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1. Environmental DNA detects Spawning Habitat of an ephemeral migrant fish (Anadromous Rainbow Smelt: Osmerus mordax)

   https://doi.org/10.1186/s12862-022-02073-y  

   Holmes, Vaughn; Aman, Jacob; York, Geneva; Kinnison, Michael T. (December 2022, BMC Ecology and Evolution)

   Abstract Background Anadromous rainbow smelt ( Osmerus mordax ) have experienced a large range reduction in recent decades and the status of remnant spawning populations is poorly known in Maine, where these fish have significant ecological, cultural, and commercial relevance. Defining the remnant range of anadromous smelt is more difficult than for many declining fish species because adults are only ephemerally present while spawning in small coastal streams at night during spring runoff periods when traditional assessments can be unreliable or even hazardous. We hypothesized that eDNA might facilitate improved survey efforts to define smelt spawning habitat, but that detection could also face challenges from adult eDNA quickly flushing out of these small stream systems. We combined daytime eDNA sampling with nighttime fyke netting to ascertain a potential window of eDNA detection before conducting eDNA surveys in four streams of varying abundance. Hierarchical occupancy modeling was in turn employed to estimate eDNA encounter probabilities relative to numbers of sampling events (date), samples within events, and qPCR replicates within samples. Results Results from the combined eDNA and fyke net study indicated eDNA was detectable over an extended period, culminating approximately 8–13 days following peak spawning, suggesting developing smelt larvae might be the primary source of eDNA. Subsequently, smelt eDNA was readily detected in eDNA surveys of four streams, particularly following remediation of PCR inhibitors. Hierarchical occupancy modeling confirmed our surveys had high empirical detection for most sites, and that future surveys employing at least three sampling events, three samples per event, and six qPCR replicates can afford greater than 90% combined detection capability in low abundance systems. Conclusions These results demonstrate that relatively modest eDNA sampling effort has high capacity to detect this ephemerally present species of concern at low to moderate abundances. As such, smelt eDNA detection could improve range mapping by providing longer survey windows, safer sampling conditions, and lower field effort in low density systems, than afforded by existing visual and netting approaches. 

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2. Harnessing stemflow as a diagnostic tool for canopy disease detection and monitoring

   https://doi.org/10.1016/j.foreco.2025.122674  

   Gordon, D; Burke, David J; Carino-Kyker, Sarah R; Bashian-Victoroff, Claudia; Mabrouk, Adam I; Van_Stan, John T (June 2025, Forest Ecology and Management)

   Monitoring diseases within tree canopies is challenging due to their inaccessibility and the complexity of canopy ecosystems. Here, we explore the potential of stemflow sampling as a novel, ground-based method for detecting and monitoring canopy-associated pathogens. In a case study focused on Litylenchus crenatae ssp. mccannii (LCM), the nematode associated with Beech Leaf Disease (BLD), we collected stemflow samples from 18 Fagus grandifolia Ehrh. (American beech) trees across 12 storm events. eDNA assays detected LCM presence in 7 of those storms, with quantitative PCR-derived gene concentrations ranging from 80 to 158,000 copies mL−1. Higher detections and concentrations coincided with leaf senescence and bud formation periods, and they correlated conditionally with event rainfall amount and pre-storm changes in relative humidity. Although based on a single site and season, these findings demonstrate the potential for stemflow sampling to capture a pathogen’s eDNA (i.e., canopy distress signals) at ground level. This method could complement traditional monitoring, offering another affordable, non-invasive tool for pathogen detection. Additional validation, particularly regarding live versus dead organisms and across varied site conditions, will be essential to evaluate the breadth of value stemflow eDNA offers for canopy disease management and ecological research. 

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3. Microbial communities of the Laurentian Great Lakes reflect connectivity and local biogeochemistry

   https://doi.org/10.1111/1462-2920.14862  

   Paver, Sara_F; Newton, Ryan_J; Coleman, Maureen_L (December 2019, Environmental Microbiology)

   Summary The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI‐B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by aChloroflexioligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to anActinobacteriaoligotype (acI‐C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations. 

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4. Hidden in plain sight: The invasive macroalga Caulerpa prolifera evades detection by environmental DNA methods

   https://doi.org/10.1002/edn3.496  

   Waters, Tanner; Langlois, Kylie; Gold, Zachary; Theroux, Susanna; Eagle, Robert A. (January 2024, Environmental DNA)

   Abstract Environmental managers need a rapid and cost‐effective monitoring tool for tracking the spread of invasive species, particularly at the onset of introduction. The macroalgaeCaulerpa proliferais considered an invasive species outside its native range, colonizing large patches of seafloor, reducing native species, and altering ecosystem functioning. Here, we developed a droplet digital PCR assay for detection ofC. proliferafrom environmental DNA seawater samples using the internal transcribed spacer (ITS) region. While the assay itself was confirmed to be highly efficient, we discovered concentrations ofC. proliferaeDNA were present below detectable levels in the water column surrounding an outbreak. To understand why, we conducted tank‐based experiments for two California invasive algae species,Caulerpa proliferaandSargassum horneri. The steady‐state eDNA concentration (eDNA copies/ gram of biomass detected) ofC. proliferawas found to be two orders of magnitude lower thanS. horneri. A meta‐analysis of steady‐state concentrations reported in the literature showed a remarkable range from ~10⁴–10¹¹(copies/g), revealing C. proliferato have the lowest recorded steady‐state concentrations of eDNA of any known species. We attributeC. prolifera'slow steady‐state eDNA concentration to its unique biology as a unicellular macroscopic algae which reduces the possible modes of eDNA release compared to similarly sized multicellular organisms. Critically our results demonstrate the potential limits of eDNA approaches, the influence of shedding rates in the reliability of species detections, and the vital importance of benchmarking and validating eDNA assays in both field and laboratory settings. 

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5. Early Holocene ice retreat from Isle Royale in the Laurentian Great Lakes constrained with ¹⁰ Be exposure-age dating

   https://doi.org/10.5194/gchron-5-413-2023  

   Portenga, Eric W.; Ullman, David J.; Corbett, Lee B.; Bierman, Paul R.; Caffee, Marc W. (January 2023, Geochronology)

   Abstract. The timing of the Laurentide Ice Sheet's final retreat from North America's Laurentian Great Lakes is relevant to understanding regional meltwater routing, changing proglacial lake levels, and lake-bottom stratigraphy following the Last Glacial Maximum. Recessional moraines on Isle Royale, the largest island in Lake Superior, have been mapped but not directly dated. Here, we use the mean of 10 new 10Be exposure ages of glacial erratics from two recessional moraines (10.1 ± 1.1 ka, one standard deviation; excluding one anomalously young sample) to constrain the timing of Isle Royale's final deglaciation. This 10Be age is consistent with existing minimum-limiting 14C ages of basal organic sediment from two inland lakes on Isle Royale, a sediment core in Lake Superior southwest of the island, and an estimated deglaciation age of the younger of two subaqueous moraines between Isle Royale and Michigan's Keweenaw Peninsula. Relationships between Isle Royale's landform ages and Lake Superior bottom stratigraphy allow us to delineate the retreat of the Laurentide ice margin across and through Lake Superior in the early Holocene. We suggest that Laurentide ice was in contact with the southern shorelines of Lake Superior later than previously thought. 

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