Reproducibility is a key tenet of the scientific process that dictates the reliability and generality of results and methods. The complexities of ecological observations and data present novel challenges in satisfying needs for reproducibility and also transparency. Ecological systems are dynamic and heterogeneous, interacting with numerous factors that sculpt natural history and that investigators cannot completely control. Observations may be highly dependent on spatial and temporal context, making them very difficult to reproduce, but computational reproducibility can still be achieved. Computational reproducibility often refers to the ability to produce equivalent analytical outcomes from the same data set using the same code and software as the original study. When coded workflows are shared, authors and editors provide transparency for readers and allow other researchers to build directly and efficiently on primary work. These qualities may be especially important in ecological applications that have important or controversial implications for science, management, and policy. Expectations for computational reproducibility and transparency are shifting rapidly in the sciences. In this work, we highlight many of the unique challenges for ecology along with practical guidelines for reproducibility and transparency, as ecologists continue to participate in the stewardship of critical environmental information and ensure that research methods demonstrate integrity.

Ancient lakes are among the best archivists of past environmental change, having experienced more than one full glacial cycle, a wide range of climatic conditions, tectonic events, and long association with human settlements. These lakes not only record long histories of environmental variation and human activity in their sediments, but also harbor very high levels of biodiversity and endemism. Yet, ancient lakes are faced with a familiar suite of anthropogenic threats, which may degrade the unusual properties that make them especially valuable to science and society. In all ancient lakes for which data exist, significant warming of surface waters has occurred, with a broad range of consequences. Eutrophication threatens both native species assemblages and regional economies reliant on clean surface water, fisheries, and tourism. Where sewage contributes nutrients and heavy metals, one can anticipate the occurrence of less understood emerging contaminants, such as pharmaceuticals, personal care products, and microplastics that negatively affect lake biota and water quality. Human populations continue to increase in most of the ancient lakes’ watersheds, which will exacerbate these concerns. Further, human alterations of hydrology, including those produced through climate change, have altered lake levels. Co‐occurring with these impacts have been intentional and unintentional species introductions, altering biodiversity. Given that the distinctive character of each ancient lake is strongly linked to age, there may be few options to remediate losses of species or other ecosystem damage associated with modern ecological change, heightening the imperative for understanding these systems.

Food production hinges largely upon access to phosphorus (P) fertilizer. Most fertilizer P used in the global agricultural system comes from mining of nonrenewable phosphate rock deposits located within few countries. However, P contained in livestock manure or urban wastes represents a recyclable source of P. To inform development of P recycling technologies and policies, we examined subnational, national, and global spatial patterns for two intersections of land use affording high P recycling potential: (a) manure‐rich cultivated areas and (b) populous cultivated areas. In turn, we examined overlap between P recycling potential and nation‐level P fertilizer import dependency. Populous cultivated areas were less abundant globally than manure‐rich cultivated areas, reflecting greater segregation between crops and people compared to crops and livestock, especially in the Americas. Based on a global hexagonal grid (290‐km² grid cell area), disproportionately large shares of subnational “hot spots” for P recycling potential occurred in India, China, Southeast Asia, Europe, and parts of Africa. Outside of China, most of the remaining manure‐rich or populous cultivated areas occurred within nations that had relatively high imports of P fertilizer (net P import:consumption ratios ≥0.4) or substantial increases in fertilizer demand between the 2000s (2002–2006) and 2010s (2010–2014). Manure‐rich cultivated grid cells (those above the 75th percentiles for both manure and cropland extent) represented 12% of the global grid after excluding cropless cells. Annually, the global sum of animal manure P was at least 5 times that contained in human excreta, and among cultivated cells the ratio was frequently higher (median = 8.9). The abundance of potential P recycling hot spots within nations that have depended on fertilizer imports or experienced rising fertilizer demand could prove useful for developing local P sources and maintaining agricultural independence.

Millions of lakes worldwide are distributed at latitudes or elevations resulting in the formation of lake ice during winter. Lake ice affects the transfer of energy, heat, light, and material between lakes and their surroundings creating an environment dramatically different from open‐water conditions. While this fundamental restructuring leads to distinct gradients in ions, dissolved gases, and nutrients throughout the water column, surprisingly little is known about the resulting effects on ecosystem processes and food webs, highlighting the lack of a general limnological framework that characterizes the structure and function of lakes under a gradient of ice cover. Drawing from the literature and three novel case studies, we present the Lake Ice Continuum Concept (LICC) as a model for understanding how key aspects of the physical, chemical, and ecological structure and function of lakes vary along a continuum of winter climate conditions mediated by ice and snow cover. We examine key differences in energy, redox, and ecological community structure and describe how they vary in response to shifts in physical mixing dynamics and light availability for lakes with ice and snow cover, lakes with clear ice alone, and lakes lacking winter ice altogether. Global change is driving ice covered lakes toward not only warmer annual average temperatures but also reduced, intermittent or no ice cover. The LICC highlights the wide range of responses of lakes to ongoing climate‐driven changes in ice cover and serves as a reminder of the need to understand the role of winter in the annual aquatic cycle.

The duration of winter ice cover on lakes varies substantially with climate variability, and has decreased over the last several decades in many temperate lakes. However, little is known of how changes in seasonal ice cover may affect biogeochemical processes under ice. We examined winter nitrogen (N) dynamics under ice using a 30+ yr dataset from five oligotrophic/mesotrophic north temperate lakes to determine how changes in inorganic N species varied with ice duration. Nitrate accumulated during winter and was strongly related to the number of days since ice‐on. Exogenous inputs accounted for less than 3% of nitrate accumulation in four of the five lakes, suggesting a paramount role of nitrification in regulating N transformation and the timing of chemical conditions under ice. Winter nitrate accumulation rates ranged from 0.15 μg N L⁻¹ d⁻¹ to 2.7 μg N L⁻¹ d⁻¹ (0.011–0.19 μM d⁻¹), and the mean for intermediate depths was 0.94 μg N L⁻¹ d⁻¹ (0.067 μM d⁻¹). Given that winters with shorter ice duration (< 120 d) have become more frequent in these lakes since the late 1990s, peak winter nitrate concentrations and cumulative nitrate production under ice may be declining. As ice extent and duration change, the physical and chemical conditions supporting life will shift. This research suggests we may expect changes in the form and amount of inorganic N, and altered dissolved nitrogen : phosphorus ratios, in lakes during winters with shorter ice duration.

In lakes that experience seasonal ice cover, understanding of nitrogen–oxygen coupling and nitrification has been dominated by observations during open water, ice-free conditions. To address knowledge gaps about nitrogen–oxygen linkages under ice, we examined long-term winter data (30 + years, 2–3 sample events per winter) in 7 temperate lakes of forested northern Wisconsin, USA. Across lakes and depths, there were strong negative relationships between dissolved oxygen (DO) and the number of days since ice-on, reflecting consistent DO consumption rates under ice. In two bog lakes that routinely experience prolonged winter DO concentrations below 1.0 mg L⁻¹, nitrate accumulated near the ice surface mainly in late winter, suggesting nitrification may depend on biogenic oxygen from photosynthesis. In contrast, within five oligotrophic-mesotrophic lakes, nitrate accumulated more consistently over winter and often throughout the water column, especially at intermediate depths. Exogenous inputs of nitrate to these lakes were minimal compared to rates of nitrate accumulation. To produce the nitrate via in-lake nitrification, substantial oxygen consumption by ammonium oxidizing microbes would be required. Among lakes and depths that had significant DO depletion over winter, the stoichiometric nitrifier oxygen demand ranged from 1 to 25% of the DO depletion rate. These estimates of nitrifier-driven DO decline are likely conservative because we did not account for nitrate consumed by algal uptake or denitrification. Our results provide an example of nitrification at temperatures < 5 degrees C having a substantial influence on ecosystem-level nitrogen and oxygen availability in seasonally-frozen, northern forested lakes. Consequently, models of under-ice dissolved oxygen dynamics may be advanced through consideration of nitrification, and more broadly, coupled nitrogen and oxygen cycling.