Jonathan Cole

Cary Institute of Ecosystem Studies | CIES · Research

Aim: We discuss the biogeochemistry of carbon in lakes and illustrate its main flows and transformation processes. We cover how and in what forms carbon enters lake ecosystems, how carbon is transformed within lakes, and the pathways through which it is transported out. We describe the main processes involved in the transformation of carbon between...

Freshwater reservoirs are a known source of greenhouse gas (GHG) to the atmosphere, but their quantitative significance is still only loosely constrained. Although part of this uncertainty can be attributed to the difficulties in measuring highly variable fluxes, it is also the result of a lack of a clear accounting methodology, particularly about...

Ecosystem regime shifts are abrupt changes from one dynamical state to another, such as the shift from a clear-water state to an algal bloom state in lakes. These transitions are hard to forecast but theory suggests early warning indicators can predict impending regime shifts which may allow for management intervention to prevent or mitigate an unw...

Significance Blooms of cyanobacteria in lakes and reservoirs cause fish kills and pose toxicity risk for humans, livestock, and wildlife. Theory suggests that blooms may be anticipated in advance by calculating resilience indicators using high-frequency observations of pigments in lake water. However, it is not known whether management can prevent...

CO2 emissions from inland waters are commonly determined by indirect methods that are based on the product of a gas transfer coefficient and the concentration gradient at the air water interface (e.g., wind-based gas transfer models). The measurements of concentration gradient are typically collected during the day in fair weather throughout the co...

It is well established that lakes are typically sources of CO2 to the atmosphere. However, it remains unclear what portion of CO2 efflux is from endogenously processed organic carbon or from exogenously produced CO2 transported into lakes. We estimated high frequency CO2 and O2 efflux from three north temperate lakes in summer to determine the prop...

Terrestrial organic matter can be assimilated by aquatic consumers but implications for biomass and production are unresolved. An ecosystem model was fit to estimate effects of phosphorus (P) load, planktivory, and supply rate of terrestrial particulate organic carbon (TPOC) on phytoplankton and zooplankton in five whole-lake experiments. Phytoplan...

Many ecosystems are likely to experience abrupt changes and extreme conditions due to forces such as climate change. These events and their consequences - including the loss of ecosystem services - may be predictable or may occur without warning. Given these considerations, greater efforts are needed in two areas of research: improvements in early...

Hydrogen stable isotopes (δ2H) are used for quantifying resources supporting food webs. However, application of δ2H in mixing models requires; (1) correction for environmental water (ω) in consumer tissues, (2) consideration of differential fractionation among biochemical constituents, and (3) consideration of differential H-exchange among samples...

Theory suggests that alternative resources may begin to support a food web when highly used resources become less available relative to alternatives. To test the potential for alternative resources to support consumers, we experimentally darkened a lake whose consumers had relied heavily on algal resources (phytoplankton and benthic algae). We esti...

Many lakes have positive, heterograde vertical oxygen (O2) profiles with a metalimnetic maximum usually assumed to be the result of biological O2 production. However, supersaturated metalimnetic O2 maxima are formed by biological processes (net photosynthetic production of O2) and physical processes (warming of gasses trapped below the thermocline)...

Dissolved inorganic carbon (DIC) is present in all natural waters. The concentration of DIC varies from less than 20μM in acidic soft waters to more than 5000μM in highly alkaline hard waters, but ranges between 100 and 1000μM in most systems. DIC is usually the most abundant form of C in water. DIC consists of three main constituents: free CO2 (a...

A Global Lake Ecological Observatory Network (GLEON; www.gleon.org) has formed to provide a coordinated response to the need for scientific understanding of lake processes, utilising technological advances available from autonomous sensors. The organisation embraces a grassroots approach to engage researchers from varying disciplines, sites spannin...

Like many large-river ecosystems, the Hudson River has been changing rapidly, chiefly as a result of human activities. Many of these changes take place on a decadal timescale, longer than the duration of most ecological studies. We use long-term studies of the Hudson to describe decadal-scale change in this ecosystem. Major impacts on the Hudson...

Resources in lakes are vertically partitioned due to stratification and trophic interactions. Metalimnetic phytoplankton could be an important resource for zooplankton that either reside in the metalimnion or migrate through this layer. However, it is difficult to estimate metalimnetic resource use, especially using isotope approaches, because surf...

Studies designed to assess the resources supporting aquatic consumers using stable isotope analysis require measure-ments of the potential end members (basal resources). While some basal resources are easily measured, it is often difficult to physically separate phytoplankton (one potential end member) from other components in seston. Further, terr...

Artificial reservoirs likely accumulate more carbon than natural lakes due to their unusually high sedimentation rates. Nevertheless, the actual magnitude of carbon accumulating in reservoirs is poorly known due to a lack of whole-system studies of carbon burial. We determined the organic carbon (OC) burial rate and the total OC stock in the sedime...

Based on empirical and synthetic research, lakes make, store, and mineralize organic carbon (OC) at rates that are significant and relevant to regional and global carbon budgets. Although some global-scale studies have examined specific processes such as carbon burial and CO2 exchange with the atmosphere, most studies of lake carbon cycling are fro...

Massive changes to ecosystems sometimes cross thresholds from which recovery can be difficult, expensive and slow. These thresholds are usually discovered in post hoc analyses long after the event occurred. Anticipating these changes prior to their occurrence could give managers a chance to intervene. Here we present a novel approach for anticipati...

Significance Large changes can occur when ecosystems cross certain thresholds. Crossing such thresholds poses a challenge to ecosystem management because the positions of the threshold are uncertain and change over time. However, as an ecosystem approaches a threshold its resilience declines, resulting in changes in system dynamics that increase va...

Lake food webs can be supported by primary production from within the lake, organic matter imported from the catchment or some mixture of these two sources. Generalisations about food‐web subsidies to lake ecosystems are often based on data from only a few ecosystems and therefore do not consider the potential variability of subsidies among diverse...

Background/Question/Methods: Lake food webs can be supported by primary production from within the lake, organic matter imported from the watershed, or some mixture of these two sources. Current debates about food web subsidies to lake ecosystems often depend on data from only a few ecosystems, and therefore do not consider the potential variabilit...

Background/Question/Methods A large portion of the total organic matter in many lakes is terrestrial in origin, and lake consumers can be supported by both terrestrial (allochthonous) and aquatic (autochthonous) resources. With the progression of global climate change, freshwaters may receive higher loadings of allochthonous organic matter, which...

Phytoplankton populations often exhibit cycles associated with nuisance blooms of cyanobacteria and other algae that cause toxicity, odor problems, oxygen depletion, and fish kills. Models of phytoplankton blooms used for management and basic research often contain critical transitions from stable points to cycles, or vice-versa. It would be useful...

[1] Aquatic ecosystems are hotspots of decomposition and sources of carbon dioxide to the atmosphere that are globally significant. Carbon exported from land (allochthonous) also supplements the carbon fixed by photosynthesis in aquatic ecosystems (autochthonous), contributing to the organic matter (OM) that supports aquatic consumers. Although the...

A surprising fraction of Earth's element cycling takes place in inland waters. Jonathan Cole suggests that interactions between these water bodies and the terrestrial biosphere are more extensive and interesting than previously thought.

The book is in 5 Chapters that seek to review how the carbon cycle works in freshwater ecosystems; how the terrestrial and aquatic carbon cycles interact; and how terrerstrial inputs of organic matter sometimes subsidze the food webs of lakes, streams and rivers

The Hudson River is a strongly heterotrophic system in which the invasive zebra mussel (Dreissena polymorpha) comprises >90% of total metazoan biomass. Using a Bayesian mixing model, with isotope ratios of C, N, and H, and four basal resources (phytoplankton, benthic algae, submersed aquatic vegetation [SAV], and terrestrial inputs), we estimated t...

To characterize the spatial variability of metabolism estimates (gross primary production [GPP], respiration [R], and net ecosystem production [NEP]) in two Northern Wisconsin lakes, we collected data from 27 and 35 dissolved oxygen sensors placed in a two-dimensional array throughout the upper mixed layers over a period of 10 d per lake in midsumm...

A Bayesian mixing model and stable isotopes of carbon, nitrogen, and hydrogen were used to evaluate the extent to which six consumers (three fishes, two zooplankton, and a snail) in a naturally productive lake used terrestrial resources, epilimnetic and metalimnetic phytoplankton, benthic algae, and macrophytes. Resource use varied with consumer ha...

Determining the effects of species loss on ecosystems has received considerable attention given the current threats many ecosystems are facing. A significant body of research has yielded many insights to this question, but this work has been limited by a focus on ecosystems where primary production plays a significant role in energy transfer. As ma...

1] High-frequency physical observations from 40 temperate lakes were used to examine the relative contributions of wind shear (u *) and convection (w *) to turbulence in the surface mixed layer. Seasonal patterns of u * and w * were dissimilar; u * was often highest in the spring, while w * increased throughout the summer to a maximum in early fall...

Measurements of the production and consumption of organic material have been a focus of aquatic science for more than 80years. Over the last century, a variety of approaches have been developed and employed for measuring rates of gross primary production (Pg), respiration (R), and net ecosystem production (Pn=Pg−R) within aquatic ecosystems. Here,...

Dissolved organic matter (DOM) influ-ences inland water ecosystems through its light absorbing qualities. We investigated how pH affects light absorption by DOM with pH manipulation experiments and with data from two lake surveys. We hypothesized that: (1) light absorption and photoble-aching of DOM would increase with increasing pH, and (2) as a r...

Diel vertical migration of zooplankton is influenced by a variety of factors including predation, food, and temperature. Research has recently shifted from a focus on factors influencing migration to how migration affects nutrient cycling and habitat coupling. Here we evaluate the potential for Daphnia migrations to incorporate metalimnetic product...

Large differences in δ 2H of primary producers between aquatic and terrestrial ecosystems are used to identify subsidies, discriminate organic matter sources, and reduce uncertainty in food web studies. Previous investigations of hydrogen isotope ratios suggest there may be predictable differences between the δ 2H of water and organic matter for di...

High-frequency measurements are increasingly available and used to model ecosystem processes. This growing capability provides the opportunity to resolve key drivers of ecosystem processes at a variety of scales. We use a unique series of high-frequency measures of potential predictors to analyze daily variation in rates of gross primary production...

Hydroelectric reservoirs cover an area of 3.4× 10 5 km 2 and comprise about 20% of all reservoirs. In addition, they contain large stores of formerly terrestrial organic carbon. Significant amounts of greenhouse gases are emitted, especially in the early years following reservoir creation, but the global extent of these emissions is poorly known. P...

Catastrophic ecological regime shifts may be announced in advance by statistical early warning signals such as slowing return rates from perturbation and rising variance. The theoretical background for these indicators is rich, but real-world tests are rare, especially for whole ecosystems. We tested the hypothesis that these statistics would be ea...

Previous studies have used sondes to measure diel changes in dissolved oxygen and thereby estimate gross primary production (GPP), ecosystem respiration (R), and net ecosystem production (NEP). Most of these studies estimate rates for the surface layer and require knowing the depth of the mixed layer (Zmix), which is usually determined from discret...

Fluxes of organic matter across habitat boundaries are common in food webs. These fluxes may strongly influence community dynamics, depending on the extent to which they are used by consumers. Yet understanding of basal resource use by consumers is limited, because describing trophic pathways in complex food webs is difficult. We quantified resourc...

A series of whole-lake manipulations of both food web structure and nutrient loading rate revealed that the downward vertical P flux was significantly affected by food web structure. Food webs and nutrient input rates of two lakes were manipulated while a third lake served as a reference system. Phosphorus transport to the sediments was examined by...

A simplified method for the determination of dissolved organic carbon is based upon the ampoule–persulfate wet digestion procedure. The modification proposed involves use of a continuous stream of sparging gas (technical grade oxygen) during the ampoule sealing process to minimize entry of combustion products from the sealing flame. The method prov...

In this rapidly changing world, improving the capacity to predict future dynamics of ecological systems and their services is essential for better stewardship of the earth system. Prediction relies on models that describe our understanding of the major processes that underlie system dynamics and data about these processes and the present state of e...

Cross-ecosystem subsidies to food webs can alter metabolic balances in the receiving (subsidized) system and free the food web, or particular consumers, from the energetic constraints of local primary production. Although cross-ecosystem subsidies between terrestrial and aquatic systems have been well recognized for benthic organisms in streams, ri...

At the 2009 Annual Meeting of the Ecological Society of America, investigators of ecosystem science and biogeochemistry gathered in a series of sessions sponsored by the National Science Foundation to examine what is known about the coupling of chemical elements in biochemistry and thus in global biogeochemical cycles. As an introduction to the top...

The analysis of coupled biogeochemical cycles (CBCs) addresses the scientific basis for some of today's major environmental problems. Drawing from information presented at a series of sessions on CBCs held at the 2009 Annual Meeting of the Ecological Society of America and from the research community's expertise, we identify several principal resea...

Degassing of carbon dioxide (CO2) from small streams draining forest landscapes have come under close scrutiny as potentially significant sources of CO2 relative to the net ecosystem exchange (NEE) of carbon. Quantifying such losses is essential to our understanding of how temperate forest ecosystems function as carbon sinks. The concentration of C...

Significant improvements have been made in estimating gross primary production (GPP), ecosystem respiration (R), and net ecosystem production (NEP) from diel, "free-water" changes in dissolved oxygen (DO). Here we evaluate some of the assumptions and uncertainties that are still embedded in the technique and provide guidelines on how to estimate re...

In inland waters, transparent exopolymer particles (TEP) can affect carbon export and sequestration in sediments with consequences for lake C budgets. We measured TEP concentration in 32 lakes from two contrasting lake districts covering wide ranges in biological and chemical characteristics. North temperate lakes, located in a wet region, have low...

Recent studies indicate that highly aged material is a major component of organic matter transported by most rivers. However, few studies have used natural 14C to trace the potential entry of this aged material into modern river food webs. Here we use natural abundance 14C, 13C, and deuterium (2H) to trace the contribution of aged and contemporary...

We performed a series of gas exchange measurements in 12 diverse aquatic systems to develop the direct relationship between near-surface turbulence and gas transfer velocity. The relationship was log-linear, explained 78% of the variation in instantaneous gas transfer velocities, and was valid over a range of turbulent energy dissipation rates span...

The rate of gas exchange between air and water is an essential quantity in a number of contexts, from mass balances to the calculation of whole-system metabolism. The exchange of a gas between water and the atmosphere is controlled by differential partial pressures of gases in air and in water (both straightforward to measure) and by the amount of...

Inland waters, just as the world's oceans, play an important role in the global carbon cycle. While lakes and reservoirs typically emit CO2, they also bury carbon in their sediment. The net CO2 emission is largely the result of the decomposition or preservation of terrestrially supplied carbon. What regulates the balance between CO2 emission and ca...

Hydroelectric reservoirs generate energy without significant combustion of fossil fuels. However, these systems can, potentially, emit greenhouse gases (GHG’s) at a rate which may be significant at the global scale, and, possible, co-equal, per kilowatt-hour, to that from conventional coal or oil-fired systems. Although much of the new construction...

Using high-frequency measurements of free water dissolved oxygen (O(2)), we assessed gross primary production (GPP), respiration (R), and net aquatic production (NAP) in the shallow-water Everglades peatland between 1996 and 2005. We distinguish NAP from net ecosystem production since the boundary for shallow aquatic ecosystems may include abovegro...

Using high-frequency measurements of free water dissolved oxygen (O2), we assessed gross primary production (GPP), respiration (R), and net aquatic production (NAP) in the shallow-water Everglades peatland between 1996 and 2005. We distinguish NAP from net ecosystem production since the boundary for shallow aquatic ecosystems may include abovegroun...