Comparing Quantitative Methods for Analyzing Sediment DNA Records of Cyanobacteria in Experimental and Reference Lakes

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

Response of Lacustrine Biota to Late Holocene Climate and Environmental Conditions in Northernmost Ungava (Canada)

Sediment cores from three lakes located in the northernmost region of Ungava, Québec (Canada) were examined to define aquatic community and ecosystem variability during the Late Holocene period. A chironomid-based transfer function was used to reconstruct August air temperature trends, and lacustrine primary production was inferred from sedimentary biogenic silica content and siliceous microfossil abundances. Trends in primary production, sediment organic matter content (estimated through loss on ignition), and chironomid-inferred temperature were compared to explore potential effects of environmental change on biotic assemblage composition at centennial to millennial time scales. Although no direct correlation between chironomid-inferred August air temperature and primary production was observed, we found indications that both chironomid and diatom communities were responding to the same overarching regional climatic and environmental processes. Over the last decade, northern Québec has been undergoing notable, rapid warming that contrasts with the relative inertia of the past few millennia. This study provides a baseline against which recent and future environmental changes in this region can be compared. Les archives sédimentaires couvrant la période de l’Holocène tardif ont été examinées dans trois lacs situés dans la région du nord de l’Ungava, au Québec (Canada). Un modèle d’inférence basé sur les assemblages de chironomides a été utilisé pour reconstruire la variabilité des températures de l’air du mois d’août, et la production primaire lacustre a été inférée par le contenu sédimentaire en silice biogénique et les abondances des microfossiles siliceux. Les variations historiques de la production primaire, du contenu organique du sédiment (évalué par la perte au feu) et les températures inférées ont été comparées afin d’explorer les effets potentiels des changements environnementaux sur la composition des assemblages à différentes échelles temporelles (centenaires à millénaires). Malgré le fait qu’aucune corrélation directe n’ait été observée entre les températures inférées en août et la productivité primaire, certaines indications suggèrent que les communautés de chironomides et de diatomées répondaient aux mêmes processus climatiques et environnementaux régionaux. Au cours de la dernière décennie, le nord du Québec a connu un réchauffement rapide et marqué, contrastant avec l’inertie relative des derniers millénaires. Cette étude fournit le scénario de référence par rapport auquel les changements environnementaux actuels et futurs pourront être comparés dans cette région

Reconstructing changes in macrophyte cover in lakes across the northeastern United States based on sedimentary diatom assemblages

Abstract Macrophytes are a critical component of lake ecosystems affecting nutrient and contaminant cycling, food web structure, and lake biodiversity. The long-term (decades to centuries) dynamics of macrophyte cover are, however, poorly understood and no quantitative estimates exist for pre-industrial (pre-1850) macrophyte cover in northeastern North America. Using a 215 lake dataset, we tested if surface sediment diatom assemblages significantly differed among lakes that have sparse (<10% cover; group 1), moderate (10-40% cover; group 2) or extensive (>40% cover; group 3) macrophyte cover. Analysis of similarity indicated that the diatom assemblages of these a priori groups of macrophyte cover were significantly different from one another (i.e., difference between: groups 1 and 3, R statistic = 0.31, P < 0.001; groups 1 and 2, R statistic = 0.049, P < 0.01; groups 3 and 2, R statistic = 0.112, P < 0.001). We then developed an inference model for macrophyte cover from lakes classified as sparse or extensive cover (145 lakes) based on the surface sediment diatom assemblages, and applied this model using the top-bottom paleolimnological approach (i.e., comparison of recent sediments to pre-disturbance sediments). We used the second axis of our correspondence analysis, which significantly divided sparse and extensive macrophyte cover sites, as the independent variable in a logistic regression to predict macrophyte cover as either sparse or extensive. Cross validation, using 48 randomly chosen sites that were excluded from model development, indicated that our model accurately predicts macrophyte cover 79% of the time (r 2 = 0.32, P < 0.001). When applied to the top and bottom sediment samples, our model predicted that 12.5% of natural lakes and 22.4% of reservoirs in the dataset have undergone a ! 30% change in macrophyte cover. For the sites with an inferred change in macrophyte cover, the majority of natural lakes (64.3%) increased in cover, while the majority of reservoirs (87.5%) decreased in macrophyte cover. This study demonstrates that surface sediment diatom assemblages from profundal zones differ in lakes based on their macrophyte cover and that diatoms are useful indicators for quantitatively reconstructing changes in macrophyte cover

Land-Use Legacies Are Important Determinants of Lake Eutrophication in the Anthropocene

Background: A hallmark of the latter half of the 20 th century is the widespread, rapid intensification of a variety of anthropogenically-driven environmental changes—a ‘‘Great Acceleration.’ ’ While there is evidence of a Great Acceleration in a variety of factors known to be linked to water quality degradation, such as conversion of land to agriculture and intensification of fertilizer use, it is not known whether there has been a similar acceleration of freshwater eutrophication. Methodology/Principal Findings: Using quantitative reconstructions of diatom-inferred total phosphorus (DI-TP) as a proxy for lake trophic state, we synthesized results from 67 paleolimnological studies from across Europe and North America to evaluate whether most lakes showed a pattern of eutrophication with time and whether this trend was accelerated after 1945 CE, indicative of a Great Acceleration. We found that European lakes have experienced widespread increases in DI-TP over the 20 th century and that 33 % of these lakes show patterns consistent with a post-1945 CE Great Acceleration. In North America, the proportion of lakes that increased in DI-TP over time is much lower and only 9 % exhibited a Great Acceleration of eutrophication. Conclusions/Significance: The longer and more widespread history of anthropogenic influence in Europe, the leading cause for the relatively pervasive freshwater eutrophication, provides an important cautionary tale; our current path of intensive agriculture around the world may lead to an acceleration of eutrophication in downstream lakes that could tak

Long-Term Hydrologic Fluctuations and Dynamics of Primary Producers in a Tropical Crater Lake

Aquatic ecosystems in tropical regions remain understudied and their long-term dynamics poorly understood. In East Africa, a better understanding of how natural communities of primary producers in small freshwater ecosystems respond to climatic variability is needed to improve management and conservation of aquatic resources. This study explored the response of algae and bacteria communities to marked hydrological variation over the past 1,500 years in a small western Ugandan crater lake, Lake Nkuruba. We analyzed sedimentary algal and bacterial pigments to evaluate the magnitude and direction of change in the autotrophic community in response to severe climatic perturbations in the region. The lithology of the Lake Nkuruba sediment core indicated that external forcing in the form of a major drought, associated with the Medieval Climate Anomaly, caused a heavy, short-lived detrital pulse to the basin that led to a brief but substantial disruption of the lake system in the second half of the Thirteenth century. The system appears to have recovered rapidly, and then transitioned to a more productive state than the one preceding the drought. The considerable variation observed in the sedimentary pigment biomarkers is likely linked with climatically-induced changes in the water column structure of this small crater lake. Our results highlight the challenge of defining appropriate baselines or reference conditions in climatically-sensitive East African aquatic ecosystems and disentangling long-term anthropogenic impacts from the strong regional hydrological flux at the decadal to centennial scale

Diverse perspectives on interdisciplinarity from Members of the College of the Royal Society of Canada

Various multiple-disciplinary terms and concepts (although most commonly interdisciplinarity, which is used herein) are used to frame education, scholarship, research, and interactions within and outside academia. In principle, the premise of interdisciplinarity may appear to have many strengths; yet, the extent to which interdisciplinarity is embraced by the current generation of academics, the benefits and risks for doing so, and the barriers and facilitators to achieving interdisciplinarity, represent inherent challenges. Much has been written on the topic of interdisciplinarity, but to our knowledge there have been few attempts to consider and present diverse perspectives from scholars, artists, and scientists in a cohesive manner. As a team of 57 members from the Canadian College of New Scholars, Artists, and Scientists of the Royal Society of Canada (the College) who self-identify as being engaged or interested in interdisciplinarity, we provide diverse intellectual, cultural, and social perspectives. The goal of this paper is to share our collective wisdom on this topic with the broader community and to stimulate discourse and debate on the merits and challenges associated with interdisciplinarity. Perhaps the clearest message emerging from this exercise is that working across established boundaries of scholarly communities is rewarding, necessary, and is more likely to result in impact. However, there are barriers that limit the ease with which this can occur (e.g., lack of institutional structures and funding to facilitate cross-disciplinary exploration). Occasionally, there can be significant risk associated with doing interdisciplinary work (e.g., lack of adequate measurement or recognition of work by disciplinary peers). Solving many of the world\u27s complex and pressing problems (e.g., climate change, sustainable agriculture, the burden of chronic disease, and aging populations) demands thinking and working across long-standing, but in some ways restrictive, academic boundaries. Academic institutions and key support structures, especially funding bodies, will play an important role in helping to realize what is readily apparent to all who contributed to this paper-that interdisciplinarity is essential for solving complex problems; it is the new norm. Failure to empower and encourage those doing this research will serve as a great impediment to training, knowledge, and addressing societal issues

Prioritizing taxa for genetic reference database development to advance inland water conservation

Biodiversity loss has accelerated over the past century and freshwater species overall are among those experiencing greatest declines. Genetic resources have the potential to help evaluate the full magnitude of this loss and represent a key tool to effectively allocate conservation resources and monitor the success of restoration efforts. The full power of genetic resources will be realized when the daunting task of referencing all DNA sequences of freshwater organisms is complete. Here, we quantified the availability and distribution of barcode and genome data for freshwater macroscopic organisms in Canada, a country rich in inland water resources and thus particularly vulnerable to aquatic species losses. Impressively, most inland water species (86 %) were represented by barcodes recorded in the BOLD Systems database, while very few had full genomes available (<4 %) in the NCBI database. We identified barcode data deficiencies in northern regions and for taxa assessed as most at risk or without sufficient information for conservation status classification. As expected, the speciose insect group had a lower-than-average number of records per species and a high proportion of data deficient species without adequate barcode coverage. This study highlights where future sequencing resources should be prioritized within initiatives such as the Canada BioGenome Project and BIOSCAN Canada and provides a workflow that could be applied internationally to inform conservation management plans and to mitigate biodiversity loss

First human impacts and responses of aquatic systems: a review of palaeolimnological records from around the world

Lake sediments constitute natural archives of past environmental changes. Historically, research has focused mainly on generating regional climate records, but records of human impacts caused by land use and exploitation of freshwater resources are now attracting scientific and management interests. Long-term environmental records are useful to establish ecosystem reference conditions, enabling comparisons with current environments and potentially allowing future trajectories to be more tightly constrained. Here we review the timing and onset of human disturbance in and around inland water ecosystems as revealed through sedimentary archives from around the world. Palaeolimnology provides access to a wealth of information reflecting early human activities and their corresponding aquatic ecological shifts. First human impacts on aquatic systems and their watersheds are highly variable in time and space. Landscape disturbance often constitutes the first anthropogenic signal in palaeolimnological records. While the effects of humans at the landscape level are relatively easily demonstrated, the earliest signals of human-induced changes in the structure and functioning of aquatic ecosystems need very careful investigation using multiple proxies. Additional studies will improve our understanding of linkages between human settlements, their exploitation of land and water resources, and the downstream effects on continental water

Diverse perspectives on interdisciplinarity from the Members of the College of the Royal Society of Canada

Various multiple-disciplinary terms and concepts (although most commonly “interdisciplinarity”, which is used herein) are used to frame education, scholarship, research, and interactions within and outside academia. In principle, the premise of interdisciplinarity may appear to have many strengths; yet, the extent to which interdisciplinarity is embraced by the current generation of academics, the benefits and risks for doing so, and the barriers and facilitators to achieving interdisciplinarity represent inherent challenges. Much has been written on the topic of interdisciplinarity, but to our knowledge there have been few attempts to consider and present diverse perspectives from scholars, artists, and scientists in a cohesive manner. As a team of 57 members from the Canadian College of New Scholars, Artists, and Scientists of the Royal Society of Canada (the College) who self-identify as being engaged or interested in interdisciplinarity, we provide diverse intellectual, cultural, and social perspectives. The goal of this paper is to share our collective wisdom on this topic with the broader community and to stimulate discourse and debate on the merits and challenges associated with interdisciplinarity. Perhaps the clearest message emerging from this exercise is that working across established boundaries of scholarly communities is rewarding, necessary, and is more likely to result in impact. However, there are barriers that limit the ease with which this can occur (e.g., lack of institutional structures and funding to facilitate cross-disciplinary exploration). Occasionally, there can be significant risk associated with doing interdisciplinary work (e.g., lack of adequate measurement or recognition of work by disciplinary peers). Solving many of the world’s complex and pressing problems (e.g., climate change, sustainable agriculture, the burden of chronic disease, and aging populations) demand thinking and working across long-standing, but in some ways restrictive, academic boundaries. Academic institutions and key support structures, especially funding bodies, will play an important role in helping to realize what is readily apparent to all who contributed to this paper—that interdisciplinarity is essential for solving complex problems; it is the new norm. Failure to empower and encourage those doing this research will serve as a great impediment to training, knowledge, and addressing societal issues

The Changing Landscape for Stroke\ua0Prevention in AF: Findings From the GLORIA-AF Registry Phase 2

Background GLORIA-AF (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients with Atrial Fibrillation) is a prospective, global registry program describing antithrombotic treatment patterns in patients with newly diagnosed nonvalvular atrial fibrillation at risk of stroke. Phase 2 began when dabigatran, the first non\u2013vitamin K antagonist oral anticoagulant (NOAC), became available. Objectives This study sought to describe phase 2 baseline data and compare these with the pre-NOAC era collected during phase&nbsp;1. Methods During phase 2, 15,641 consenting patients were enrolled (November 2011 to December 2014); 15,092 were eligible. This pre-specified cross-sectional analysis describes eligible patients\u2019 baseline characteristics. Atrial fibrillation&nbsp;disease characteristics, medical outcomes, and concomitant diseases and medications were collected. Data were analyzed using descriptive statistics. Results Of the total patients, 45.5% were female; median age was 71 (interquartile range: 64, 78) years. Patients were from Europe (47.1%), North America (22.5%), Asia (20.3%), Latin America (6.0%), and the Middle East/Africa (4.0%). Most had high stroke risk (CHA2DS2-VASc [Congestive heart failure, Hypertension, Age&nbsp; 6575 years, Diabetes mellitus, previous Stroke, Vascular disease, Age 65 to 74 years, Sex category] score&nbsp; 652; 86.1%); 13.9% had moderate risk (CHA2DS2-VASc&nbsp;= 1). Overall, 79.9% received oral anticoagulants, of whom 47.6% received NOAC and 32.3% vitamin K antagonists (VKA); 12.1% received antiplatelet agents; 7.8% received no antithrombotic treatment. For comparison, the proportion of phase 1 patients (of N&nbsp;= 1,063 all eligible) prescribed VKA was 32.8%, acetylsalicylic acid 41.7%, and no therapy 20.2%. In Europe in phase 2, treatment with NOAC was more common than VKA (52.3% and 37.8%, respectively); 6.0% of patients received antiplatelet treatment; and 3.8% received no antithrombotic treatment. In North America, 52.1%, 26.2%, and 14.0% of patients received NOAC, VKA, and antiplatelet drugs, respectively; 7.5% received no antithrombotic treatment. NOAC use was less common in Asia (27.7%), where 27.5% of patients received VKA, 25.0% antiplatelet drugs, and 19.8% no antithrombotic treatment. Conclusions The baseline data from GLORIA-AF phase 2 demonstrate that in newly diagnosed nonvalvular atrial fibrillation patients, NOAC have been highly adopted into practice, becoming more frequently prescribed than VKA in&nbsp;Europe and North America. Worldwide, however, a large proportion of patients remain undertreated, particularly in&nbsp;Asia&nbsp;and North America. (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients With Atrial Fibrillation [GLORIA-AF]; NCT01468701