100 years of anthropogenic impact causes changes in freshwater functional biodiversity

Despite efforts from scientists and regulators, biodiversity is declining at an alarming rate. Unless we find transformative solutions to preserve biodiversity, future generations may not be able to enjoy nature's services. We have developed a conceptual framework that establishes the links between biodiversity dynamics and abiotic change through time and space using artificial intelligence. Here, we apply this framework to a freshwater ecosystem with a known history of human impact and study 100 years of community-level biodiversity, climate change and chemical pollution trends. We apply explainable network models with multimodal learning to community-level functional biodiversity measured with multilocus metabarcoding, to establish correlations with biocides and climate change records. We observed that the freshwater community assemblage and functionality changed over time without returning to its original state, even if the lake partially recovered in recent times. Insecticides and fungicides, combined with extreme temperature events and precipitation, explained up to 90% of the functional biodiversity changes. The community-level biodiversity approach used here reliably explained freshwater ecosystem shifts. These shifts were not observed when using traditional quality indices (e.g. Trophic Diatom Index). Our study advocates the use of high-throughput systemic approaches on long-term trends over species-focused ecological surveys to identify the environmental factors that cause loss of biodiversity and disrupt ecosystem functions.

Time after time: Detecting annual patterns in stream bacterial biofilm communities

To quantify the major environmental drivers of stream bacterial population dynamics, we modelled temporal differences in stream bacterial communities to quantify community shifts, including those relating to cyclical seasonal variation and more sporadic bloom events. We applied Illumina MiSeq 16S rRNA bacterial gene sequencing of 892 stream biofilm samples, collected monthly for 36‐months from six streams. The streams were located a maximum of 118 km apart and drained three different catchment types (forest, urban and rural land uses). We identified repeatable seasonal patterns among bacterial taxa, allowing their separation into three ecological groupings, those following linear, bloom/trough and repeated, seasonal trends. Various physicochemical parameters (light, water and air temperature, pH, dissolved oxygen, nutrients) were linked to temporal community changes. Our models indicate that bloom events and seasonal episodes modify biofilm bacterial populations, suggesting that distinct microbial taxa thrive during these events including non‐cyanobacterial community members. These models could aid in determining how temporal environmental changes affect community assembly and guide the selection of appropriate statistical models to capture future community responses to environmental change.

Reconstructing Long-Term Changes in Avian Populations Using Lake Sediments: Opening a Window Onto the Past

The lack of long-term monitoring data for many wildlife populations is a limiting factor in establishing meaningful and achievable conservation goals. Even for well-monitored species, time series are often very short relative to the timescales required to understand a population’s baseline conditions before the contemporary period of increased human impacts. To fill in this critical information gap, techniques have been developed to use sedimentary archives to provide insights into long-term population dynamics over timescales of decades to millennia. Lake and pond sediments receiving animal inputs (e.g., feces, feathers) typically preserve a record of ecological and environmental information that reflects past changes in population size and dynamics. With a focus on bird-related studies, we review the development and use of several paleolimnological proxies to reconstruct past colony sizes, including trace metals, isotopes, lipid biomolecules, diatoms, pollen and non-pollen palynomorphs, invertebrate sub-fossils, pigments, and others. We summarize how animal-influenced sediments, cored from around the world, have been successfully used in addressing some of the most challenging questions in conservation biology, namely: How dynamic are populations on long-term timescales? How may populations respond to climate change? How have populations responded to human intrusion? Finally, we conclude with an assessment of the current state of the field, challenges to overcome, and future potential for research.

Sediment archives reveal irreversible shifts in plankton communities after World War II and agricultural pollution

To evaluate the stability and resilience¹ of coastal ecosystem communities to perturbations that occurred during the Anthropocene,² pre-industrial biodiversity baselines inferred from paleoarchives are needed.^3,4 The study of ancient DNA (aDNA) from sediments (sedaDNA)⁵ has provided valuable information about past dynamics of microbial species^6-8 and communities^9-18 in relation to ecosystem variations. Shifts in planktonic protist communities might significantly affect marine ecosystems through cascading effects,^19-21 and therefore the analysis of this compartment is essential for the assessment of ecosystem variations. Here, sediment cores collected from different sites of the Bay of Brest (northeast Atlantic, France) allowed ca. 1,400 years of retrospective analyses of the effects of human pollution on marine protists. Comparison of sedaDNA extractions and metabarcoding analyses with different barcode regions (V4 and V7 18S rDNA) revealed that protist assemblages in ancient sediments are mainly composed of species known to produce resting stages. Heavy-metal pollution traces in sediments were ascribed to the World War II period and coincided with community shifts within dinoflagellates and stramenopiles. After the war and especially from the 1980s to 1990s, protist genera shifts followed chronic contaminations of agricultural origin. Community composition reconstruction over time showed that there was no recovery to a Middle Ages baseline composition. This demonstrates the irreversibility of the observed shifts after the cumulative effect of war and agricultural pollutions. Developing a paleoecological approach, this study highlights how human contaminations irreversibly affect marine microbial compartments, which contributes to the debate on coastal ecosystem preservation and restoration.

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

Landscape Setting Drives the Microbial Eukaryotic Community Structure in Four Swedish Mountain Lakes over the Holocene

On the annual and interannual scales, lake microbial communities are known to be heavily influenced by environmental conditions both in the lake and in its terrestrial surroundings. However, the influence of landscape setting and environmental change on shaping these communities over a longer (millennial) timescale is rarely studied. Here, we applied an 18S metabarcoding approach to DNA preserved in Holocene sediment records from two pairs of co-located Swedish mountain lakes. Our data revealed that the microbial eukaryotic communities were strongly influenced by catchment characteristics rather than location. More precisely, the microbial communities from the two bedrock lakes were largely dominated by unclassified Alveolata, while the peatland lakes showed a more diverse microbial community, with Ciliophora, Chlorophyta and Chytrids among the more predominant groups. Furthermore, for the two bedrock-dominated lakes-where the oldest DNA samples are dated to only a few hundred years after the lake formation-certain Alveolata, Chlorophytes, Stramenopiles and Rhizaria taxa were found prevalent throughout all the sediment profiles. Our work highlights the importance of species sorting due to landscape setting and the persistence of microbial eukaryotic diversity over millennial timescales in shaping modern lake microbial communities.

Anthropogenic impact on the historical phytoplankton community of Lake Constance reconstructed by multimarker analysis of sediment-core environmental DNA

During the 20th century, many lakes in the Northern Hemisphere were affected by increasing human population and urbanization along their shorelines and catchment, resulting in aquatic eutrophication. Ecosystem monitoring commenced only after the changes became apparent, precluding any examination of timing and dynamics of initial community change in the past and comparison of pre- and postimpact communities. Peri-Alpine Lake Constance (Germany) underwent a mid-century period of eutrophication followed by re-oligotrophication since the 1980s and is now experiencing warm temperatures. We extended the period for which monitoring data of indicator organisms exist by analysing historical environmental DNA (eDNA) from a sediment core dating back some 110 years. Using three metabarcoding markers-for microbial eukaryotes, diatoms and cyanobacteria-we revealed two major breakpoints of community change, in the 1930s and the mid-1990s. In our core, the latest response was exhibited by diatoms, which are classically used as palaeo-bioindicators for the trophic state of lakes. Following re-oligotrophication, overall diversity values reverted to similar ones of the early 20th century, but multivariate analysis indicated that the present community is substantially dissimilar. Community changes of all three groups were strongly correlated to phosphorus concentration changes, whereas significant relationships to temperature were only observed when we did not account for temporal autocorrelation. Our results indicate that each microbial group analysed exhibited a unique response, highlighting the particular strength of multimarker analysis of eDNA, which is not limited to organisms with visible remains and can therefore discover yet unknown responses and abiotic-biotic relationships.

Assessing the response of micro-eukaryotic diversity to the Great Acceleration using lake sedimentary DNA

Long-term time series have provided evidence that anthropogenic pressures can threaten lakes. Yet it remains unclear how and the extent to which lake biodiversity has changed during the Anthropocene, in particular for microbes. Here, we used DNA preserved in sediments to compare modern micro-eukaryotic communities with those from the end of the 19th century, i.e., before acceleration of the human imprint on ecosystems. Our results obtained for 48 lakes indicate drastic changes in the composition of microbial communities, coupled with a homogenization of their diversity between lakes. Remote high elevation lakes were globally less impacted than lowland lakes affected by local human activity. All functional groups (micro-algae, parasites, saprotrophs and consumers) underwent significant changes in diversity. However, we show that the effects of anthropogenic changes have benefited in particular phototrophic and mixotrophic species, which is consistent with the hypothesis of a global increase of primary productivity in lakes.