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Coronavirus disease 2019 (COVID-19) is an infectious disease that is mainly spread through aerosolized droplets containing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is excreted in feces by infected individuals. Sewage surveillance has been applied widely to obtain data on the prevalence of COVID-19 in whole communities. We used SARS-CoV-2 gene targets N1, N2, and E to determine the prevalence of COVID-19 at both municipal and building levels. Frequency analysis of wastewater testing indicated that single markers detected only 85% or less of samples that were detected as positive for SARS-CoV-2 with the three markers combined, indicating the necessity of pairing markers to lower the false-negative rate. The best pair of markers in both municipal and building level monitoring was N1 and N2, which correctly identified 98% of positive samples detected with the three markers combined. The degradation rates of all three targets were assessed at two different temperatures (25 and 35 °C) as a possible explanation for observed differences between markers in frequency. Results indicated that all three RNA targets degrade at nearly the same rate, indicating that differences in degradation rate are not responsible for the observed differences in marker frequency. HIGHLIGHTS There is a knowledge gap regarding the expression frequency and degradation of SARS-CoV-2 in wastewater.; This study looks at the frequency and degradation of three RNA molecular markers commonly used in wastewater-based epidemiology (WBE).; Results indicate the best combination of RNA markers and their average decay kinetics.; This study will aid in future WBE monitoring and modeling efforts for SARS-CoV-2.;

Abstract Background Urban areas are often built along large rivers and surrounded by agricultural land. This may lead to small tributary streams that have agricultural headwaters and urbanized lower reaches. Our study objectives assessed are as follows: (1) landscape, geomorphic, and water quality variables that best explained variation in aquatic communities and their integrity in a stream system following this agricultural-to-urban land use gradient; (2) ways this land use gradient caused aquatic communities to differ from what would be expected for an idealized natural stream or other longitudinal gradients; and (3) whether the impacts of this land use gradient on aquatic communities would grow larger in a downstream direction through the agricultural and urban developments. Our study area was an impaired coldwater stream in Michigan, USA. Results Many factors structured the biological communities along the agricultural-to-urban land use gradient. Instream woody debris had the strongest relationship with EPT (Ephemeroptera, Plecoptera, and Trichoptera) abundance and richness and were most common in the lower, urbanized watershed. Fine streambed substrate had the strongest relationship with Diptera taxa and surface air breather macroinvertebrates and was dominant in agricultural headwaters. Fish community assemblage was influenced largely by stream flow and temperature regimes, while poor fish community integrity in lower urban reaches could be impacted by geomorphology and episodic urban pollution events. Scraping macroinvertebrates were most abundant in deforested, first-order agricultural headwaters, while EPT macroinvertebrate richness was the highest downstream of agricultural areas within the urban zone that had extensive forest buffers. Conclusion Environmental variables and aquatic communities would often not conform with what we would expect from an idealized natural stream. EPT richness improved downstream of agricultural areas. This shows promise for the recovery of aquatic systems using well-planned management in watersheds with this agricultural-to-urban land use pattern. Small patches of forest can be the key to conserving aquatic biodiversity in urbanized landscapes. These findings are valuable to an international audience of researchers and water resource managers who study stream systems following this common agricultural-to-urban land use gradient, the ecological communities of which may not conform with what is generally known about land use impacts to streams.

Abstract Explaining spatiotemporal variability in metacommunities is challenging because conducting empirical studies that link mechanisms across scales is difficult. We developed a stochastic model of epilithic algal succession in streams to better understand the underlying interactions that drive patch dynamics at three levels of spatial hierarchy: patch, channel habitat, and reach. The state of an algal patch is specified by one of nine community types, which are defined by growth form. Ninety‐two empirical data sets of epilithic succession were used to estimate Markov transition probabilities among patch types as functions of inputs for light, nutrients, and current. Two additional probability matrices determine the effects of herbivory and disturbance based on user inputs. Testing model predictions of patch composition against independent empirical data indicated good correspondence based on resemblance metrics. Early in succession, most patches were occupied by prostrate and erect diatoms. These persisted under low light and nutrient conditions. Motile and stalked diatom patches characterized later stages when resources were moderate. Succession proceeded to mostly filamentous green algal patches under high resource levels. Sensitivity simulations indicated light most affected succession. Herbivory and disturbance increased the probability of prostrate diatom patches. We then used the model to examine how changes in abiotic and biotic parameters affect patch dynamics at different scales. Changes in nutrients or light affected patch diversity differently at the habitat vs. reach scale. Interactions with local resource levels within a channel habitat determined its alpha diversity. The proportion of channel habitat types within a reach, and their collective response to changes, determined beta diversity. Patch diversity within channel habitats generated by herbivory followed the predation hypothesis only when nutrients were low. At the reach scale, herbivory always increased patch similarity among channel habitats, lowering beta diversity. Diversity within channel habitats followed the intermediate disturbance hypothesis for a variety of habitats. Effects of disturbance on beta diversity at the reach scale depended on channel habitat heterogeneity. The stability of patches at the reach scale was highest when disturbance created high patch diversity, supporting the insurance hypothesis. The ideas generated can improve stream bioassessment methods and provide insight into mechanisms underlying patch dynamics in other ecosystems.

Draft method C is a standardized method for quantifying E. coli densities in recreational waters using quantitative polymerase chain reaction (qPCR). The method includes a Microsoft Excel workbook that automatically screens for poor-quality data using a set of previously proposed acceptance criteria, generates weighted linear regression (WLR) composite standard curves, and calculates E. coli target gene copies in test samples. We compared standard curve parameter values and test sample results calculated with the WLR model to those from a Bayesian master standard curve (MSC) model using data from a previous multi-lab study. The two models’ mean intercept and slope estimates from twenty labs’ standard curves were within each other’s 95% credible or confidence intervals for all labs. E. coli gene copy estimates of six water samples analyzed by eight labs were highly overlapping among labs when quantified with the WLR and MSC models. Finally, we compared multiple labs’ 2016−2018 composite curves, comprised of data from individual curves where acceptance criteria were not used, to their corresponding composite curves with passing acceptance criteria. Composite curves developed from passing individual curves had intercept and slope 95% confidence intervals that were often narrower than without screening and an analysis of covariance test was passed more often. The Excel workbook WLR calculation and acceptance criteria will help laboratories implement draft method C for recreational water analysis in an efficient, cost-effective, and reliable manner.

Streambank erosion is difficult to quantify; models and field methods are needed to assess this important sediment source to streams. Our objectives were to (1) evaluate and compare three techniques for quantifying streambank erosion: erosion pins, total station, and laser scanning, (2) spatially assess streambank erosion rates in the Indian Mill Creek watershed of Michigan, USA, and (3) relate results with modeling of nonpoint source pollution. We found large absolute and relative errors between the different measurement techniques. However, we were unable to determine any statistically significant differences between techniques and only observed a correlation between total station and laser scanner. This suggests that the three methods have limited comparability and differences between measurements were largely not systemic. Further, the application of each technique should be dependent on site conditions, project goals, desired resolution, and resources. The laser scanner collected high-resolution data on clear, barren streambanks, but the erosion pin and total station were more representative of complex vegetated banks. Streambank erosion rates varied throughout the watershed and were influenced by fluvial processes. We estimate that streambank erosion contributed 28.5% of the creek’s total sediment load. These findings are important to address sources of watershed impairments related to sedimentation, as choosing an applicable technique for individual purposes can help reduce the challenges and costs of a streambank erosion study.

The 2-sample mark-recapture method with Chapman's estimator is often used by inland fishery managers to estimate the reach-scale abundance of stream fish. An important assumption of this method is that no dispersal into or out of the study reach occurs between the two samples. Violations of this assumption are probably common in practice, but their effect on bias (systematic error) of abundance estimates is poorly understood, especially in small populations. Estimation methods permitting dispersal exist but, for logistical reasons, often are infeasible for routine assessments in streams. The purpose of this paper is to extend available results regarding effects of dispersal on the bias of Chapman's estimator as applied to reach-scale studies of stream fish abundance. We examine for the first time the joint effects of dispersal and sampling variation on the bias of this estimator. To reduce the bias effects of dispersal, we propose a modified sampling scheme in which the original study reach is expanded, a central subreach is sampled during the mark session (sample 1), and the entire reach is sampled during the recapture session (sample 2). This modified sampling scheme can substantially reduce bias effects of dispersal without requiring unique marking of individual fish or additional site visits. Analytical and simulation results show that sampling variation tends to create negative bias with respect to study-reach abundance, while dispersal tends to create positive bias; the net effect can be positive, negative, or zero, depending on the true abundance, capture probabilities, and amount and nature of dispersal. In most cases, simply expanding the study reach is an effective way to reduce dispersal-related bias of Chapman's estimator, but expanding the study reach and employing the modified sampling scheme we propose is a better alternative for accurately estimating abundance with the same level of sampling effort.