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.

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.

A reduction in macrophage (MPhi) function with aging makes mice less responsive to bacterial capsular polysaccharides, such as those present in the pneumococcal polysaccharide vaccine, a model of thymus independent (TI) antigen (Ag). Using trinitrophenol (TNP)-lipopolysaccharide (LPS) and TNP-Ficoll, two other well-studied TI Ag, we studied the mechanistic basis of reduced MPhi function in the aged. We show that aged mice are profoundly hyporesponsive to these TI Ag. As a result of a requirement for MPhi, highly purified B cells from young-adult mice do not respond to TI Ag. When purified, young B cells were immunized with TNP-Ficoll, the antibody production from those cultures reconstituted with MPhi from aged mice was significantly lower than that seen with young MPhi. Consequently, this unresponsiveness can be overcome by a mixture of interleukin (IL)-1beta and IL-6. Upon stimulation with LPS, in comparison with young MPhi, aged MPhi secreted reduced amounts of IL-6, tumor necrosis factor alpha, IL-1beta, and IL-12, cytokines necessary for B cells to respond to TI Ag. LPS also induced aged MPhi to produce an excess of IL-10. Neutralization of IL-10 enhanced the production of proinflamatory cytokines by MPhi upon LPS stimulation and also induced Ab production by aged splenocytes. Thus, the inability of aged MPhi to help the B cell response appears to be caused by an excess of IL-10. As aged MPhi have a reduced number of cells expressing Toll-like receptor 4 and CD14, the imbalance in cytokine production might be partly a result of fewer cells expressing key components of the LPS receptor complex.

Abstract. Headwater streams remove, transform, and store inorganic nitrogen (N) delivered from surrounding watersheds, but excessive N inputs from human activity can saturate removal capacity. Most research has focused on quantifying N removal from the water column over short periods and in individual reaches, and these ecosystem-scale measurements suggest that assimilatory N uptake accounts for most N removal. However, cross-system comparisons addressing the relative role of particular biota responsible for incorporating inorganic N into biomass are lacking. Here we assess the importance of different primary uptake compartments on reach-scale ammonium (NH 4 + -N) uptake and storage across a wide range of streams varying in abundance of biota and local environmental factors. We analyzed data from 17 15 N-NH 4 + tracer addition experiments globally, and found that assimilatory N uptake by autotrophic compartments (i.e., epilithic biofilm, filamentous algae, bryophytes/macrophytes) was higher but more variable than for heterotrophic microorganisms colonizing detrital organic matter (i.e., leaves, small wood, and fine particles). Autotrophic compartments played a disproportionate role in N uptake relative to their biomass, although uptake rates were similar when we rescaled heterotrophic assimilatory N uptake associated only with live microbial biomass. Assimilatory NH 4 + -N uptake, either estimated as removal from the water column or from the sum uptake of all individual compartments, was four times higher in open-than in closed-canopy streams. Using Bayesian Model Averaging, we found that canopy cover and gross primary production (GPP) controlled autotrophic assimilatory N uptake while ecosystem respiration (ER) was more important for the heterotrophic contribution. The ratio of autotrophic to heterotrophic N storage was positively correlated with metabolism (GPP: ER), which was also higher in open-than in closed-canopy streams. Our analysis shows riparian canopy cover influences the relative abundance of different biotic uptake compartments and thus GPP:ER. As such, the simple categorical variable of canopy cover explained differences in assimilatory N uptake among streams at the reach scale, as well as the relative roles of autotrophs and heterotrophs in N storage. Finally, this synthesis links cumulative N uptake by stream biota to reach-scale N demand and provides a mechanistic and predictive framework for estimating and modeling N cycling in other streams.

Neonates do not respond to thymus-independent (TI) antigens (Ag), making them vulnerable to infection with encapsulated bacteria. The antibody (Ab) response of adult and neonatal B cells to TI Ag requires certain cytokines, which are provided by T cells or macrophages (MPhi). Lipopolysaccharide (LPS) failed to induce neonatal MPhi to produce interleukin (IL)-1beta and tumor necrosis factor alpha (TNF-alpha) mRNA and to secrete IL-1beta, IL-12, and TNF-alpha. However, LPS induced neonates to secrete some IL-6 and three- to fivefold more IL-10 than adults. Accordingly, adding adult but not neonatal MPhi could restore the response of purified adult B cells to trinitrophenol (TNP)-LPS, a TI Ag. Increased IL-10 is causally related to decreased IL-1beta and IL-6 production, as IL-10(-/-) neonatal MPhi responded to LPS by secreting more IL-1beta and IL-6 than wild-type (WT) neonatal MPhi. When cultures were supplemented with a neutralizing Ab to IL-10, WT neonatal MPhi secreted increased amounts of IL-6 and allowed neonatal MPhi to promote adult B cells to mount an Ab response against TNP-LPS. Thus, neonates do not respond to TI Ag as a result of the inability of neonatal MPhi to secrete cytokines, such as IL-1beta and IL-6, probably as a result of an excess production of IL-10. This dysregulated cytokine secretion by neonatal MPhi may be a result of a reduction in expression of Toll-like receptor-2 (TLR-2) and TLR-4 and CD14.

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The United States (U.S.) has faced major environmental changes in recent decades, including agricultural intensification and urban expansion, as well as changes in atmospheric deposition and climate-all of which may influence eutrophication of freshwaters. However, it is unclear whether or how water quality in lakes across diverse ecological settings has responded to environmental change. We quantified water quality trends in 2913 lakes using nutrient and chlorophyll (Chl) observations from the Lake Multi-Scaled Geospatial and Temporal Database of the Northeast U.S. (LAGOS-NE), a collection of preexisting lake data mostly from state agencies. LAGOS-NE was used to quantify whether lake water quality has changed from 1990 to 2013, and whether lake-specific or regional geophysical factors were related to the observed changes. We modeled change through time using hierarchical linear models for total nitrogen (TN), total phosphorus (TP), stoichiometry (TN:TP), and Chl. Both the slopes (percent change per year) and intercepts (value in 1990) were allowed to vary by lake and region. Across all lakes, TN declined at a rate of 1.1% year , while TP, TN:TP, and Chl did not change. A minority (7%-16%) of individual lakes had changing nutrients, stoichiometry, or Chl. Of those lakes that changed, we found differences in the geospatial variables that were most related to the observed change in the response variables. For example, TN and TN:TP trends were related to region-level drivers associated with atmospheric deposition of N; TP trends were related to both lake and region-level drivers associated with climate and land use; and Chl trends were found in regions with high air temperature at the beginning of the study period. We conclude that despite large environmental change and management efforts over recent decades, water quality of lakes in the Midwest and Northeast U.S. has not overwhelmingly degraded or improved.

Growth of macroscale limnological research has been accompanied by an increase in secondary datasets compiled from multiple sources. We examined patterns of data availability in LAGOS-NE, a dataset derived from 87 sources, to identify biases in availability of lake water quality data and to consider how such biases might affect perceived patterns at a subcontinental scale. Of eight common water quality parameters, variables indicative of trophic state (Secchi, chlorophyll, and total P) were most abundant in terms of total observations, lakes sampled, and long-term records, whereas carbon variables (true color and dissolved organic carbon) were scarcest. Most data were collected during summer from larger (≥ 20 ha) lakes over 1-3 yr. Approximately 80% of data for each variable is derived from~20% of sampled lakes. Long-term (≥ 20 yr) records were rare and spatially clustered. Data availability is linked to major management challenges (eutrophication and acid rain), citizen science, and a few programs that quantify C and N variables. Resampling exercises suggested that correcting for the surface area sampling bias did not substantially change statistical distributions of the eight variables. Further, estimating a lake's long-term median Secchi, chlorophyll, and total P using average record lengths had high uncertainty, but modest increases in sample size to > 5 yr yielded estimates with manageable error. Although the specific nature of sampling biases may vary among regions, we expect that they are widespread. Thus, large integrated datasets can and should be used to identify tendencies in how lakes are studied and to address these biases as part broad-scale limnological investigations.