Pervasive changes in algal indicators since pre-industrial times: A paleolimnological study of changes in primary production and diatom assemblages from ~200 Canadian lakes

Phytoplankton responses to reduced freshwater inflow and acid conditions in a Ramsar estuarine lake

Global change pressures influence estuarine functionality, driving structural shifts that threaten ecosystem resilience. Estuarine lakes are inherently susceptible to these pressures given their tendency to experience prolonged periods of water residency and mouth closure. As such, this study aimed to investigate water quality and phytoplankton responses to drastic shifts in abiotic conditions during the transition from a dry to wet cycle in the Verlorenvlei Estuarine Lake, South Africa. Initially, drought- and human-induced hydrological constraints resulted in extreme environmental conditions, characterised by low water levels and acidification. These low water levels reduced connectivity, resulting in hypersaline conditions and phytoplankton blooms (>20 μg Chl-a L-1) in the lower reaches, while the main basin became brackish, highly acidic (pH < 4), and ammonium-rich (>10 mg/L). Conversely, increased flow improved connectivity, although the lower reaches remained hypersaline and pH in the main basin remained low. When the mouth was open, conditions became homogenous and oligohaline, with neutralised pH levels (>6.5) and low phytoplankton biomass (<5 μg Chl-a L-1). Upon mouth closure, the lower reaches shifted to mesohaline conditions, the main basin became acidic (pH < 5) and supported high-biomass (>60 μg Chl-a l-1) bloom conditions of non-siliceous taxa, and the upper reaches became disconnected. As such, it is critical for catchment-scale interventions to be implemented that conserve and restore freshwater inflow to dilute acidity and replenish the buffering capacity of the system. Without intervention, ongoing anthropogenic and climate change stressors may push the system towards an irreversible ecological tipping point.

Surface sediment elemental compositions of 167 Canadian lakes show widespread exceedance of quality guidelines for metals

Sediments form a key part of lake ecosystems and play important roles in biological and chemical processes. Yet in the most lake-rich country in the world, Canada, there was no standardized portrait of lake sediment elemental compositions and knowledge was lacking about how frequently field data exceeded sediment quality guidelines. To address these gaps and generate a more comprehensive understanding of large-scale spatial patterns in surface sediment geochemistry, we undertook an analysis of 167 lakes sampled by the NSERC Canadian Lake Pulse Network. We analyzed sediment elemental compositions and identified three geographic regions with distinct sediment geochemistry by applying a cascade multivariate regression tree analysis (cMRT). Of these regions, sediments in eastern Canada had relatively high concentrations of metals, while central Canada and southwestern Ontario lakes had relatively high concentrations of detrital elements. Urbanization was correlated with elevated sediment metal concentrations whereas agricultural and pastoral activities were correlated with elevated concentrations of detrital elements. Comparisons between sites with low and high levels of anthropogenic land use indicated limited differences in sediment elemental compositions. However, 70 % of all sites exceeded the guidelines for at least one of the six potentially toxic elements with published sediment quality guidelines that we examined. Since these guidelines were designed to be conservative, we recommend the development of regional sediment quality guidelines for implementation across Canada.

Diatom species responses along gradients of dissolved inorganic carbon, total phosphorus, and lake depth from lakes across Canada

Diatoms are key components of freshwater ecosystems and are regularly used for paleolimnological reconstructions, in which defining species optima and tolerances is fundamental for interpreting assemblage shifts in a sediment record. Here, we examined responses of diatoms across three major environmental gradients-dissolved inorganic carbon (range: 0.1-230.5 mg · L-1), total phosphorus (range: 3-326 μg · L-1), and maximum lake depth (range: 0.9-55.0 m)-taken from 158 lakes from across Canada. The lakes were sampled as part of the LakePulse Network, which conducted a standardized sampling of lakes spanning 12 Canadian ecozones. Hierarchical logistic regression was used to model the species responses of 37 common taxa, and species optima and tolerances were calculated with weighted average modeling. The most common response detected was the symmetrical unimodal model, suggesting we likely captured the full environmental ranges for many species, although skewed unimodal responses were also common. Indicator species analyses identified taxa with high predictive values and fidelities to particular ecozones, with high-nutrient-adapted taxa such as Stephanodiscus spp. and Cyclotella meneghiniana characteristic of the agriculturally productive Prairie region. The Prairies stood out in the dataset as the region with the most unique flora from the local contribution to beta diversity analysis. Overall, the autecological data provided by our study will allow for improved interpretations of paleolimnological records and other biomonitoring efforts, addressing management concerns and contributing to a better understanding of our changing environment.

Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long-term microscopy-based monitoring of the phytoplankton community

Palaeolimnological records provide valuable information about how phytoplankton respond to long-term drivers of environmental change. Traditional palaeolimnological tools such as microfossils and pigments are restricted to taxa that leave sub-fossil remains, and a method that can be applied to the wider community is required. Sedimentary DNA (sedDNA), extracted from lake sediment cores, shows promise in palaeolimnology, but validation against data from long-term monitoring of lake water is necessary to enable its development as a reliable record of past phytoplankton communities. To address this need, 18S rRNA gene amplicon sequencing was carried out on lake sediments from a core collected from Esthwaite Water (English Lake District) spanning ~105 years. This sedDNA record was compared with concurrent long-term microscopy-based monitoring of phytoplankton in the surface water. Broadly comparable trends were observed between the datasets, with respect to the diversity and relative abundance and occurrence of chlorophytes, dinoflagellates, ochrophytes and bacillariophytes. Up to 20% of genera were successfully captured using both methods, and sedDNA revealed a previously undetected community of phytoplankton. These results suggest that sedDNA can be used as an effective record of past phytoplankton communities, at least over timescales of <100 years. However, a substantial proportion of genera identified by microscopy were not detected using sedDNA, highlighting the current limitations of the technique that require further development such as reference database coverage. The taphonomic processes which may affect its reliability, such as the extent and rate of deposition and DNA degradation, also require further research.

A genome catalogue of lake bacterial diversity and its drivers at continental scale

Lakes are heterogeneous ecosystems inhabited by a rich microbiome whose genomic diversity is poorly defined. We present a continental-scale study of metagenomes representing 6.5 million km2 of the most lake-rich landscape on Earth. Analysis of 308 Canadian lakes resulted in a metagenome-assembled genome (MAG) catalogue of 1,008 mostly novel bacterial genomospecies. Lake trophic state was a leading driver of taxonomic and functional diversity among MAG assemblages, reflecting the responses of communities profiled by 16S rRNA amplicons and gene-centric metagenomics. Coupling the MAG catalogue with watershed geomatics revealed terrestrial influences of soils and land use on assemblages. Agriculture and human population density were drivers of turnover, indicating detectable anthropogenic imprints on lake bacteria at the continental scale. The sensitivity of bacterial assemblages to human impact reinforces lakes as sentinels of environmental change. Overall, the LakePulse MAG catalogue greatly expands the freshwater genomic landscape, advancing an integrative view of diversity across Earth's microbiomes.