100 years of anthropogenic impact causes changes in freshwater functional biodiversity

Reviewer #1 (Public Review):

This study presents a conceptual and analytical framework for tracking the impacts of human activities on freshwater ecosystems over time. It demonstrates the application of the framework to a 100-year record of community-level biodiversity, climate change, and chemical pollution from sediments cores of Lake Ring, Denmark. By reconstructing biodiversity using environmental DNA (eDNA) and pollutant inputs using mass spectrometry, the authors identify the taxonomic groups responding positively and negatively in different phases of the lake's environmental history. Furthermore, they identify the independent and additive effects of climate variables and pollutants on biodiversity throughout the 100-year record.

Strengths:

The advances in paired molecular and machine learning analyses are an important step towards a better understanding of 20th/21st century trajectories of biodiversity and pollution.

The finding that taxonomic groups so central to ecosystem assessment in Europe (i.e., diatoms) do not appear to respond to degradation or amelioration - providing at least a partial explanation as to why "ecological status" (as defined under the EU Water Framework Directive) has proved so difficult to improve.

The framework shows how both taxonomic and functional indicators can be used to better understand ecological degradation and recovery.

The identification of individual biocides and climate variables driving observed changes is a particular strength.

Limitations:

The analytical framework is not sufficiently explained in the main text.

The significance of findings in relation to functional changes is not clear. What are the consequences of enrichment of RNA transport or ribosome biogenesis pathways between pesticides and recovery stages, for example?

The impact of individual biocides and climate variables, and their additive effects, are assessed but there is no information offered on non-additive interactions (e.g., synergistic, antagonistic).

The level of confidence associated with results is not made explicit. The reader is given no information on the amount of variability involved in the observations, or the level of uncertainty associated with model estimates.

The major implications of the findings for regulatory ecological assessment are missed. Regulators may not be primarily interested in identifying past "ecosystem shifts". What they need are approaches which give greater confidence in monitoring outcomes by better reflecting the ecological impact of contemporary environmental change and ecosystem management. The real value of the work in this regard is that: (1) it shows that current approaches are inappropriate due to the relatively stable nature of the indicators used by regulators, despite large changes in pollutant inputs; (2) it presents some better alternatives, including both taxonomic and functional indicators; and (3) it provides a new reference (or baseline) for regulators by characterizing "semi-pristine" conditions.

Reviewer #2 (Public Review):

This study highlights the importance of including not only spatio-termporal scales to biodiversity assessments, but also to include some of the possible drivers of biodiversity loss and to study their joint contribution as environmental stressors.

Introduction - Well written and placed within the current trends of unprecedented biodiversity loss, with an emphasis on freshwater ecosystems. The authors identify three important points as to why biodiversity action plans have failed. Namely, community changes occur over large spatio-temporal scales and monitoring programs capture a fraction of these long-term dynamics (e.g. few decades) which although good at capturing trends in biodiversity change, they often fail at identifying the drivers of these changes. Additionally, most of these rely on manual sorting of samples, overlooking cryptic diversity, or state-of-the-art techniques such as sedimentary DNA (sedaDNA) which allow studying decade-long dynamics, usually focus on specific taxonomic groups unable to represent community-level changes. Secondly, the authors identify that biodiversity is threatened by multiple factors and are rarely studied in tandem. Finally, the authors stress the need for high-throughput approaches to study biodiversity changes since historically, most conservation efforts rely on highly specialized skills for biodiversity monitoring, and even well-studied species have relatively short time series data. The authors identify a model freshwater lake (Lake Ring, Denmark) - suitable due to its well-documented history over the last 100 years - to present a comprehensive framework using metabarcoding, chemical analysis and climatic records for identifying past and current impacts on this ecosystem arising from multiple abiotic environmental stressors.

Results - They are brief and should expand some more. Particularly, there are no results regarding metabarcoding data (number of reads, filtering etc.). These details are important to know the quality of the data which represents the bulk of the analyses. Even the supplementary material gives little information on the metabarcoding results (e.g. number of ASVs - whether every ASV of each family were pooled etc.). The drivers of biodiversity change section could be restructured and include main text tables showing the families positively or negatively correlated with the different variables (akin to table S2 but simplified).

Discussion
The discussion is well written, identifying first some of the possible caveats of this study, particularly regarding the classification of metabarcoding data, its biases and the possible DNA degradation of ancient sediment DNA. The authors discuss how their results fit to general trends showing how agricultural runoff and temperature drive changes in freshwater functional biodiversity primarily due to their synergistic effects on bioavailability, adsorption, etc. The authors highlight the advantage of using a system-level approach rather than focusing on taxa-specific studies due to their indicator status. Similarly, the authors justify the importance of studying community composition as far back as possible since it reveals unexpected patterns of ecosystem resilience. Lake Ring, despite its partially recovered status, has not returned to its semi-pristine levels of biodiversity and community assemblage. Additionally, including enzyme activity allows to assess the functional diversity of the studied environment, although reference databases of these pathways are still lacking. Finally, the authors discuss the implications of their findings under a conservation and land management framework suggesting that by combining these different approaches, drivers of biodiversity stressors can be derived with high accuracy allowing for better-informed mitigation and conservation efforts.