Timely and accurate biodiversity analysis poses an ongoing challenge for the success of biomonitoring programs. Morphology-based identification of bioindicator taxa is time consuming, and rarely supports species-level resolution especially for immature life stages. Much work has been done in the past decade to develop alternative approaches for biodiversity analysis using DNA sequence-based approaches such as molecular phylogenetics and DNA barcoding. On-going assembly of DNA barcode reference libraries will provide the basis for a DNA-based identification system. The use of recently introduced next-generation sequencing (NGS) approaches in biodiversity science has the potential to further extend the application of DNA information for routine biomonitoring applications to an unprecedented scale. Here we demonstrate the feasibility of using 454 massively parallel pyrosequencing for species-level analysis of freshwater benthic macroinvertebrate taxa commonly used for biomonitoring. We designed our experiments in order to directly compare morphology-based, Sanger sequencing DNA barcoding, and next-generation environmental barcoding approaches. Our results show the ability of 454 pyrosequencing of mini-barcodes to accurately identify all species with more than 1% abundance in the pooled mixture. Although the approach failed to identify 6 rare species in the mixture, the presence of sequences from 9 species that were not represented by individuals in the mixture provides evidence that DNA based analysis may yet provide a valuable approach in finding rare species in bulk environmental samples. We further demonstrate the application of the environmental barcoding approach by comparing benthic macroinvertebrates from an urban region to those obtained from a conservation area. Although considerable effort will be required to robustly optimize NGS tools to identify species from bulk environmental samples, our results indicate the potential of an environmental barcoding approach for biomonitoring programs.

Biological monitoring has failed to develop from simple binary assessment outcomes of the impacted/unimpacted type, towards more diagnostic frameworks, despite significant scientific effort over the past fifty years. It is our assertion that this is largely because of the limited information content of biological samples processed by traditional morphology‐based taxonomy, which is a slow, imprecise process, focused on restricted groups of organisms. We envision a new paradigm in ecosystem assessment, which we refer to as ‘Biomonitoring 2.0’. This new schema employs DNA‐based identification of taxa, coupled with high‐throughput DNA sequencing on next‐generation sequencing platforms. We discuss the transformational nature of DNA‐based approaches in biodiversity discovery and ecosystem assessment and outline a path forward for their future widespread application.

Summary1. Species traits have been frequently used in ecological studies in an attempt to develop a general ecological framework linking biological communities to habitat pressures. The trait approach offers a mechanistic alternative to traditional taxonomy-based descriptors. This review focuses on research employing traits as biomonitoring tools for freshwater ecosystems, although the lessons learned have wider application in the assessment of other ecosystem types. 2. We review the support from ecological theory to employ species traits for biomonitoring purposes (e.g. the habitat templet concept, landscape filtering hypothesis), and the subsequent studies that test the hypotheses arising from these theories, and apply this knowledge under real freshwater biomonitoring scenarios. We also include studies that deal with more specific issues such as trait trade-offs and trait syndromes. 3. We highlight the functional trait approach as one of the most promising tools emerging for biomonitoring freshwater ecosystems. Several technical issues are addressed and solutions are proposed. We discuss the need for: a broader unified trait biomonitoring tool; a more accurate understanding of the natural variation of community patterns of trait expression; approaches to diminish the effects of trait trade-offs and trait syndromes; additional life history and ecological requirement studies; and the detection of specific impacts under multiple stressor scenarios. 4. Synthesis and applications. This review provides biologists with the conceptual underpinning for the use of species traits as community descriptors and for freshwater biomonitoring and management. We expect that the functional trait approach will ultimately improve communication to managers and legislators of the importance of protecting freshwater ecosystem functions.

Biodiversity metrics are critical for assessment and monitoring of ecosystems threatened by anthropogenic stressors. Existing sorting and identification methods are too expensive and labour-intensive to be scaled up to meet management needs. Alternately, a high-throughput DNA sequencing approach could be used to determine biodiversity metrics from bulk environmental samples collected as part of a large-scale biomonitoring program. Here we show that both morphological and DNA sequence-based analyses are suitable for recovery of individual taxonomic richness, estimation of proportional abundance, and calculation of biodiversity metrics using a set of 24 benthic samples collected in the Peace-Athabasca Delta region of Canada. The high-throughput sequencing approach was able to recover all metrics with a higher degree of taxonomic resolution than morphological analysis. The reduced cost and increased capacity of DNA sequence-based approaches will finally allow environmental monitoring programs to operate at the geographical and temporal scale required by industrial and regulatory end-users.

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For the past 20 years, research on biodiversity and ecosystem functioning (B-EF) has only implicitly considered the underlying role of environmental change. We illustrate that explicitly re-introducing environmental change drivers in B-EF research is needed to predict the functioning of ecosystems facing changes in biodiversity. Next, we show how this reintroduction improves experimental control over community composition and structure, which helps to obtain mechanistic insight about how multiple aspects of biodiversity relate to function, and how biodiversity and function relate in food-webs. We also highlight challenges for the proposed re-introduction, and suggest analyses and experiments to better understand how random biodiversity changes, as studied by classic approaches in B-EF research, contribute to the shifts in function that follow environmental change.

Predator-generated variation in prey energy intake remains the dominant explanation of adaptive response to predation risk in prey life history, morphology and physiology across a wide range of taxa. This "behavioural hypothesis" suggest that chemical or visual signals of predation risk reduce prey energy intake leading to a life history characterized by a small size and late age at maturity. However, size-selective predation can induce either smaller size-early age or large size-late age life history. The alternative "physiological hypothesis" suggests that size-selective cues decouple the relationship between energy and life history, acting instead directly on development. Here we use a series of experiments in a fish-daphnid predator-prey system to ask whether size-selective predator cues induce a physiological mediation of development, overshadowing behaviourally based changes in food intake. We found fish chemical cues reduce the net energy intake in Daphnia magna, suggesting a behaviourally mediated reduction in energy. Experimental manipulation of food levels show further that reductions in food lead to later but smaller size at maturity. However, in line with the physiological hypothesis, we show that D. magna matures earlier and at a smaller size when exposed to fish predation cues. Furthermore, our data shows that they do this by increasing their development rate (earlier maturity) for a given growth rate, resulting in a smaller size at maturity. Our data, from a classic size-selective predation system, indicate that predator-induced changes in this system are driven by physiological mediation of development rather than behavioural mediation of energy intake.

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