Clive G. Jones

Organisms as ecosystem engineers

Interactions between organisms are a major determinant of the distribution and abundance of species. Ecology textbooks (e.g., Ricklefs 1984, Krebs 1985, Begon et al. 1990) summarise these important interactions as intra- and interspecific competition for abiotic and biotic resources, predation, parasitism and mutualism. Conspicuously lacking from the list of key processes in most text books is the role that many organisms play in the creation, modification and maintenance of habitats. These activities do not involve direct trophic interactions between species, but they are nevertheless important and common. The ecological literature is rich in examples of habitat modification by organisms, some of which have been extensively studied (e.g. Thayer 1979, Naiman et al. 1988).

Mechanism of dye response and interference in the Bradford protein assay

Bradford Coomassie brilliant blue G-250 protein-binding dye exists in three forms: cationic, neutral, and anionic. Although the anion is not freely present at the dye reagent pH, it is this form that complexes with protein. Dye binding requires a macromolecular form with certain reactive functional groups. Interactions are chiefly with arginine rather than primary amino groups; the other basic (His, Lys) and aromatic residues (Try, Tyr, and Phe) give slight responses. The binding behavior is attributed to Van der Waals forces and hydrophobic interactions. Assay interference by bases, detergents, and other compounds are explained in terms of their effects upon the equilibria between the three dye forms.

An ecosystem engineer, the beaver, increases species richness at the landscape scale

Abstract. Ecosystem engineering – the physical modification of habitats by organisms – has been proposed as an important mechanism for maintaining high species richness at the landscape scale by increasing habitat heterogeneity. Dams built by beaver (Castor canadensis) dramatically alter riparian landscapes throughout much of North America. In the central Adirondacks, New York, USA, ecosystem engineering by beaver leads to the formation of extensive wetland habitat capable of supporting herbaceous plant species not found elsewhere in the riparian zone. We show that by increasing habitat heterogeneity, beaver increase the number of species of herbaceous plants in the riparian zone by over 33% at a scale that encompasses both beaver-modified patches and patches with no history of beaver occupation. We suggest that ecosystem engineers will increase species richness at the landscape scale whenever there are species present in a landscape that are restricted to engineered habitats during at least some stages of their life cycle.

Urbanization effects on tree growth in the vicinity of New York City.

Plants in urban ecosystems are exposed to many pollutants and higher temperatures, CO2 and nitrogen deposition than plants in rural areas. Although each factor has a detrimental or beneficial influence on plant growth, the net effect of all factors and the key driving variables are unknown. We grew the same cottonwood clone in urban and rural sites and found that urban plant biomass was double that of rural sites. Using soil transplants, nutrient budgets, chamber experiments and multiple regression analyses, we show that soils, temperature, CO2, nutrient deposition, urban air pollutants and microclimatic variables could not account for increased growth in the city. Rather, higher rural ozone (O3) exposures reduced growth at rural sites. Urban precursors fuel the reactions of O3 formation, but NOx scavenging reactions resulted in lower cumulative urban O3 exposures compared to agricultural and forested sites throughout the northeastern USA. Our study shows the overriding effect of O3 despite a diversity of altered environmental factors, reveals ‘footprints’ of lower cumulative urban O3 exposures amidst a background of higher regional exposures, and shows a greater adverse effect of urban pollutant emissions beyond the urban core.

Natural products – a simple model to explain chemical diversity

A simple evolutionary model is presented which explains why organisms produce so many natural products, why so many have low biological activity, why enzymes involved in natural product synthesis have the properties they do and why natural product metabolism is shaped as it is.

Insect Defoliation and Nitrogen Cycling in Forests

O of defoliating insects can have dramatic effects on forest ecosystems. Studies have shown that defoliation can decrease transpiration and tree growth and increase tree mortality, light penetration to the forest floor, and water drainage (Stephens et al. 1972, Campbell and Sloan 1977, Houston 1981). The allocation of carbon to various parts of the tree may be altered, production of defensive compounds in foliage may increase (Schultz and Baldwin 1982), and seed production may decline for many years after defoliation (McConnell 1988, Gottschalk 1990). Shifts in tree species composition (Doane and McManus 1981, Glitzenstein et al. 1990) and changes in the population size of insectivorous birds and other wildlife may also occur (Holmes et al. 1986, USDA Forest Service 1994). Several studies of insect outbreaks have also indicated an increased loss of nitrogen (N) from forest ecosystems in drainage water following defoliation, suggesting an increase in soil-available nitrogen that is subject to leaching (Swank et al. 1981, McDonald et al. 1992, Webb et al. 1995, Eshleman et al. 1998, Reynolds et al. 2000). Large losses of nitrogen via leaching would reduce long-term forest production in Nlimited ecosystems. In addition, the export of nitrate (NO3 –) to stream water can acidify downstream waters (Webb et al. 1995) and contribute to eutrophication of coastal waters and estuaries (Fisher and Oppenheimer 1991). At first glance, the view held by many investigators that forest ecosystems leak N in large quantities after defoliation fits the general notion of nitrogen behavior in disturbed ecosystems. Significant nitrogen losses have been observed in response to disturbances such as intensive harvesting (Likens et al. 1970), fire (Bayley and Schindler 1991), and severe windstorms (Schaefer et al. 1996). However, defoliation differs qualitatively from these other disturbances in three ways. First, most of the trees usually remain alive with their woody structure intact after defoliation by insects. (Exceptions are the high mortality rates caused by repeated severe defoliations of hardwood trees or by severe defoliation of conifers.) Second, physical disturbance of the soil is minimal and significant erosion is therefore unlikely to occur. And third, if the trees are not killed, the time for substantial canopy recovery is often measured in weeks rather than years. In this article we examine the mechanisms and magnitudes of N-cycle perturbations by defoliation, drawing heavily on the considerable body of research on the gypsy moth (Lymantria dispar L.), an introduced lepidopteran that has been the major defoliator of hardwood forests in the northeastern United States during the last 5 or 6 decades (Doane and McManus 1981). We attempt to establish a more coherent view of the likely consequences of defoliation for N cycling, and we make the case that, contrary to the commonly held view, the response of forest ecosystems to defoliation is primarily one of redistribution, rather than loss, of nitrogen.

The evolution of secondary metabolism – a unifying model

Why do microbes make secondary products? That question has been the subject of intense debate for many decades. There are two extreme opinions. Some argue that most secondary metabolites play no role in increasing the fitness of an organism. The opposite view, now widely held, is that every secondary metabolite is made because it possesses (or did possess at some stage in evolution) a biological activity that endows the producer with increased fitness. These opposing views can be reconciled by recognizing that, because of the principles governing molecular interactions, potent biological activity is a rare property for any molecule to possess. Consequently, in order for an organism to evolve the rare potent, biologically active molecule, a great many chemical structures have to be generated, most of which will possess no useful biological activity. Thus, the two sides of the debate about the role and evolution of secondary metabolism can be accommodated within the view that the possession of secondary metabolism can enhance fitness, but that many products of secondary metabolism will not enhance the fitness of the producer. It is proposed that secondary metabolism will have evolved such that traits that optimize the production and retention of chemical diversity at minimum cost will have been selected. Evidence exists for some of these predicted traits. Opportunities now exist to exploit these unique properties of secondary metabolism to enhance secondary product diversity and to devise new strategies for biotransformation and bioremediation.

Measuring plant protein with the Bradford assay

The suitability of the Bradford protein assay for measuring plant protein was evaluated and a standard method developed. The assay involves extraction of dried, fresh, or frozen plant material in 0.1 NaOH for 30 min. Replicate 100-μl aliquots of centrifuged supernatant are assayed with 5 ml Bio-Rad Bradford dye reagent (Coomassie brilliant blue G-250) diluted 1:4 and containing 3 mg/ml soluble polyvinylpyrollidone. Absorbance at 595 nm is recorded after 15 min against an NaOH blank. Samples are calibrated against a ribulose 1,5-diphosphate carboxylase-oxygenase standard in NaOH. Procedures for plant preparation, extraction stability, the effects of phenol removal and quinone formation, and assay recovery are evaluated. Assay absorbance stability and techniques for increasing absorbance stability are reported. Changes in protein quality are briefly discussed.

Effects of Damage to Living Plants on Leaf Litter Quality

The leaves of plants in nature are commonly subjected to damage from a wide variety of agents, including herbivory, air pollutants, and simple physical damage. Despite the attention paid to damage effects on living plants, the potential effects on the quality of litter derived from damaged leaves has not been considered. We used controlled laboratory assays of decomposition to show that both ozone (0.2 mL/m3, 4 h) and mite damage, but not ultraviolet radiation (UV-B) exposure, to living leaves of cottonwood plants resulted in a decrease in decomposition rate of litter derived from damaged leaves. De- composition rates were -50% slower for litter from damaged plants, and there was a twofold increase in the refractory fraction. Contrary to expectation, there was a negative relationship between rate of decomposition and litter nitrogen content. Our finding of slow decompo- sition of high-nitrogen litter is explained by a general mechanism whereby cellular damage causes increases in complex phenolic material. Such materials can lead to reductions in decomposition and binding of available nitrogen. We suggest that this mechanism can translate a common occurrence, damage by a diversity of processes, into long-term and possibly large-scale alterations in detritus processing.

Linking Species and Ecosystems: Organisms as Ecosystem Engineers

Ecosystem engineers are organisms that directly or indirectly modulate the availability of resources to other species, by causing physical state changes in biotic or abiotic materials. In so doing they modify, maintain, and create habitats. Autogenic engineers (e.g., corals, or trees) change the environment via their own physical structures (i.e., their living and dead tissues). Allogenic engineers (e.g., woodpeckers, beavers) change the environment by transforming living or nonliving materials from one physical state to another, via mechanical or other means. Here we define and explain engineering, and provide a classification and some general, conceptual models of the processes involved. We show how organismal engineering is related to human engineering and to ecological concepts such as keystone species. We then identify the factors scaling the impact of engineers. The biggest effects are attributable to species with large per capita impacts, living at high densities, over large areas for a long time, giving rise to structures that persist for millennia and that modulate many resource flows. We argue that all habitats on earth support, and are influenced to some degree, by ecosystem engineers, and we raise some general questions about organismal engineering that are worth pursuing.