Environmental unpredictability is known to result in the evolution of bet‐hedging traits. Variable dormancy enhances survival through harsh conditions, and is widely cited as a diversification bet‐hedging trait. The floating aquatic plant, Spirodela polyrhiza (Greater Duckweed), provides an opportunity to study diversification because although partially reliable seasonal cues exist, its growing season is subject to an unpredictable and literally “hard” termination when the surface water freezes, and overwinter survival depends on a switch from production of normal daughter fronds to production of dense, sinking “turions” prior to freeze‐over. The problem for S. polyrhiza is that diversified dormancy behavior must be generated among clonally produced, genetically identical offspring. Variation in phenology has been observed in the field, but its sources are unknown. Here, we investigate sources of phenological variation in turion production, and test the hypothesis that diversification in turion phenology is generated within genetic lineages through effects of parental birth order. As expected, phenotypic plasticity to temperature is expressed along a thermal gradient; more interestingly, parental birth order was found to have a significant and strong effect on turion phenology: Turions are produced earlier by late birth‐order parents. These results hold regardless of whether turion phenology is measured as first turion birth order, time to first turion, or turion frequency. This study addresses a question of current interest on potential mechanisms generating diversification, and suggests that consistent phenotypic differences across birth orders generate life history variation.

Freshwater biodiversity is declining at an unprecedented rate. Freshwater conservationists and environmental managers have enough evidence to demonstrate that action must not be delayed but have insufficient evidence to identify those actions that will be most effective in reversing the current trend. Here, the focus is on identifying essential research topics that, if addressed, will contribute directly to restoring freshwater biodiversity through supporting ‘bending the curve’ actions (i.e. those actions leading to the recovery of freshwater biodiversity, not simply deceleration of the current downward trend). The global freshwater research and management community was asked to identify unanswered research questions that could address knowledge gaps and barriers associated with ‘bending the curve’ actions. The resulting list was refined into six themes and 25 questions. Although context‐dependent and potentially limited in global reach, six overarching themes were identified: (i) learning from successes and failures; (ii) improving current practices; (iii) balancing resource needs; (iv) rethinking built environments; (v) reforming policy and investments; and (vi) enabling transformative change. Bold, efficient, science‐based actions are necessary to reverse biodiversity loss. We believe that conservation actions will be most effective when supported by sound evidence, and that research and action must complement one another. These questions are intended to guide global freshwater researchers and conservation practitioners, identify key projects and signal research needs to funders and governments. Our questions can act as springboards for multidisciplinary and multisectoral collaborations that will improve the management and restoration of freshwater biodiversity.

Sediment DNA (sedDNA) analyses are rapidly emerging as powerful tools for the reconstruction of environmental and evolutionary change. While there are an increasing number of studies using molecular genetic approaches to track changes over time, few studies have compared the coherence between quantitative polymerase chain reaction (PCR) methods and metabarcoding techniques. Primer specificity, bioinformatic analyses, and PCR inhibitors in sediments could affect the quantitative data obtained from these approaches. We compared the performance of droplet digital polymerase chain reaction (ddPCR) and high-throughput sequencing (HTS) for the quantification of target genes of cyanobacteria in lake sediments and tested whether the two techniques similarly reveal expected patterns through time. Absolute concentrations of cyanobacterial 16S rRNA genes were compared between ddPCR and HTS using dated sediment cores collected from two experimental (Lake 227, fertilized since 1969 and Lake 223, acidified from 1976 to 1983) and two reference lakes (Lakes 224 and 442) in the Experimental Lakes Area (ELA), Canada. Relative abundances of Microcystis 16S rRNA (MICR) genes were also compared between the two methods. Moderate to strong positive correlations were found between the molecular approaches among all four cores but results from ddPCR were more consistent with the known history of lake manipulations. A 100-fold increase in ddPCR estimates of cyanobacterial gene abundance beginning in ~1968 occurred in Lake 227, in keeping with experimental addition of nutrients and increase in planktonic cyanobacteria. In contrast, no significant rise in cyanobacterial abundance associated with lake fertilization was observed with HTS. Relative abundances of Microcystis between the two techniques showed moderate to strong levels of coherence in top intervals of the sediment cores. Both ddPCR and HTS approaches are suitable for sedDNA analysis, but studies aiming to quantify absolute abundances from complex environments should consider using ddPCR due to its high tolerance to PCR inhibitors.

Analyses of sedimentary DNA (sedDNA) have increased exponentially over the last decade and hold great potential to study the effects of anthropogenic stressors on lake biota over time. Herein, we synthesise the literature that has applied a sedDNA approach to track historical changes in lake biodiversity in response to anthropogenic impacts, with an emphasis on the past c. 200 years. We identified the following research themes that are of particular relevance: (1) eutrophication and climate change as key drivers of limnetic communities; (2) increasing homogenisation of limnetic communities across large spatial scales; and (3) the dynamics and effects of invasive species as traced in lake sediment archives. Altogether, this review highlights the potential of sedDNA to draw a more comprehensive picture of the response of lake biota to anthropogenic stressors, opening up new avenues in the field of paleoecology by unrevealing a hidden historical biodiversity, building new paleo‐indicators, and reflecting either taxonomic or functional attributes. Broadly, sedDNA analyses provide new perspectives that can inform ecosystem management, conservation, and restoration by offering an approach to measure ecological integrity and vulnerability, as well as ecosystem functioning.

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The analysis of sediment DNA has emerged as a promising alternative to classical paleolimnological proxies, which typically rely on hard fossils to reconstruct environmental change. In recent studies, the timing and causes of apparent increases in toxic cyanobacterial blooms in lakes around the world have been identified by high‐throughput sequencing of cyanobacterial 16S rRNA genes from decadal‐ and centennial‐scale sediment records. However, the reconstruction of ecological time series can be influenced by DNA degradation processes interfering with taxonomic resolution and quantification of target genes. To determine whether some cyanobacterial taxa degrade more rapidly than others, a one‐year incubation experiment was performed to estimate degradation rates in sediments under contrasting environmental conditions of temperature (4°C vs. 25°C) and sediment redox (oxic vs. anoxic). Using sediments collected from an oligotrophic lake, serum bottles were inoculated with either Microcystis aeruginosa, Synechococcus sp., or Trichormus variabilis. These cyanobacteria were chosen because they are widespread yet exhibit contrasting morphologies. The absolute concentrations of the target genes were measured over time through droplet digital PCR. The three taxa exhibited log‐linear declines with different rates of decay. Based on first‐order linear decay models, Microcystis exhibited faster decay under oxic conditions, whereas Synechococcus sp. and Trichormus were both temperature and anoxic dependent. Overall, cyanobacterial decay rates were lowest under 4°C anoxic conditions, corresponding to conditions in deep temperate lakes. Under 4°C, Synechococcus exhibited the lowest degradation rates followed by Trichormus, then Microcystis. These findings will be useful in the interpretation of population and community structure data based on sediment DNA and advances our current understanding of cyanobacterial preservation in sediment.

Background SARS-CoV-2 can be detected from the built environment (e.g., floors), but it is unknown how the viral burden surrounding an infected patient changes over space and time. Characterizing these data can help advance our understanding and interpretation of surface swabs from the built environment. Methods We conducted a prospective study at two hospitals in Ontario, Canada between January 19, 2022 and February 11, 2022. We performed serial floor sampling for SARS-CoV-2 in rooms of patients newly hospitalized with COVID-19 in the past 48 hours. We sampled the floor twice daily until the occupant moved to another room, was discharged, or 96 hours had elapsed. Floor sampling locations included 1 metre (m) from the hospital bed, 2 m from the hospital bed, and at the room’s threshold to the hallway (typically 3 to 5 m from the hospital bed). The samples were analyzed for the presence of SARS-CoV-2 using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR). We calculated the sensitivity of detecting SARS-CoV-2 in a patient with COVID-19, and we evaluated how the percentage of positive swabs and the cycle threshold of the swabs changed over time. We also compared the cycle threshold between the two hospitals. Results Over the 6-week study period we collected 164 floor swabs from the rooms of 13 patients. The overall percentage of swabs positive for SARS-CoV-2 was 93% and the median cycle threshold was 33.4 (interquartile range [IQR]: 30.8, 37.2). On day 0 of swabbing the percentage of swabs positive for SARS-CoV-2 was 88% and the median cycle threshold was 33.6 (IQR: 31.8, 38.2) compared to swabs performed on day 2 or later where the percentage of swabs positive for SARS-CoV-2 was 98% and the cycle threshold was 33.2 (IQR: 30.6, 35.6). We found that viral detection did not change with increasing time (since the first sample collection) over the sampling period, Odds Ratio (OR) 1.65 per day (95% CI 0.68, 4.02; p = 0.27). Similarly, viral detection did not change with increasing distance from the patient’s bed (1 m, 2 m, or 3 m), OR 0.85 per metre (95% CI 0.38, 1.88; p = 0.69). The cycle threshold was lower (i.e., more virus) in The Ottawa Hospital (median quantification cycle [Cq] 30.8) where floors were cleaned once daily compared to the Toronto hospital (median Cq 37.2) where floors were cleaned twice daily. Conclusions We were able to detect SARS-CoV-2 on the floors in rooms of patients with COVID-19. The viral burden did not vary over time or by distance from the patient’s bed. These results suggest floor swabbing for the detection of SARS-CoV-2 in a built environment such as a hospital room is both accurate and robust to variation in sampling location and duration of occupancy.

Background Environmental surveillance of SARS-CoV-2 via wastewater has become an invaluable tool for population-level surveillance of COVID-19. Built environment sampling may provide a more spatially refined approach for surveillance of COVID-19 in congregate living settings and other high risk settings (e.g., schools, daycares). Methods We conducted a prospective study in 10 long-term care homes (LTCHs) across three cities in Ontario, Canada between September 2021 and May 2022. Floor surfaces were sampled weekly at multiple locations (range 10 to 24 swabs per building) within each building and analyzed for the presence of SARS-CoV-2 using RT-qPCR. The exposure variable was detection of SARS-CoV-2 on floors. The primary outcome was the presence of a COVID-19 outbreak in the week that floor sampling was performed. Results Over the 9-month study period, we collected 3848 swabs at 10 long-term care homes. During the study period, 19 COVID-19 outbreaks occurred with 103 cumulative weeks under outbreak. During outbreak periods, the proportion of floor swabs positive for SARS-CoV-2 was 50% (95% CI: 47-53) with a median quantification cycle of 37.3 (IQR 35.2-38.7). During non-outbreak periods the proportion of floor swabs positive was 18% (95% CI:17-20) with a median quantification cycle of 38.0 (IQR 36.4-39.1). Using the proportion of positive floor swabs for SARS-CoV-2 to predict COVID-19 outbreak status in a given week, the area under the receiver operating curve (AUROC) was 0.85 (95% CI: 0.78-0.92). Using thresholds of ≥10%, ≥30%, and ≥50% of floor swabs positive for SARS-CoV-2 yielded positive predictive values for outbreak of 0.57 (0.49-0.66), 0.73 (0.63-0.81), and 0.73 (0.6-0.83) respectively and negative predictive values of 0.94 (0.87-0.97), 0.85 (0.78-0.9), and 0.75 (0.68-0.81) respectively. Among 8 LTCHs with an outbreak and swabs performed in the antecedent week, 5 had positive floor swabs exceeding 10% at least five days prior to outbreak identification. For 3 of these 5 LTCHs, positivity of floor swabs exceeded 10% more than 10 days before the outbreak being identified. Conclusions Detection of SARS-CoV-2 on floors is strongly associated with COVID-19 outbreaks in LTCHs. These data suggest a potential role for floor sampling in improving early outbreak identification.