Search for: All records

<sc>Abstract</sc> Experiments on entire ecosystems have contributed knowledge on effects of atmospheric CO₂and climate change, environmental pollutants, trophic cascades, response of fisheries to management, consumer interactions, ecosystem resilience and stability, and early warning indicators of critical transitions in ecosystem state. Rate of change in external drivers of an ecosystem such as climate warming, inflow of water or nutrients, or harvest of apex predators may affect signals of critical transitions but rates of change of drivers are rarely considered in whole-ecosystem studies. We studied effects of drivers’ rates of change on indicators of critical transitions using models for whole lake manipulations of nutrient enrichment, light-absorbing substances, and apex predators. Results show that times of signals from indicators relative to times of critical transitions can vary depending on the rate of external drivers, including the rate of manipulation in whole-ecosystem experiments. 

Abstract Many ecosystems can abruptly shift between states, and shallow lakes are a classic example. Biomanipulation via the removal of benthivores can shift a shallow lake from a turbid to a clear-water macrophyte-dominated state, but the limited number of long-term studies indicates that persistence in this state rarely lasts beyond 5–10 years. We analyzed 12 years of pre-removal (1996–2007) and 17 years of post-removal (2008–2024) data to assess the ecological impacts of a common carp (Cyprinus carpio) removal from Lake Wingra, a shallow eutrophic lake in Madison, Wisconsin, USA. Summer water clarity abruptly increased following the winter 2008 carp removal, resulting in a 64% increase in mean Secchi depth in post-removal summers and a major expansion of the littoral zone. Fast growing submerged macrophytes (for example,Ceratophyllum demersumand invasiveMyriophyllum spicatum) rapidly expanded into deeper zones, reaching the maximum colonization depth of 3.96 m within four summers. Post-removal nutrient concentrations declined by 24–34% and became more correlated with precipitation, suggesting a shift from internal to external regulation of nutrient loading. Three likely interacting mechanisms for maintaining water clarity include predation by centrarchids maintaining low carp populations, the high and stable coverage of submerged macrophytes, and abundant filamentous algae that provide an additional nutrient sink. However, high biomass of invasive species and filamentous algae can degrade ecosystem services and function, and increased variability of precipitation-driven nutrient inputs may destabilize the macrophyte-dominated state in the future. We demonstrate with long-term data the sustained shift of a shallow eutrophic lake out of the turbid state with a single biomanipulation. 

ABSTRACT AimGlobal change can impact the stability of biological communities by affecting species richness and synchrony. While most studies focus on terrestrial ecosystems, our research includes both terrestrial and aquatic realms. Previous works measure overall community synchrony as co‐variation among co‐occurring species, ignoring the tail dependence—when species fluctuate together at extreme abundance levels. We used community time‐series data to test two hypotheses across realms: a positive relationship between diversity (richness) and stability, and a negative relationship between synchrony and stability. Additionally, we explored how tail‐dependent synchrony contributes to variations in community stability. LocationGlobal. Time Period1923–2020. Major Taxa Studied7 taxa across freshwater (fish, plants, invertebrates) and terrestrial (birds, plants, invertebrates, mammals) realms. MethodsWe synthesised 20+ years of species abundance/biomass data from 2668 communities across seven taxonomic groups. Using a variance‐ratio approach and copula models, we measured overall and tail‐dependent synchrony. Hierarchical linear mixed‐effects models in a Bayesian framework were used to assess the effects of richness and both synchrony types on stability. ResultsWe found a positive diversity–stability relationship in terrestrial but not in freshwater communities, with terrestrial stability being nearly three times higher. A negative synchrony –stability relationship was found in both realms. The best model explaining stability included realm differences, richness and both types of synchronies. For freshwater, only overall synchrony significantly impacted stability, while richness and both synchrony types were key predictors for terrestrial stability. Notably, the model overestimates terrestrial stability when tail‐dependent synchrony is excluded. Main ConclusionsRichness strongly enhanced terrestrial stability, offering the most extensive support for this relationship to date. In addition, tail‐dependent synchrony provides key insights into stability differences across ecosystems. As extreme environmental events increase, incorporating tail‐dependent synchrony in future stability studies is crucial. 

Abstract Disturbance ecology is underdeveloped in marine pelagic ecosystems relative to terrestrial and aquatic benthic habitats, in part because, when measured relative to a fixed location, postdisturbance recovery involves the advection of entire communities in addition to biotic interactions. A Lagrangian frame-of-reference perspective alleviates this issue. Using results from the California Current Ecosystem, we highlight three approaches: in situ Lagrangian, synthetic Lagrangian, and simulated Lagrangian studies. Within a Lagrangian context, extratropical marine heatwaves and El Niños represent press disturbances or alterations to the disturbance regime. Individual upwelling events are more appropriately viewed as pulse disturbances. Upwelling disturbances stimulate rapid growth of pioneer species (diatoms), with herbivores (copepods) lagging these blooms by approximately 3 weeks. The climax community is an assemblage of small low-nutrient specialists with high Shannon diversity. We suggest that pelagic ecosystems can be ideal systems for investigating disturbance recovery because of the rapid response times of marine primary producers and herbivores. 

Abstract The ecological literature often features phenomenological dynamic models lacking robust validation against observational data. Reverse engineering ecological models from data is an alternative approach, where time series data are utilized to infer or fit a stochastic differential equation. This process, known as system reconstruction, presents significant challenges especially when data resolution is low. This paper addresses the estimation of the (often) non‐linear deterministic and stochastic parts of Langevin models from sparsely sampled time series.We introduce a maximum likelihood estimation (MLE) inference method, termed Euler reconstruction, tailored for time series data with high resolution. However, the Euler approach is not reliable for low‐resolution data. To fill the gap for sparsely sampled data, we present an MLE inference method pioneered by Aït‐Sahalia that we term Hermite reconstruction. We employ splines to detect inherent nonlinearities in the unknown data‐generating system with high accuracy and acceptable computational burden.We applied both methods to a range of simulated, ecological, and climate datasets, with different data resolutions. We provide a practical measure (‘relaxation time’) to distinguish between different data resolutions. For simulated data, we show that the Euler reconstruction can accurately reveal the underlying system when data resolution is high, while Hermite reconstruction can recover the system even with low resolution. We recommend using Hermite reconstruction for real data even when the resolution is relatively high. Only when the resolution of real data is exceptionally high might Euler reconstruction suffice.We provide a MATLAB package and a tutorial to assist researchers in applying the method to their own data. 

Abstract Aquatic heatwaves are increasing in frequency, intensity, and duration worldwide. While increases in mean water temperatures are linked to enhanced phytoplankton biomass, it is unclear how heatwaves alter phytoplankton dynamics in lakes at an ecosystem scale. We investigated changes in surface chlorophyll during 29 summer heatwaves between 2008 and 2019 in 3 north temperate lakes. These lakes vary in staining and were either references or manipulated with nutrients and top predator additions. The manipulations provided a variety of nutrient, grazing, and light conditions during heatwave and non‐heatwave conditions. Surface chlorophyll concentrations increased during 24 out of 29 heatwaves. In the low‐nutrient reference lake the mean increase in chlorophyll was 57% while in the two experimental lakes the mean increases were 127% and 183%. Overall, the effects of the whole‐lake experiments were variable but still provided context for possible patterns amid a diverse set of food web and nutrient conditions. 

ABSTRACT The potential for extracellular electron transfer (EET) is a prevailing genomic feature of humic lake bacterioplankton. However, there has been little evidence for the substantial ecological contribution predicted by genetics. We hypothesized that anoxygenic phototrophic electrotrophs and accompanying heterotrophic electrogens cycle dissolved organic matter (DOM) between oxidized and reduced states. We predicted that such bacterioplankton would exhibit diel-scale oscillations due to the light dependency of photosynthesis. Using Trout Bog Lake in Wisconsin, USA, as our model ecosystem, we profiled the water column with depth-discrete metagenomic, physiochemical, and electrochemical analyses. We observed variation in oxidation reduction potential (ORP) in response to sunlight, initiating at depths populated by anoxygenic phototrophs with EET genes. We developed an automated buoy to measure electric current flow between many pairs of electrodes simultaneously, observing correlation in electron consumption to sunlight. Our results, combined with published metatranscriptomic analysis, indicate the occurrence of electron cycling between phototrophic oxidation (electrotrophic metabolism) byChlorobiumand anaerobic respiration (electrogenic metabolism) byGeothrix, involving DOM. We also repeatedly observed gradual seasonal increases in hypolimnion ORP throughout summer. These diel and seasonal patterns imply that electroactive DOM mediates the ecology of electroactive bacteria in lakes, controlling humic lake methane emissions.IMPORTANCEWe investigated the physical, chemical, and redox characteristics of a bog lake and electrodes hung therein to test the hypothesis that dissolved organic matter is being cycled between oxidized and reduced states by electroactive bacterioplankton powered by phototrophy. To do so, we performed field-based analyses on multiple timescales using both established and novel instrumentation. We paired these analyses with recently developed bioinformatics pipelines for metagenomics data to investigate genes that enable electroactive metabolism and accompanying metabolisms. Our results are consistent with our hypothesis and yet upend some of our other expectations. Our findings have implications for understanding greenhouse gas emissions from lakes, including electroactivity as an integral part of lake metabolism throughout more of the anoxic parts of lakes and for a longer portion of the summer than expected. Our results also give a sense of what electroactivity occurs at given depths and provide a strong basis for future studies. 

Abstract BackgroundViruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied. ResultsHere, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes had greater species richness and total viral genome abundances than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment. ConclusionsOverall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits. 

ABSTRACT MotivationFreshwater ecosystems have been heavily impacted by land‐use changes, but data syntheses on these impacts are still limited. Here, we compiled a global database encompassing 241 studies with species abundance data (from multiple biological groups and geographic locations) across sites with different land‐use categories. This compilation will be useful for addressing questions regarding land‐use change and its impact on freshwater biodiversity. Main Types of Variables ContainedThe database includes metadata of each study, sites location, sample methods, sample time, land‐use category and abundance of each taxon. Spatial Location and GrainThe database contains data from across the globe, with 85% of the sites having well‐defined geographical coordinates. Major Taxa and Level of MeasurementThe database covers all major freshwater biological groups including algae, macrophytes, zooplankton, macroinvertebrates, fish and amphibians. 

Abstract BackgroundProtists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world’s best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last 20 years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community and to hypothesize about their interactions with bacteria. ResultsBased on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukaryotic phytoplankton community over time, which we predict to be a consequence of reduced zooplankton grazing pressures after the invasion of a invasive predator (the spiny water flea) to the lake. The metagenomic data also reveal the presence of the spiny water flea and the zebra mussel, a second invasive species to Lake Mendota, prior to their visual identification during routine monitoring. Furthermore, we use species co-occurrence and co-abundance analysis to connect the protistan community with bacterial taxa. Correlation analysis suggests that protists and bacteria may interact or respond similarly to environmental conditions. Cryptophytes declined in the second decade of the timeseries, while many alveolate groups (e.g., ciliates and dinoflagellates) and diatoms increased in abundance, changes that have implications for food web efficiency in Lake Mendota. ConclusionsWe demonstrate that metagenomic sequence-based community analysis can complement existing efforts to monitor protists in Lake Mendota based on microscopy-based count surveys. We observed patterns of seasonal abundance in microeukaryotes in Lake Mendota that corroborated expectations from other systems, including high abundance of cryptophytes in winter and diatoms in fall and spring, but with much higher resolution than previous surveys. Our study identified long-term changes in the abundance of eukaryotic microbes and provided context for the known establishment of an invasive species that catalyzes a trophic cascade involving protists. Our findings are important for decoding potential long-term consequences of human interventions, including invasive species introduction.