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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. 

Abstract Limnological understanding of the role snow plays in under‐ice thermal dynamics is mainly based on studies of clear‐water lakes. Very little is known about the role snow plays in the thermal dynamics of dystrophic lakes. We conducted a whole lake experiment on a small, 8 m deep dystrophic bog lake in northern Wisconsin, where we removed all snowfall over two consecutive winters. Due to weather variability, only 1 year had predominantly black ice. Under these conditions, the lake rapidly cooled in early and mid‐winter, compared to snow covered conditions that insulated the lake from heat loss. The lake also rapidly gained heat in late winter resulting in isothermal conditions well in advance of ice‐off. These results show how water clarity modulates the influence of snow on under‐ice thermal dynamics, which is relevant to futures with snow droughts. 

Abstract Cisco (Coregonus artedi) are a widespread, cold‐water zooplanktivore native to North America. Although Cisco are generally referred to as an “obligate zooplanktivore,” there is some evidence that the species exhibits considerable variability in trophic niche. Here, we assessed how Cisco body size relates to trophic position, that is, trophic ontogeny. We analysed¹³C and¹⁵N isotopes from Cisco ranging from 127 to 271 mm in body length (n = 66) from Trout Lake, Vilas County, Wisconsin, USA.¹⁵N isotopes showed smaller Cisco had a trophic position of ~3, which steadily increased to ~3.5 for larger Cisco. Further,¹³C isotope signatures showed Cisco transitioned to be more pelagically reliant (lower¹³C signatures). Using gillnet catch data, we found that larger Cisco were using deeper habitats than smaller Cisco. Our results support that Cisco have significant variability in trophic niche even though they are traditionally thought of as an obligate planktivore. Overall, we emphasize that researchers should be cautious when generalizing Cisco trophic function, particularly when considering the broader food web. 

Abstract Water temperature dynamics in large inland lakes are interrelated with internal lake physics, ecosystem function, and adjacent land surface meteorology and climatology. Models for simulating and forecasting lake temperatures often rely on remote sensing andin situdata for validation.In situmonitoring platforms have the benefit of providing relatively precise measurements at multiple lake depths, but are often sparser (temporally and spatially) than remote sensing data. Here, we address the challenge of synthesizingin situlake temperature data by creating a standardized database of near-surface and subsurface measurements from 134 sites across 29 large North American lakes, with the primary goal of supporting an ongoing lake model validation study. We utilize data sources ranging from federal agency repositories to local monitoring group samples, with a collective historical record spanning January 1, 2000 through December 31, 2022. Our database has direct utility for validating simulations and forecasts from operational numerical weather prediction systems in large lakes whose extensive surface area may significantly influence nearby weather and climate patterns. 

ABSTRACT Ecosystems are abruptly changing due to invasive species and global climate change. In lakes, invasive Rainbow Smelt Osmerus mordax can cause negative ecosystem effects through competitive and predatory interactions with native species leading to food web shifts away from native species dominance, altered zooplankton communities, and the decline or extirpation of native cool and coldwater fishes. We conducted two whole-lake removals of invasive Rainbow Smelt and simultaneous introductions of native Cisco Coregonus artedi through stocking. About 327 and 1.6 adult Rainbow Smelt/ha were removed and about 45 adult Cisco/ha were stocked over 4 years into the two experimental lakes. In one system, native Yellow Perch Perca flavscens relative abundance and density significantly increased by 556% and 143% post-manipulation, respectively. In the other system, native Walleye Sander vitreus relative abundance increased by 26% and became consistently present in the pelagic zone post-manipulation (allowing for density estimation). Rainbow Smelt relative abundance and density decreased by >85% in both experimental lakes. The two ecosystems shifted to native species dominance while invasive Rainbow Smelt became insignificant components of the food webs. In these two intensive whole-lake manipulations, we applied the Resist–Accept–Direct (RAD) climate adaptation framework to test an applicable ecological adaptation strategy and used panarchy theory as an ecologically grounded pathway to purposefully direct ecosystem transformation. We used this holistic management framework to better understand and manage undesired ecological change—“food web thinking.” In the context of our study, two ecosystems were purposefully directed towards native food web structures, species interactions, and processes, which mitigated Rainbow Smelt driven negative effects. 

Abstract Freshwater ecosystems can serve as model systems that reveal insights into biological invasions. In this article, we summarize nine lessons about aquatic invasive species from the North Temperate Lakes Long-Term Ecological Research program and affiliated projects. The lessons about aquatic invasive species are as follows: Invasive species are more widespread than has been documented; they are usually at low abundance; they can irrupt from low-density populations in response to environmental triggers; they can occasionally have enormous and far-reaching impacts; they can affect microbial communities; reservoirs act as invasive species hotspots; ecosystem vulnerability to invasion can be estimated; invasive species removal can produce long-term benefits; and the impacts of invasive species control may be greater than the impacts of the invasive species. This synthesis highlights how long-term research on a freshwater landscape can advance our understanding of invasions. 

Abstract Resilience, measured by the distribution of passage times between alternate states, indicates persistence of a state in stochastic dynamic systems such as blooms of cyanobacteria in lakes. We used high‐frequency datasets to compare the resilience of low and high states of phycocyanin, a pigment indicator of cyanobacteria, in Lake Mendota, Wisconsin, USA, for three growing seasons that ranged sevenfold in external phosphorus (P) load. Each year we observed 139–265 passage times across the unstable threshold that separated the low‐ from high‐phycocyanin states. Each sample of passage times is highly skewed with low median, larger mean, much larger SD, and wide tails extending to long lifetimes of a state. About 25% of events, whether low or high phycocyanin, lasted a day or more. Among these 3 years of contrasting external P load, there were no discernible differences in the resilience of either ecosystem state. We attribute this lack of contrast to the sustained recycling of P from sediments and the high stochasticity of phycocyanin in this lake. 

Abstract Terrestrial plants are sensitive indicators of global warming because their annual cycles of growth and senescence are changing as warming proceeds. Single celled algae are distinct life forms capable of population bursts in any season, so there is uncertainty about phytoplankton phenology as a comparable indicator of global warming. We analyzed 4+ decades of monthly chlorophyllameasurements at two sites in San Francisco Bay and found abrupt shifts during summer months leading to a 48‐day advance in the annual pattern of chlorophyll‐a accumulation at one site and a 36‐day delay at the other. These large phenological changes were not associated with changing temperature, but they were associated with changes in top–down control by bivalve filter feeders as biological communities were restructured by (1) introduction of a non‐native clam, and (2) a shift in atmospheric forcing of the NE Pacific. This study illustrates that changes in phytoplankton phenology are not necessarily responses to or indicators of global warming. However, they can be indicators of human disturbances and natural climate oscillations having effects large enough to mask the effect of climate warming.