In the past 50 years, there has been an apparent increase in the frequency and magnitude of abrupt change in large freshwater ecosystems, including from altered nutrient fluxes, invasive species, and climate. However, often relatively little is known of historical changes in ecosystem function due to difficulties in representative sampling. We used paleoecological analysis of multiple biological (diatoms, chironomids, fossil pigments), geochemical (organics, carbonates, mineral, biogenic silica, C/N isotopes), and sedimentary DNA (sedDNA, specifically botulinum neurotoxin BONT/E gene copies) proxies in three sediment cores to quantify timing, extent, and causes of ecosystem change over the past 150 years in northeast Lake Michigan and evaluate the role of nearshore food-web variability in recent botulism outbreaks. Sediment cores preserved records of nearshore food web changes including shifting phytoplankton, historical eutrophication and recent oligotrophication, nearshore energy shunt, and restructuring of the nearshore food web and ecology. The deepest station sediments recorded significant changes in the early 1900s in response to Euro-American settlement, catchment development, and whole-lake eutrophication. Principal coordinates analysis of biological sediment proxies also identified unprecedented historical changes in primary and secondary producer communities in the late 1990s–early 2000s at all nearshore stations, with particularly marked changes in diatom community structure, primary producer biomass, and chironomid assemblages. Further, sedimentary analyses implicate changes in Cladophora abundance and the nearshore benthic food-web as important recent covariates of increased prevalence of Clostridium botulinum. Together, these findings suggest that large-scale changes in offshore ecosystems are amplified in coastal regions in large lakes and may be important regulators of aquatic disease transmission.

Headwater streams are reliant on riparian tree leaf litterfall to fuel brown food webs. Terrestrial agents like herbivores and contaminants can alter plant growth, litter production, litter quality, and the timing of litterfall into streams, influencing aspects of the brown food web. At Mount St. Helens (USA), early successional streams are developing willow (Salix sitchensis) riparian zones. The willows are attacked by stem-boring herbivores, altering litter quality and the timing of litterfall. Within a established experimental plots, willows (male and female plants) were protected from herbivores using insecticides and provided with experimental additions of nitrogen. This enabled us to test the interacting influences of herbivores, nitrogen deposition, and willow sex on leaf litter quality, aquatic litter decomposition, and microbial and invertebrate detritivores. We found weak litter quality effects (higher N and lower C:N) for the herbivore treatment, but no effect of nitrogen deposition. Although litter decomposition rates were not strongly affected by litter treatments, detritivore communities were altered by all treatments. Nitrogen deposition resulted in decreased bacterial richness and decreased fungal diversity in-stream. Aquatic macroinvertebrate communities were influenced by the interacting effects of herbivory and nitrogen addition, with abundances highest in herbivore litter with the greatest N addition. Shredders showed the highest abundance in male, herbivore-attacked litter. The establishment of riparian willows along early successional streams and their interacting effects with herbivores and nitrogen deposition may be influencing detritivore community assembly at Mount St. Helens. More broadly, global changes like increased wet and dry N deposition and expanded ranges of key herbivores might influence tree litter decomposition in many ecosystems.

Determining how streams develop naturally, particularly the ecological role of newly developed riparian canopy cover, is essential to understanding the factors that structure new stream communities and provides valuable information for restoring highly disturbed ecosystems. However, attempts to understand primary succession in riverine ecosystems have been hindered by a lack of data owing to the infrequent formation of new rivers on the landscape. In the present study, we used five streams formed following the 1980 eruption of Mount St. Helens (WA, USA) to examine the influence of canopy cover development on algal and benthic macroinvertebrate assemblages, biomass, and organic matter processing. Newly established closed canopy reaches had less available light, but no significant differences in algal biomass or macroinvertebrate assemblages compared to open canopy reaches. Instead, algal and macroinvertebrate communities were structured mainly by hydrologic differences among watersheds. In contrast, organic matter processing rates were sensitive to canopy cover development, and rates were faster under closed canopies, especially in late summer or after terrestrial preconditioning. After 40 years of stream and riparian primary successional development, canopy cover strongly influences ecosystem function, but aquatic organism assembly was more influenced by physio-chemical and hydrologic variation. Our findings provide insight into the development of in-stream assemblages and ecosystem functions, which is also relevant to efforts to address major disturbances to stream channels, such as volcanic eruptions, floods, forest fires, and clear-cut logging.

The eruption of Mount St. Helens in 1980 resulted in a cataclysmic restructuring of its surrounding landscapes. The Pumice Plain is one of these landscapes, where tree species such as Sitka willow (Salix sitchensis) and their dependent communities have been established along newly-formed streams. Thus, the study of these dependent communities provides a unique and rare opportunity to investigate factors influencing metacommunity assembly during true primary succession. We analyzed the influence of landscape connectivity on metacommunity assembly through a novel application of circuit theory, alongside the effects of other factors such as stream locations, willow leaf chemistry, and leaf area. We found that landscape connectivity structures community composition on willows across the Pumice Plain, where the least connected willows favored active flyers such as the western tent caterpillar (Malacosoma fragilis) or the Pacific willow leaf beetle (Pyrrhalta decora carbo). We also found that multiple levels of spatial habitat structure linked via landscape connectivity can predict the presence of organisms lacking high rates of dispersal, such as the invasive stem-boring poplar weevil (Cryptorhynchus lapathi). This is critical for management as we show that the maintenance of a heterogeneous mixture of landscape connectivity and resource locations can facilitate metacommunity dynamics to promote ecosystem function and mitigate the influences of invasive species.

Major disturbances fundamentally alter ecosystems through the transformation of both biotic and abiotic factors. The eruption of Mount St. Helens in 1980 resulted in a cataclysmic restructuring of its surrounding landscapes. The Pumice Plain is one of these landscapes, where tree species such as Sitka willow (Salix sitchensis) and their dependent communities have established along newly-formed streams. Thus, the study of these dependent communities provides a unique opportunity to investigate factors influencing metacommunity assembly during true primary succession. We analyzed the influence of landscape connectivity on metacommunity assembly through a novel application of circuit theory, alongside the effects of other factors such as stream locations, willow leaf chemistry, and leaf area. We found that landscape connectivity structures community composition on willows across the Pumice Plain, while our other factors had varied effects. Most importantly, multiple levels of spatial habitat structure linked via landscape connectivity can predict the presence of organisms lacking high rates of dispersal, such as the invasive stem-boring poplar weevil (Cryptorhynchus lapathi). This is critical for management as we show that the maintenance of a heterogeneous mixture of landscape connectivities and resource locations can facilitate meta-community dynamics to promote ecosystem function and mitigate the influences of invasive species.

Leaf litter inputs can influence the structure and function of both terrestrial and adjacent aquatic ecosystems. Dioecy and herbivory are two factors that together have received little attention, yet have the potential to affect the quantity, quality, and timing of riparian litterfall, litter chemistry, and litter decomposition processes. Here, we explore litter chemistry differences for the dioecious Sitka willow (Salix sitchensis Sanson ex. Bong), which is establishing on primary successional habitats at Mount St. Helens (WA, USA) and is heavily infested with a stem-boring weevil (Cryptorhynchus lapathi). Weevil-attacked branches produced summer senesced litter that had significantly higher %N, lower C:N ratios, and lower condensed tannins than litter from branches that were unattacked by the weevil and senesced naturally in the autumn. Weevils more often attack female willows; however, these common litter chemicals did not significantly differ between males and females within the weevil-attacked and -unattacked groups. High-resolution mass spectrometry was used to isolate compounds in litter from 10 Sitka willow individuals with approximately 1500-1600 individual compounds isolated from each sample. There were differences between weevil-attacked litter and green leaf samples, but at this level, there was no clustering of male and female samples. However, further exploration of the isolated compounds determined a suite of compounds present only in either males or females. These findings suggest some variation in more complex litter chemistry between the sexes, and that significant differences in weevil-attacked litter chemistry, coupled with the shift in seasonality of litter inputs to streams, could significantly affect in-stream ecological processes, such as decomposition and detritivore activity.

We examined the recent paleolimnological diatom record from 109 mostly Minnesota (USA) lakes to determine whether anthropogenic impacts could be detected across a large geographic region and associated with a known stressor such as agriculture or climate change. Four periods of diatom assemblage reorganization were observed: (1) a pre-impact period; (2) a period of early Euro-American settlement and development; (3) a mid-20th century period of stabilization in impacts likely related to remediation and landscape recovery; and (4) a recent period of rapid change likely due to multiple stressors. Shallow and deep lakes expressed variations in their taxonomic character and historical changes in the diatom assemblages, but the amount of change was not specifically associated with contemporary agricultural or modern in-lake nutrient status. Lake depth is a major determinant of how a lake will respond to stressors and manifest change in primary producers; however, lake- or ecoregion-specific considerations will continue to inform lake management. Cultural eutrophication caused several of these historical changes to algal communities, but it is apparent that the amount of recent assemblage reorganization is a result of multiple concurrent stressors that may include climate change and the effects of non-native species infestations.

Lakes in protected or remote regions are not immune to anthropogenic impacts and face a variety of stressors ranging from atmospheric deposition of pollutants to global climate change. Monitoring programs in these lakes can be limited in scope due to sampling logistics, leaving an incomplete picture of how the systems may be impacted by environmental stressors. Here, we used diatoms as early indicators of change in relatively undisturbed lakes from five national park units in the US Great Lakes region. Surface sediment samples were collected repeatedly over more than a decade to analyze the diatom community turnover. This diatom community assemblage data were compared with the measured water quality data collected over the same period in order to identify the predominant drivers of ecological change. Even though the parks in this study span two biomes, and lake characteristics vary between and within parks, we found synchronicity in measured water quality trends and diatom responses. Changes in the thermal regime and water-column mixing appeared to drive much of the change across parks, although much of the diatom turnover also followed a sulfate or pH gradient. Nutrients did not appear to play a major role in diatom community change. This method of using diatoms in conjunction with water quality monitoring allows for an integrated response over a number of years and provides managers with a complementary tool to determine which environmental parameters are having the biggest effect on lake ecology.

Evidence suggests that boreal-lake ecosystems are changing rapidly, but with variable ecological responses, due to climate warming. Paleolimnological analysis of 27 undeveloped northern forested lakes showed significant and potentially climate-mediated shifts in diatom communities and increased carbon and biogenic silica burial. We hypothesize the sensitivity of northern forested lakes to climate change will vary along two physical gradients: one reflecting direct, in-lake climate effects (propensity to thermally stratify), the other reflecting indirect watershed effects (watershed to lake-surface area ratio). We focus on the historical response of algal communities to test our two-dimensional sensitivity framework. Historical algal response was summarized by measures of diatom community turnover, changes in species and diagnostic species groups, and measures of siliceous algal and overall primary production (biogenic silica, carbon burial). Measures of algal production increased across all lake types, with carbon burial proportionately higher in polymictic lakes. Greater diatom community change occurred in deep, stratified lakes with smaller watersheds, whereas diatom species groups showed variable responses along our two-dimensional sensitivity framework. Physical characteristics of lakes and watersheds could serve as predictors of sensitivity to climate change based on paleo-indicators that are mechanistically linked to direct and indirect limnological effects of climate change.

The influences of inter- and intraspecific variation in leaf litter quality on aquatic food webs are well understood. However, the timing and type of organic matter inputs also varies within a species based on plant phenophase, including litterfall and flowering, which may influence instream communities and ecosystem processes including decomposition. We investigated how leaf and flower litters of a willow shrub species (Salix sitchensis) influenced decomposition and aquatic invertebrate colonization in a headwater stream. We collected abscised willow catkins and leaves from female plants, analyzed their initial chemistry, constructed litterbags, and incubated them at our stream site for five weeks. A subset of litterbags of each litter type was retrieved at 7, 22, and 37 days and analyzed for litter decomposition and invertebrate colonization. We found significant differences between catkins and leaves. Catkins had lower initial condensed tannin concentrations and higher invertebrate colonization compared to leaves. Initial leaching losses were faster for leaves, but overall decomposition rates were comparable. Catkin structural complexity supported higher invertebrate abundance and diversity as well as altered community composition, indicating their unique contribution to stream ecosystems. Although the ratio of reproductive to leaf inputs is low, we argue that the sequential availability of these two litter types may provide complementary energy inputs to consumers in headwater stream ecosystems dependent on organic matter.

Abstract A growing body of research shows that plant genetic factors can influence ecosystem processes and structure communities, but one aspect that has received little study is sex differentiation in dioecious plants. Since headwater streams are reliant on riparian leaf litterfall, plant sex differences in leaf traits may influence in‐stream processes. Sitka willow (Salix sitchensis) at Mount St. Helens is dioecious and heavily infested with the stem‐boring weevil (Cryptorhynchus lapathi), which causes branch dieback and summer litterfall. We found that female willow shrubs tend to grow closer to the stream bank, are more likely to be infected by the weevil, and have 42% higher litter C:N than male willows. These factors may lead to increased litter inputs and slower litter mass loss for female willows. The combination of colonization location, herbivore attack, altered litter quality, and slower mass loss results in female shrubs providing more sustained carbon and nutrient resources to microbes and invertebrates in the early successional streams at Mount St. Helens. In addition, since dioecy is a relatively common trait in riparian habitats, it is possible that plant sex plays a far more interesting role in structuring linked terrestrial–aquatic communities and ecosystem processes than previously understood.

Climate disrupts aquatic ecosystems directly through changes in temperature, wind, and precipitation, and indirectly through watershed effects. Climate-induced changes in northern lakes include longer ice-free season, stronger stratification, browning, shifts in algae, and more cyanobacterial blooms. We compared retrospective temperature-depth relationships modeled using MINLAKE2012 with biogeochemical changes recorded in sediment cores. Four lakes in Voyageurs National Park (VOYA) and four lakes in Isle Royale National Park (ISRO) were studied. Meteorological data from International Falls and Duluth, Minnesota, were used for VOYA and ISRO, respectively. Model output was processed to analyze epilimnetic and hypolimnetic water temperatures and thermal gradients between two periods (1962–1986, 1987–2011). Common trends were increased summer epilimnion temperatures and, for deep lakes, increased frequency and duration of thermoclines. Changes in diatom communities differed between shallow and deep lakes and the parks. Based on changes in benthic and tychoplanktonic communities, shallow lake diatoms respond to temperature, mixing events, pH, and habitat. Changes in deep lakes are evident in the deep chlorophyll layer community of Cyclotella and Discostella species, mirroring modeled changes in thermocline depth and stability, and in Asterionella and Fragilaria species, reflecting the indirect effects of in-lake and watershed nutrient cycling and spring mixing.

Understanding what constitutes a reference (background) nutrient condition for lakes is important for National Park Service managers responsible for preserving and protecting aquatic resources. For this study we characterize water quality conditions in 29 lakes across four national parks, and compare their nutrient status to U.S. Environmental Protection Agency (USEPA) nutrient reference criteria and alternative criteria recently proposed by others. Where appropriate we also compare the nutrient status of these 29 lakes to state or tribal nutrient reference criteria or standards. For lakes that exceed reference criteria we investigate physical and chemical patterns, and for a subset of lakes compare modern nutrient conditions to paleolimnological (i.e., diatom‐inferred [DI]) nutrient reconstructions. Many lakes exceeded USEPA nutrient reference criteria, but met alternative less restrictive criteria. Modern nutrient conditions were also largely consistent with DI historic (pre‐1900) nutrient conditions. Lakes exceeding alternative nutrient criteria and with elevated nutrient levels relative to DI historic conditions were mostly small, shallow, and dystrophic; continued attention to their nutrient dynamics and biological response is warranted. Coupling modern and paleolimnological data offer an innovative and scientifically defensible approach to understand long‐term nutrient trends and provide greater context for comparison with reference conditions.

Ecological shifts in shallow lakes from clear-water macrophyte-dominated to turbid-water phytoplankton-dominated are generally thought of as rapid short-term transitions. Diatom remains in sediment records from shallow lakes in the Prairie Pothole Region of North America provide new evidence that the long-term ecological stability of these lakes is defined by the legacy of large regime shifts. We examine the modern and historical stability of 11 shallow lakes. Currently, four of the lakes are in a clear-water state, three are consistently turbid-water, and four have been observed to change state from year to year (transitional). Lake sediment records spanning the past 150-200 yr suggest that (1) the diatom assemblage is characteristic of either clear or turbid lakes, (2) prior to significant landscape alteration, all of the lakes existed in a regime of a stable clear-water state, (3) lakes that are currently classified as turbid or transitional have experienced one strong regime shift over the past 150-200 yr and have since remained in a regime where turbid-water predominates, and (4) top-down impacts to the lake food-web from fish introductions appear to be the dominant driver of strong regime shifts and not increased nutrient availability. Based on our findings we demonstrate a method that could be used by lake managers to identify lakes that have an ecological history close to the clear-turbid regime threshold; such lakes might more easily be returned to a clear-water state through biomanipulation. The unfortunate reality is that many of these lakes are now part of a managed landscape and will likely require continued intervention.

The roles of both landscape alteration and in-lake processes need to be considered in conservation strategies for shallow lakes in the prairie regions of North America. Here we focus on shallow lakes in west-central Minnesota, USA, highlighting the long-term ecological history and response to known landscape changes of a clear-water, macrophyte-dominated, shallow lake. Contemporary limnological data suggest the aquatic ecosystem has been very stable and fishless for the last ~15 years. Sediment proxies for primary production and ecological change confirm that a stable ecosystem likely prevailed for the last ~200 years. However, sedimentary indicators of catchment erosion detail a distinct response to land-use change during the conversion of native grassland to agricultural land, and following establishment of a protected waterfowl production area (WPA) around the lake. Post-WPA, the rate of sediment accrual decreased dramatically within 5–10 years and sources of organic matter were similar to those of the pre-settlement period. The aquatic ecosystem has been able to withstand nutrient enrichment and allochthonous inputs because stable trophic interactions have likely been in place for more than 200 years. We conclude that lack of hydrologic connectivity and isolated, small catchments are important factors in the promotion of clear-water shallow lake ecosystems, mainly because they prevent colonization by fish and associated ecological consequences. This study highlights the importance of managing both the landscape and in-lake processes to maintain stable, clear-water, shallow lakes.

Intensive agricultural practices can dramatically change the landscape, thereby increasing the concentrations and rates at which nutrients are delivered to aquatic ecosystems. In the United States, concerns about accelerating rates of lake eutrophication related to increases in nutrient loading require a method of quantifying ecological changes that have occurred since European settlement. Because the application of traditional quantitative total phosphorus transfer functions in paleolimnology has proven difficult in shallow, hypereutrophic lakes, we used several approaches in this study to assess ecosystem changes associated with eutrophication of 32 natural lakes in the state of Iowa, USA. In addition to traditional transfer function methods, we estimated changes in primary productivity from the flux of biogenic silica (BSi) and organic carbon accumulation rates (OC AR). Additionally, we compared pre-disturbance diatom communities to modern diatom communities, i.e. floristic change, using non-metric multi-dimensional scaling and square chord distance. OC AR and BSi fluxes increased over time and were positively correlated with the time period of agricultural intensification in the region (post-1940). Ninety-one percent of the lakes in this study showed evidence for eutrophication based on geochemical proxies, and 88 % of lakes showed major floristic change in the diatom community. Whereas geochemical indicators showed consistent increases in productivity across most lakes, floristic changes reflected more complex interactions between other environmental drivers. The magnitude of floristic change did not directly correlate to nutrient-driven increases in primary production, but was driven by ecological diatom assembly related to lake depth. Transfer functions consistently perform poorly, especially for shallow lakes, and other techniques that combine geochemistry and diatom ecology are recommended for reconstructions of eutrophication.

Diatoms respond rapidly to eutrophication and diatom-based models for inferring total phosphorus (TP) have found wide application in palaeolimnology, especially in tracking trajectories of past and recent nutrient enrichment and in establishing pre-disturbance targets for restoration. Using new analysis of existing training sets and sediment-cores we examine the statistical and ecological constraints of diatom-inferred TP (DI-TP) models. Although the models show an apparently strong relationship between measured and inferred TP in the training sets, even under cross-validation, the models display three fundamental weaknesses, namely (1) the relationship between TP and diatom relative abundance is heavily confounded with secondary variables such as alkalinity and lake depth, (2) the models contain many taxa that are not significantly related to TP, and (3) comparison between different models shows poor or no spatial replicability. At some sites the sediment-core diatom assemblage change tracks the TP gradient in the training sets and DI-TP reconstructions are consistent with monitored TP data and known catchment histories for the recent past. At others diatom species turnover is apparently related to variables other than TP, and DI-TP fails to even reproduce plausible trends. Pre-disturbance DI-TP values are also questionable atmost sites. We argue that these problems pervade many DI-TP models, particularly those where violations of the basic assumptions of the transfer function approach are ignored.