat to lakes worldwide, but despite being a widespread issue, little is known about its impact on biological communities at the base of the food chain.Here we used a mesocosm set‐up coupled with modern high‐frequency sensor technology to identify short‐ and longer‐term responses of phytoplankton to salinization in an oligotrophic lake. We tested the effects of salinization over a gradient of increasing salt concentrations that can be found in natural lakes exposed to road salt contamination (added salt range: from 0 to 1500 mg Cl− L−1).The high‐frequency chlorophyll‐a (chl‐a) fluorescence measurements showed an increasing divergence of chl‐a concentrations along the salinization gradient over time, with substantially lower concentrations at higher salt levels. At the sub‐daily scale, we found a profound suppression of day–night signal cycles with increasing salinity, which could be related to physiological stress due to the impairment of photosynthesis via effects on the photosystem II or potential changes in the active migration of phytoplankton. Community analyses revealed a similar decline pattern for the total phytoplankton biomass and a collapse of the total zooplankton biomass. Interestingly, we found a loss of phytoplankton diversity coupled with a compositional re‐organization involving the loss of dominant green algae but increased biomass of salt‐tolerant cyanobacteria.Altogether, these results suggest that specific cyanobacterial taxa can benefit from freshwater salinization following the collapse of dominant phytoplankton competitors and zooplankton herbivores. The results also highlight the value of autonomous sensor technology to capture novel, small‐scale ecological responses to freshwater salinization, and thereby to track fast changes in primary producer communities. [ABSTRACT FROM AUTHOR]

Recent studies have shown a decoupling in the way community composition and functions respond to environmental changes. A common pattern observed is that aggregated functions at the community level are more stable than community composition, which is likely the result of functional compensatory dynamics driven by interspecific differences in response to environmental change. However, the mechanisms by which these patterns emerge remain largely unexplored. Here we investigated in a mesocosm experiment for four weeks the compositional and functional responses of edible phytoplankton (<64 μm) and cladoceran zooplankton communities to climate warming (a constant increase of +3.5°C plus heat wave) and eutrophication (nutrient additions) from a size‐based perspective. Our results show that warming increases small‐sized taxa and decreases large‐sized taxa within both phytoplankton and zooplankton community composition. We found that such opposite responses of different‐sized taxa contributed to the stability of planktonic community functions and thereby resulted in a decoupling between compositional and functional changes. We also found that nutrient additions increased the abundance of all‐sized algal taxa, while phytoplankton community function remained stable. Nutrient additions did not alter the zooplankton community, neither compositionally nor functionally. Under the combined stress of warming and nutrient additions, the compositional and functional responses of planktonic communities were mainly driven by warming. In a broader perspective, our findings reveal a size‐dependent compensation mechanism and suggest that functional stability relies on compensatory effects among different‐sized taxa, and it is therefore important that communities host a large range of taxa differing in size to withstand an increasingly more variable environment in the future. [ABSTRACT FROM AUTHOR]

Ecological stability encompasses multiple dimensions of functional and compositional responses to environmental change. Though no single stability dimension used in isolation can fully reflect the overall response to environmental change, a common vulnerability assessment that integrates simultaneously across multiple stability components is highly desirable for ecological risk assessment.We develop both functional and compositional counterparts of a novel, integrative metric of overall ecological vulnerability (OEV). We test the framework with data from a modularized experiment replicated in five lakes over two seasons, examining functional and compositional responses to both pulse and press disturbances across three trophic groups. OEV is measured as the area under the curve integrated over the entire observation period, with the curve delimiting the difference between the disturbance treatment and undisturbed parallel controls, expressed either as the log response ratio of biomass (functional OEV) or community dissimilarity index (compositional OEV).Both, functional and compositional OEV correlated negatively with functional and compositional 'resistance', 'temporal stability' and 'final/extent of recovery' following both pulse and press disturbances, though less so with 'resilience' following a pulse disturbance. We also found a positive correlation between functional and compositional OEV, which reveals the potential to also evaluate the intricate linkage between biodiversity and functional change.Our findings demonstrate that OEV comprises a robust framework to: (a) capture simultaneously multiple functional and compositional stability components, and (b) quantify the functional consequences of biodiversity change. Our results provide the basis for an overarching framework for quantifying the overall vulnerability of ecosystems to environmental change, opening new possibilities for ecological risk assessment and management.Synthesis. Ecological stability comprises multiple dimensions that together encapsulate how ecosystems respond to environmental change. Considering these multiple aspects of stability simultaneously often poses a problem in environmental assessments, which frequently require overarching indicators of risk or vulnerability. While an analysis of multiple dimensions allows for deeper exploration of mechanisms, here we develop and test a new univariate indicator that integrates stability aspects under a broad range of disturbance regimes. Using a modularized experiment in Swedish lakes, we show that this integrative measure captures multiple stability dimensions reflecting compositional and functional vulnerability and their relationships between them. [ABSTRACT FROM AUTHOR]

Ecosystems worldwide are experiencing a range of natural and anthropogenic disturbances, many of which are intensifying as global change accelerates. Ecological responses to those disturbances are determined by both the vulnerabilities of species and their interspecific interactions. Understanding how individual species contribute to the (in‐)stability of an aggregated community property, or function, is fundamental to ecological management and conservation. Here, we present a framework to identify species contributions to stability based on their absolute and relative responses to disturbances. Using simulations, we show that these two dimensions enable identification of (de‐)stabilizing species and reveal that competitive dominance determines the magnitude of both absolute and relative contributions to stability. Applying our framework to empirical data from a multi‐site mesocosm experiment showed that species contributions varied among treatments, sites, and seasons. Despite this dependency on both biotic and abiotic contexts, species contributions were generally constrained by their relative dominance in undisturbed conditions. Rare species contributed positively to stability, while dominant species contributed negatively, indicating compensatory dynamics. Our framework offers an important step toward a more mechanistic understanding of ecological stability based on species performance. [ABSTRACT FROM AUTHOR]