Winter conditions are rapidly changing in temperate ecosystems, particularly for those that experience periods of snow and ice cover. Relatively little is known of winter ecology in these systems, due to a historical research focus on summer 'growing seasons'. We executed the first global quantitative synthesis on under-ice lake ecology, including 36 abiotic and biotic variables from 42 research groups and 101 lakes, examining seasonal differences and connections as well as how seasonal differences vary with geophysical factors. Plankton were more abundant under ice than expected; mean winter values were 43.2% of summer values for chlorophyll a, 15.8% of summer phytoplankton biovolume and 25.3% of summer zooplankton density. Dissolved nitrogen concentrations were typically higher during winter, and these differences were exaggerated in smaller lakes. Lake size also influenced winter-summer patterns for dissolved organic carbon (DOC), with higher winter DOC in smaller lakes. At coarse levels of taxonomic aggregation, phytoplankton and zooplankton community composition showed few systematic differences between seasons, although literature suggests that seasonal differences are frequently lake-specific, species-specific, or occur at the level of functional group. Within the subset of lakes that had longer time series, winter influenced the subsequent summer for some nutrient variables and zooplankton biomass.

Disturbances act as powerful structuring forces on ecosystems. To ask whether environmental microbial communities have capacity to recover after a large disturbance event, we conducted a whole-ecosystem manipulation, during which we imposed an intense disturbance on freshwater microbial communities by artificially mixing a temperate lake during peak summer thermal stratification. We employed environmental sensors and water chemistry analyses to evaluate the physical and chemical responses of the lake, and bar-coded 16S ribosomal RNA gene pyrosequencing and automated ribosomal intergenic spacer analysis (ARISA) to assess the bacterial community responses. The artificial mixing increased mean lake temperature from 14 to 20 °C for seven weeks after mixing ended, and exposed the microorganisms to very different environmental conditions, including increased hypolimnion oxygen and increased epilimnion carbon dioxide concentrations. Though overall ecosystem conditions remained altered (with hypolimnion temperatures elevated from 6 to 20 °C), bacterial communities returned to their pre-manipulation state as some environmental conditions, such as oxygen concentration, recovered. Recovery to pre-disturbance community composition and diversity was observed within 7 (epilimnion) and 11 (hypolimnion) days after mixing. Our results suggest that some microbial communities have capacity to recover after a major disturbance.

1. Dissolved organic carbon (DOC) plays a central role in the dynamics of stream and river ecosystems, affecting processes such as metabolism, the balance between autotrophy and heterotrophy, acidity, nutrient uptake and bioavailability of toxic compounds. However, despite its importance to stream processes, restoration and management activities rarely incorporate DOC as a major management criterion. 2. Lotic DOC pools reflect terrestrial organic carbon accumulation, transfer to the river channel and aquatic processing. In pristine landscapes, characteristics such as topography, climate, and landscape composition are strong predictors of terrestrial accumulation and transfer. Within aquatic systems, the quantity and form of DOC are altered by a variety of processes including primary production, microbial breakdown, sorption to particles and photodegradation. 3. Terrestrial accumulation, transfer and aquatic processing of DOC in agricultural and other human-dominated landscapes are all subject to substantial change. Consequently, DOC pools in agricultural streams likely differ from historic conditions and now include more labile material and low concentrations of a variety of ubiquitous synthetic organic compounds (e.g. pesticides, antibiotics). 4. Although DOC change in agricultural streams and associated ecological consequences are expected to be widespread, current understanding and relevant data needed to manage affected systems are surprisingly scarce. 5. Wetland and riparian restoration projects have variable effects on fluvial DOC regimes, but management at this intermediate scale is a realistic compromise between the small extent of most restoration projects and the large spatial scale over which organic carbon impairment occurs.

The development of complete regional carbon (C) budgets for different biomes is an integral step in the effort to predict global response and potential feedbacks to a changing climate regime. Wetland and lake contributions to regional C cycling remain relatively uncertain despite recent research highlighting their importance. Using a combination of field surveys and tower-based carbon dioxide (CO 2 ) flux measurements, modeling, and published literature, we constructed a complete C budget for the Northern Highlands Lake District in northern Wisconsin/ Michigan, a $6400 km 2 region rich in lakes and wetlands. This is one of the first regional C budgets to incorporate aquatic and terrestrial C cycling under the same framework. We divided the landscape into three major compartments (forests, wetlands, and surface waters) and quantified all major C fluxes into and out of those compartments, with a particular focus on atmospheric exchange but also including sedimentation in lakes and hydrologic fluxes. Landscape C storage was dominated by peat-containing wetlands and lake sediments, which make up only 20% and 13% of the landscape area, respectively, but contain 480% of the total fixed C pool (ca. 400 Tg). We estimated a current regional C accumulation of 1.1 AE 0.1 Tg yr À1 , and the largest regional flux was forest net ecosystem exchange (NEE) into aggrading forests for a total of 1.0 AE 0.1 Tg yr À1 . Mean wetland NEE (0.12 AE 0.06 Tg yr À1 into wetlands), lake CO 2 emissions and riverine efflux (each ca. 0.03 AE 0.01 Tg yr À1 ) were smaller but of consequence to the overall budget. Hydrologic transport from uplands/wetlands to surface waters within the region was an important vector of terrestrial C. Regional C fluxes and pools would be misrepresented without inclusion of surface waters and wetlands, and C budgets in heterogeneous landscapes open opportunities to examine the sensitivities of important fluxes to changes in climate and land use/land cover.

Although there are considerable site-based data for individual or groups of ecosystems, these datasets are widely scattered, have different data formats and conventions, and often have limited accessibility. At the broader scale, national datasets exist for a large number of geospatial features of land, water, and air that are needed to fully understand variation among these ecosystems. However, such datasets originate from different sources and have different spatial and temporal resolutions. By taking an open-science perspective and by combining site-based ecosystem datasets and national geospatial datasets, science gains the ability to ask important research questions related to grand environmental challenges that operate at broad scales. Documentation of such complicated database integration efforts, through peer-reviewed papers, is recommended to foster reproducibility and future use of the integrated database. Here, we describe the major steps, challenges, and considerations in building an integrated database of lake ecosystems, called LAGOS (LAke multi-scaled GeOSpatial and temporal database), that was developed at the sub-continental study extent of 17 US states (1,800,000 km2). LAGOS includes two modules: LAGOSGEO, with geospatial data on every lake with surface area larger than 4 ha in the study extent (~50,000 lakes), including climate, atmospheric deposition, land use/cover, hydrology, geology, and topography measured across a range of spatial and temporal extents; and LAGOSLIMNO, with lake water quality data compiled from ~100 individual datasets for a subset of lakes in the study extent (~10,000 lakes). Procedures for the integration of datasets included: creating a flexible database design; authoring and integrating metadata; documenting data provenance; quantifying spatial measures of geographic data; quality-controlling integrated and derived data; and extensively documenting the database. Our procedures make a large, complex, and integrated database reproducible and extensible, allowing users to ask new research questions with the existing database or through the addition of new data. The largest challenge of this task was the heterogeneity of the data, formats, and metadata. Many steps of data integration need manual input from experts in diverse fields, requiring close collaboration.Electronic supplementary materialThe online version of this article (doi:10.1186/s13742-015-0067-4) contains supplementary material, which is available to authorized users.

Ecologists are increasingly discovering that ecological processes are made up of components that are multi‐scaled in space and time. Some of the most complex of these processes are cross‐scale interactions (CSIs), which occur when components interact across scales. When undetected, such interactions may cause errors in extrapolation from one region to another. CSIs, particularly those that include a regional scaled component, have not been systematically investigated or even reported because of the challenges of acquiring data at sufficiently broad spatial extents. We present an approach for quantifying CSIs and apply it to a case study investigating one such interaction, between local and regional scaled land‐use drivers of lake phosphorus. Ultimately, our approach for investigating CSIs can serve as a basis for efforts to understand a wide variety of multi‐scaled problems such as climate change, land‐use/land‐cover change, and invasive species.

Understanding the factors that affect water quality and the ecological services provided by freshwater ecosystems is an urgent global environmental issue. Predicting how water quality will respond to global changes not only requires water quality data, but also information about the ecological context of individual water bodies across broad spatial extents. Because lake water quality is usually sampled in limited geographic regions, often for limited time periods, assessing the environmental controls of water quality requires compilation of many data sets across broad regions and across time into an integrated database. LAGOS-NE accomplishes this goal for lakes in the northeastern-most 17 US states.LAGOS-NE contains data for 51 101 lakes and reservoirs larger than 4 ha in 17 lake-rich US states. The database includes 3 data modules for: lake location and physical characteristics for all lakes; ecological context (i.e., the land use, geologic, climatic, and hydrologic setting of lakes) for all lakes; and in situ measurements of lake water quality for a subset of the lakes from the past 3 decades for approximately 2600–12 000 lakes depending on the variable. The database contains approximately 150 000 measures of total phosphorus, 200 000 measures of chlorophyll, and 900 000 measures of Secchi depth. The water quality data were compiled from 87 lake water quality data sets from federal, state, tribal, and non-profit agencies, university researchers, and citizen scientists. This database is one of the largest and most comprehensive databases of its type because it includes both in situ measurements and ecological context data. Because ecological context can be used to study a variety of other questions about lakes, streams, and wetlands, this database can also be used as the foundation for other studies of freshwaters at broad spatial and ecological scales.

Aquatic ecosystems are important components of landscape carbon budgets. In lake-rich landscapes, both lakes and streams may be important sources of carbon gases (CO 2 and CH 4 ) to the atmosphere, but the processes that control gas concentrations and emissions in these interconnected landscapes have not been adequately addressed. We use multiple data sets that vary in their spatial and temporal extent during 2001-2012 to investigate the carbon gas source strength of streams in a lake-rich landscape and to determine the contribution of lakes, metabolism, and groundwater to stream CO 2 and CH 4 . We show that streams emit roughly the same mass of CO 2 (23.4 Gg C yr À1 ; 0.49 mol CO 2 m À2 d À1 ) as lakes at a regional scale (27 Gg C yr À1 ) and that stream CH 4 emissions (189 Mg C yr À1 ; 8.46 mmol CH 4 m À2 d À1 ) are an important component of the regional greenhouse gas balance. Gas transfer velocity variability (range = 0.34 to 13.5 m d À1 ) contributed to the variability of gas flux in this landscape. Groundwater inputs and in-stream metabolism control stream gas supersaturation at the landscape scale, while carbon cycling in lakes and deep groundwaters does not control downstream gas emissions. Our results indicate the need to consider connectivity of all aquatic ecosystems (lakes, streams, wetlands, and groundwater) in lake-rich landscapes and their connections with the terrestrial environment in order to understand the full nature of the carbon cycle.