J. David Allan

University of Michigan | U-M · School of Natural Resources and Environment

The diversity of running waters is enormous, from cascading mountain streams, to meandering lowland rivers, to great rivers that occupy sub-continents. Here we set the stage for the rest of this book: first, we describe key elements of a healthy river; second, we review the many threats that rivers face; lastly, we provide an outline of forthcoming...

Streamflow gives rivers and streams their distinctive character, influencing virtually every physical, chemical, and biological process within fluvial ecosystems. Measurement of streamflow characterizes stream or river size, variability across all time scales and among seasons and river types, and the response to human intervention. Because rivers...

The decomposition of organic carbon provides key energy inputs to most food webs, and this is especially true in fluvial ecosystems. These energy pathways are referred to as detrital or detritus-based, and the immediate consumers of this material are decomposers and detritivores.

The world’s ecosystems have been extensively altered throughout the age of the Anthropocene, river ecosystems perhaps most of all.

Nutrients are inorganic compounds that plants and microbes require for the synthesis of new organic matter, and animals require for their growth and metabolism. Hence the supply of nutrients potentially limits biological activity within lotic ecosystems. Whether nutrients are acquired from the surrounding environment, as is typically the case for a...

Organic carbon is the fundamental currency of energy transfer in food webs. The study of stream ecosystem metabolism integrates all energy producing and energy consuming processes, providing a whole-ecosystem perspective of lotic ecosystems. The focus is on two central questions. First, what are the relative magnitudes of internal versus external e...

Current, substrate, and temperature strongly influence species occurrence and abundance for the denizens of running waters. Current governs the physical form of habitat and affects organisms through drag and dislodgment, but also delivers food and nutrients while removing wastes. A variety of sophisticated methods measure current and associated hyd...

The assemblage of species within a stream reach forms a network of linkages and interactions that vary in strength and the number of species affected. The basal resources of algae and detritus, with associated microorganisms, and along with external energy subsidies, sustain higher consumers including herbivores, predators, the omnivores that blur...

The assemblage of species found at a location derives from the regional pool of species, governed by the ability of each species to colonize new habitat, and the matching of individual species to available resources, habitat, and one another. Regional species richness displays intriguing geographical patterns, best described for freshwater fishes....

Microbes include heterotrophs, especially bacteria and fungi that obtain energy from detrital material as well as from organic compounds in the surrounding water, and some autotrophs. They occur on virtually all surfaces in streams as biofilms that include bacteria, fungi, algae, protists, detrital particles, various exudates, exoenzymes, and metab...

Food webs describe the network of linkages that are responsible for transfers of energy among species, and for the movement of nutrients between organisms and the abiotic environment. Food web networks ideally describe all interactions within a community of species, while recognizing that much of the energy flows through relatively few species. The...

Chemical variation among streams is primarily governed by the type and composition of rocks in the drainage, and by the amount and chemical composition of precipitation. In addition, human activities can significantly influence the chemical composition of rivers and streams, indirectly by changing land use and the chemical composition of precipitat...

Primary producers acquire energy from nonliving sources, typically sunlight and inorganic compounds, and so are also known as autotrophs. Principle autotrophs of running waters include algae, some bacteria and protists, and higher plants. Algae are diverse taxonomically and in size and growth form. Algae of running waters that occur on substrates,...

Fluvial geomorphology explores the dynamic interplay between rivers and their landscapes in the shaping of river channels and drainage networks. Many familiar features of river channels are the outcome, including meandering, an alternation of riffles, pools, and runs, and the floodplain. These features are formed by the river through cycles of eros...

The trophic categories of riverine food webs reflect the basal resources available to consumers, including benthic and planktonic algae, detritus with its associated microbial assemblage, higher plants, and other animals. Invertebrates typically are divided into functional feeding groups and fishes into guilds. Among the invertebrates, grazers inge...

Stream Ecology: Structure and Function of Running Waters is designed to serve as a textbook for advanced undergraduate and graduate students, and as a reference source for specialists in stream ecology and related fields. This Third Edition is thoroughly updated and expanded to incorporate significant advances in our understanding of environmental...

Watersheds deliver numerous pollutants to the coastline of oceans and lakes, thereby jeopardizing ecosystem services. Regulatory frameworks for stressors often focus on loading rates without accounting for the physical dynamics of the receiving water body. Here, we use a three-dimensional hydrodynamic model to simulate the transport of a generic tr...

The Laurentian Great Lakes provide a wide range of ecosystem services (ES) whose spatial distribution and extent are largely unquantified, thus limiting our understanding of ES co-occurrence, magnitude of ES supply, and the incorporation of ES into environmental planning. We mapped the spatial distribution of twelve ES in the Lake Erie Basin, inclu...

A comprehensive inventory of ecosystem services across the entire Great Lakes basin is currently lacking and is needed to make informed management decisions. A greater appreciation and understanding of ecosystem services, including both use and non-use services, may have avoided misguided resource management decisions in the past that resulted in n...

Phytoplankton communities can experience nonlinear responses to changing nutrient concentrations, but the nature of species shifts within phytoplankton is not well understood and few studies have explored responses of pelagic assemblages in large lakes. Using pelagic phytoplankton data from the Great Lakes, we assessed phytoplankton assemblage chan...

Most ecosystems are impacted by multiple local and long-distance stressors, many of which interact in complex ways. We present a framework for prioritizing ecological restoration efforts among sites in multi-stressor landscapes. Using a simple model, we show that both the economic and sociopolitical costs of restoration will typically be lower at s...

Ecological restoration programs often attempt to maintain or enhance ecosystem services (ES), but fine-scale maps of multiple ES are rarely available to support prioritization among potential projects. Here we use agency reports, citizen science, and social media as data sources to quantify the spatial distribution of five recreational elements of...

The pressures of a growing population and a fluctuating economy have caused extensive landuse transformations in the Colombian Andes, and >63% of the natural land cover has been replaced by cattle and crop fields. Despite the obvious importance of agriculture as a driver of stream degradation, the specific effects of agriculture on low-order stream...

Many initiatives since the early 1900s have been implemented to maintain water quality within the Great Lakes–St. Lawrence River basin. Despite these substantial efforts, emerging and re-emerging biological and chemical contaminants continue to pose serious human, animal, and ecosystem health risks. With over 100 biological and chemical contaminant...

Agricultural best management practices (BMPs) have been implemented in the watersheds around Lake Erie to reduce nutrient transfer from terrestrial to aquatic ecosystems and thus protect and improve the water quality of Lake Erie. However, climate change may alter the effectiveness of these BMPs by altering runoff and other conditions. Using the So...

Relieving phosphorus loading is a key management tool for controlling Lake Erie eutrophication. During the 1960s and 1970s, increased phosphorus inputs degraded water quality and reduced central basin hypolimnetic oxygen levels which, in turn, eliminated thermal habitat vital to cold-water organisms and contributed to the extirpation of important b...

Ecosystems often experience multiple environmental stressors simultaneously that can differ widely in their pathways and strengths of impact. Differences in the relative impact of environmental stressors can guide restoration and management prioritization, but few studies have empirically assessed a comprehensive suite of stressors acting on a give...

Migratory animals often transfer nutrients between ecosystems, enhancing productivity in the subsidized system. Most research on nutrient subsidies by migratory fishes has focused on Pacific salmon, whose semelparous life history is unusual among migratory fishes. To test whether iteroparous species can provide ecologically important nutrient input...

Current research has shown that reductions in nonpoint nutrient loading are needed to reduce the incidence of harmful algal blooms and hypoxia in the western and central basins of Lake Erie. We used the Soil and Water Assessment Tool (SWAT) to test various sediment and nutrient load reduction strategies, including agricultural best management pract...

Large scale, high resolution maps of stressors and ecosystem threats (e.g. habitat alteration, pollution, species invasions, and other factors) are increasingly available for many ecosystem types and geographic settings. We illustrate how patterns of stressor heterogeneity in these maps can be used to identify locations that are good candidates for...

Background/Question/Methods Effectively managing coupled human-natural systems requires understanding the effects of anthropogenic stressors on ecosystem services provisioning. Environmental stressors represent human influences on ecosystem health, while ecosystem services (particularly cultural and provisioning ones) connect ecosystem health to...

Richards, R. Peter, Ibrahim Alameddine, J. David Allan, David B. Baker, Nathan S. Bosch, Remegio Confesor, Joseph V. DePinto, David M. Dolan, Jeffrey M. Reutter, and Donald Scavia, 2012. Discussion –“Nutrient Inputs to the Laurentian Great Lakes by Source and Watershed Estimated Using SPARROW Watershed Models” by Dale M. Robertson and David A. Saad...

A key challenge in aquatic restoration efforts is documenting locations where ecological connectivity is disrupted in water bodies that are dammed or crossed by roads (road crossings). To prioritize actions aimed at restoring connectivity, we argue that there is a need for systematic inventories of these potential barriers at regional and national...

With increasing pressure placed on natural systems by growing human populations, both scientists and resource managers need a better understanding of the relationships between cumulative stress from human activities and valued ecosystem services. Societies often seek to mitigate threats to these services through large-scale, costly restoration proj...

African tilapias (Oreochromis spp.) occur in more than 100 countries outside of their native ranges and research on their invasions is largely lacking. We investigated spatiotemporal patterns of tilapia spread into 29 drainage basins in Belize and parts of Guatemala and Mexico, drawing on field data and interviews with fishermen. Habitat-suitabilit...

Catostomid fishes constitute a large portion of fish biomass in lakes and streams across North America, and millions of white and longnose suckers migrate from the Great Lakes into tributaries each spring to spawn. Worldwide, most migratory fishes are iteroparous, but studies showing that nutrients delivered by fish migrations can increase stream p...

Background/Question/Methods The Great Lakes are subject to multiple stressors, and assessing their impacts is challenging when these stressors have different spatial distributions and their impacts vary among habitats. The ability to map the presence or intensity of individual stressors across the Great Lakes, weight individual stressors for thei...

By constructing nitrogen (N) budgets from 1880 to 2002 for watersheds that have undergone urbanization, intensive agricultural specialization or experienced minimal change, we document an uneven timeline of increase in anthropogenic N inputs. N loading to the watersheds of the Lake Michigan Basin grew six-fold from 1880 to 2002, peaking in 1987. Hu...

Phosphorus (P) applied to croplands in excess of crop requirements has resulted in large-scale accumulation of P in soils worldwide, leading to freshwater eutrophication from river runoff that may extend well into the future. However, several studies have reported declines in surplus P inputs to the land in recent decades. To quantify trends in P l...

1. Stream reaches found to be impaired by physical, chemical or biological assessment generally are associated with greater extent of urban and agricultural land uses, and lesser amount of undeveloped lands. However, because stream condition commonly is influenced by multiple stressors as well as underlying natural gradients, it can be difficult to...

Allochthonous nutrients and carbon are recognized as dominant controls on biogeochemistry of low-order streams. In some systems, potamodromous fish may provide a complementary source of material as they deliver lake-derived materials to spawning streams. This study examines nutrient and carbon inputs from terrestrial ecosystems and migratory fishes...

The aim of this study was describe functional faunal assemblages occurring in streams with high influence of urbanization in USA and Brazil to answer the question whether similar biological traits of fish assemblages would be found between streams with high influence of urbanization in USA and Brazil. We compiled data on the structure and compositi...

Although the purpose of many drift studies is to describe quantitatively the abundance of drifting invertebrates and make comparisons between seasons or sites, almost no investigations have employed replicate sampling. We analyzed drift collections from a Rocky Mountain stream in order to investigate the variability of drift sampling. The data were...

Lotic systems in many regions of the country have experienced habitat degradation and biodiversity loss due to agricultural activity and urbanization. Southeastern Michigan is no exception, as agriculture in the River Raisin watershed and increased urbanization in the Huron River watershed threatens both systems. To further understand the ecologica...

We estimated net anthropogenic phosphorus inputs (NAPI) to 18 Lake Michigan (LM) and 6 Lake Erie (LE) watersheds for 1974, 1978, 1982, 1987, and 1992. NAPI quantifies all anthropogenic inputs of P (fertilizer use, atmospheric deposition, and detergents) as well as trade of P in food and feed, which can be a net input or output. Fertilizer was the d...

Laboratory simulation of acid stress to a common cladoceran, Daphnia pulex, was conducted in pond water of varying acidity due to addition of H2SO4. An acute test using exposure times of 1 to 96 h and pH levels of 3.7 and 6.5 revealed virtually no effect at 4.3 and higher, while 4.2 and lower severely reduced survivorship. Very short (3-h) exposure...

Esselman PC, Allan JD. Relative influences of catchment- and reach-scale abiotic factors on freshwater fish communities in rivers of northeastern Mesoamerica. Ecology of Freshwater Fish 2010: 19: 439–454. © 2010 John Wiley & Sons A/S Abstract – While the abiotic factors important to freshwater fish assemblages at a reach scale are well understood,...

Numerous studies have been conducted in urban centres now using sophisticated instruments that measure aerosol properties needed to determine their effects on human health, air quality and climate change) showing that a significant fraction of urban aerosols (mainly from automotive sources) are composed of organic compounds with implications for hu...

1. Protected area networks for river ecosystems must account for the highly connected nature of river habitats and the fact that conditions in distant locations can influence downstream habitats and biota. We used Marxan conservation planning software to address the unique constraints of reserve design in river ecosystems and structure a reserve ne...

A case study of atmospheric aerosol measurements exploring the impact of the vertical distribution of aerosol chemical composition upon the radiative budget in North-Western Europe is presented. Sub-micron aerosol chemical composition was measured by an Aerodyne Aerosol Mass Spectrometer (AMS) on both an airborne platform and a ground-based site at...

Results from a measurement study performed in the Tropical Atlantic on board the RHaMBLe Discovery Cruise D319 are presented. Measurements of aerosol composition, hygroscopicity and CCN activity were used to test the ability of a single parameter model to describe water uptake in sub-and supersaturated conditions. It was found that the magnitude...

Protected areas are a cornerstone of conservation and have been designed largely around terrestrial features. Freshwater species and ecosystems are highly imperiled, but the effectiveness of existing protected areas in representing freshwater features is poorly known. Using the inland waters of Michigan as a test case, we quantified the coverage of...

The NERC UK SOLAS-funded Reactive Halogens in the Marine Boundary Layer (RHaMBLe) programme comprised three field experiments. This manuscript presents an overview of the measurements made within the two simultaneous remote experiments conducted in the tropical North Atlantic in May and June 2007. Measurements were made from two mobile and one grou...

Organic matter frequently represents the single largest fraction of fine particulates in urban environments and yet the exact contributions from different sources and processes remain uncertain, owing in part to its substantial chemical complexity. Positive Matrix Factorisation (PMF) has recently proved to be a powerful tool for the purposes of sou...

Background/Question/Methods Traditionally, studies of predation have focused on the influence of predators on prey communities, and how predation might explain natural prey population oscillations via mortality. Studies carried out for nearly 40 years in one place have enabled us to evaluate the generality of traditional views of the influence of p...

The experiment presented in this paper was conducted at the Holme Moss site, which is located in the southern Pennines region in Northwestern England during November–December 2006. The strong southwesterly wind during the experimental period, which enhanced the transport of urban pollutants from the conurbations of Greater Manchester and Liverpool,...

Marine aerosol composition continues to represent a large source of uncertainty in the study of climate and atmospheric chemistry. In addition to their physical size and chemical composition, hygroscopicity plays a significant role, increasing the particles' surface areas and scattering potential. Simultaneous aerosol measurements were performed on...

River systems with impoundments are expected to experience greater nutrient removal as a consequence of enhanced nitrogen (N) loss by denitrification, settling and burial of phosphorus (P), and longer residence times of water relative to a free-flowing river. We evaluated the magnitude of N and P removal across stream reaches and impoundments, incl...

Organic aerosol chemical markers from normalized concentrations of independent measurements of mass fragments (using Aerosol Mass Spectrometry, AMS) are compared to bond-based functional groups (from Fourier Transform Infrared spectroscopy, FTIR) during eight field projects in the western hemisphere. Several field projects show weak correlations be...

The tropics emit a huge amount of volatile organic compounds (VOCs) into the Earth's atmosphere. The processes by which these gases are oxidised to form secondary organic aerosol (SOA) are currently not well understood or quantified. Intensive field measurements were carried out as part of the Oxidant and Particle Photochemical Processes (OP3) and...

Simplification of water uptake and cloud behaviour are required for large scale models owing to the complexity of a full treatment of all contributory factors to cloud activation. One widely used parameterisation aims to represent a particles hygroscopicity with a single parameter, which may hypothetically be derived from measurements of water upta...

Framework for Change Organic aerosols make up 20 to 90% of the particulate mass of the troposphere and are important factors in both climate and human heath. However, their sources and removal pathways are very uncertain, and their atmospheric evolution is poorly characterized. Jimenez et al. (p. 1525 ; see the Perspective by Andreae ) present an i...

Submicron atmospheric particles in the Amazon Basin were characterized by a high-resolution aerosol mass spectrometer during the wet season of 2008. Patterns in the mass spectra closely resembled those of secondary-organic-aerosol (SOA) particles formed in environmental chambers from biogenic precursor gases. In contrast, mass spectral indicators o...

Results from a measurement study performed in the Tropical Atlantic on board the RHaMBLe Discovery Cruise D319 are presented. Measurements of aerosol composition, hygroscopicity and CCN activity were used to test the ability of a single parameter model to describe water uptake in sub- and supersaturated conditions. It was found that the magnitude a...

The NERC UK SOLAS-funded Reactive Halogens in the Marine Boundary Layer (RHaMBLe) programme comprised three field experiments. This manuscript presents an overview of the measurements made within the two simultaneous remote experiments conducted in the tropical North Atlantic in May and June 2007. Measurements were made from two mobile and one grou...

An accurate but simple quantification of the fraction of aerosol particles that can act as cloud condensation nuclei (CCN) is needed for implementation in large-scale models. Data on aerosol size distribution, chemical composition, and CCN concentration from six different locations have been analyzed to explore the extent to which simple assumption...

Scientific findings from the last decades have clearly highlighted the need for a more comprehensive approach to atmospheric change processes. In fact, observation of atmospheric composition variables has been an important activity of atmospheric research that has developed instrumental tools (advanced analytical techniques) and platforms (instrume...