Abstract

We provide an overview of hurricane disturbance regimes in the north-eastern United States and the Caribbean, with a focus on ecological effects on temperate and tropical forests. Hurricanes in tropical regions occur with a higher frequency and reach higher intensity levels than in temperate regions. Slower movement of hurricanes in the tropics exposes forests to longer periods of damaging winds from a broader range of wind directions. At the regional to landscape level we are applying models of hurricane meteorology and topographic exposure to reconstruct wind conditions during historically important storms in order to compare these results with observations of forest damage, and to test two hypotheses: (1) regional gradients of hurricane frequency and intensity result from prevailing hurricane tracks and the configuration of coastlines and mountain ranges and (2) landscape gradients in wind exposure result from the interaction of peak wind directions and local topography. At the community level damage is controlled by windspeed, vegetation structure and composition, and site conditions. Damage patterns strongly control subsequent vegetation dynamics: (1) differential species damage determines the initial composition and structure of the vegetation, (2) leaf area establishment is controlled by damage type and forest composition, and (3) microenvironmental conditions and resource distribution are determined by the spatial pattern of residual vegetation. Field studies underline the offentimes low rate of initial mortality following catastrophic storms and the importance of releafing and sprouting in vegetation development. Changes in key ecosystem processes are often slight following even major hurricanes. Studies in Puerto Rico and New England document that nutrient retention was high, nutrient losses were minimal, soil moisture changed little, and minor changes in trace gas fluxes returned rapidly to pre-disturbance levels.

Introduction

Direct observations of microbial growth in a large number of natural ecosystems have shown that the predominant populations are attached to surfaces where they grow in glycocalyx enclosed microcolonies that develop into adherent biofilms (Costerton et al. 1987; Cheng et al. 1991; Lappin-Scott et al. 1992). In various digestive tracts, this adhesion takes the form of very specific associations with insoluble nutrients (Cheng et al. 1977; Akin 1979; Cheng et al. 1991) to form particle associated microbial populations, and with tissue surfaces to form tissue associated populations (Cheng & Costerton 1980; Cheng et al. 1981a, b). A variation of this latter mode of growth is the association of a major microbial population with the mucous blanket of secretory intestinal tissue (Rozee et al. 1982). Bacteria of the ruminant digestive tract can be divided into three distinct subpopulations, (i) those associated with the digesta, (ii) those associated with gastrointestinal tissue and (iii) those associated with gastrointestinal fluid (Cheng & Costerton 1980; Cheng et al. 1981a; Czerkawski & Cheng 1988).

General principles of microbial ecology dictate that any organism will establish itself in a favourable nutrient niche and proliferate within a physiologically integrated community. Our observations of the growth of bacteria associated with feed particles indicate that each species adheres to its own particular insoluble substrate (e.g. cellulose, protein, starch) and produces enzymes to degrade insoluble substrates to soluble nutrients (Cheng et al. 1984; McAllister et al. 1990b).

Introduction

The use of purified water in various industrial and medical applications has increased dramatically over the past 20 years. These different applications often require varying levels of water quality. Each industry sets specifications for the acceptance of purified water quality based upon their product or process demands. The aggressive nature of ionically ultrapure water (18.2 Mohm cm) can contraindicate its use in, for example, stainless steel distribution systems which are often employed in the pharmaceutical industry. While the presence of trace levels of silica in condensate polishing loop waters creates great concern in the power industry, low level silica contamination of purified waters used in the production of medical devices or photomasks, for example, may not constitute cause for alarm. If any one group of contaminants can be viewed as ‘universal’ in their distribution, significance and recalcitrance, it is the bacteria and their by-products. Their role as purified water contaminants appears to cross all boundaries of purified water application and usage.

In the semiconductor industry, the demand for contaminant free water has, to a great extent, driven ultrapure water technologies. Indeed, water purification technologies have advanced to the point whereby levels of ionic, organic, and particulate contaminants can be reduced to concentrations below current analytical detection limits. Unfortunately, this industry's ability to detect and remove biological particulates and organics has not kept pace with the needs of today's sophisticated devices. Yang & Tolliver (1989) have noted that, at the 1 megabit level where minimum circuit feature size is typically 1 μm, device yields are limited by 0.1 μm jam and larger particles.

Introduction

The disposal of sulphide bearing mine wastes (tailings) as open deposits results in the formation of unique acid generating ecosystems (Mills 1985). Acid formation occurs via biooxidation of mineral sulphides which generates dilute solutions of sulphuric acid containing soluble metalions. The microorganisms (predominantly acidophilic thiobacilli) responsible for this mineral oxidation exist as discrete biofilms obtaining energy for their metabolism from the sulphide mineral surfaces which they colonize (Norman & Snyman 1987; Southam & Beveridge 1992). Most references to biofilms conjure up images of thick layers of bacteria (>100 μm) encased in capsular material. In this chapter we will employ the term ‘discrete biofilm’ to refer to the colonization of mineral surfaces by Thiobacillus ferrooxidans which typically exist as a single cell layer that is devoid of capsule. In this context a biofilm is simply a metabolically active surface at a solid solution interface.

Bacterial leaching produces acid mine drainage (AMD) which seeps into the surrounding aquatic and terrestrial environments. AMD is of environmental concern not only because of its acidity but also because of the soluble heavy metals which may enter the eukaryotic food chain (Schofield 1976; Tamm 1976; Koryak et al. 1979; Cloutier et al. 1986). Sometimes bacterial leaching can be exploited for industrial purposes, for example in the recovery of copper or uranium (Brierly 1982). Bacterial oxidation is, then, both an economic liability due to the legislated costs associated with AMD neutralization and an economic benefit as evidenced in industrial leaching systems. Clearly, an understanding of the fundamental aspects of bacteria mineral interaction is essential for the prevention of this deleterious environmental impact and for the promotion of these industrial bio oxidative processes.

Introduction

The majority of studies on biofilms are concerned with the formation and structure of biofilms (see Korber et al., Chapter 1), the direct effects of microbial activities on surfaces, such as in metal corrosion (see Hamilton, Chapter 9), dental caries (see Marsh, Chapter 18) tissue invasion, or indirect effects of biofilms on fluid frictional resistance, heat exchange across metal surfaces, substrate transformations and biocide resistance of the biofilm organisms on biomaterials implanted in human patients (see McLean et al., Chapter 16) and on water distribution pipeline surfaces (Characklis & Marshall 1990; Anwar et al. 1992). Extensive reviews have dealt with the activities of microorganisms at surfaces (Marshall 1971; Stotzky 1986; van Loosdrecht et al. 1990; Fletcher 1991), but little on the actual genetic responses of microorganisms at surfaces. The aim of this chapter is to consider the environmental conditions existing at gel–air and solid–water interfaces, as well as in biofilms, and to relate these conditions to possible genetic responses in the immobilized bacteria.

Properties of surfaces

Bacteria at surfaces or, more broadly, at interfaces are exposed to environmental conditions not found in an aqueous phase. An interface is defined, in physicochemical terms, as the boundary between two phases in a heterogeneous system. The most common interfaces to which bacteria are exposed in nature and under laboratory conditions are solid–water interfaces (stones, soil particles, ship hulls, pipeline surfaces, glass and plastic culture vessels), although air–water (surface of bodies of water, bubbles), oil–water (oil spills) and solid–air (intertidal zones, agar surfaces) interfaces also are encountered. The concept of bacterial behaviour at various interfaces has been treated in detail by Marshall (1976).

In any scientific examination that addresses a subject as basic as the mode of growth of bacteria it is prudent to begin by considering the successful prokaryotic communities that clearly predated the development of the eukaryotic cell. During the millions of years in which bacteria constituted the only life form on Earth, we visualize an extremely oligotrophic aquatic environment in which specific ecosystems were impacted by many factors (e.g. heat, acid) hostile to their survival. It is the nature of aquatic systems to flow from one ecosystem to another and we can imagine a primitive stream connecting permissive and non-permissive bacterial habitats in the nascent Earth. Once bacterial cells had evolved, the planktonic (floating) mode of growth would deliver them from one habitat to another until they perished in the first non-permissive locus. The sessile mode of growth as attached bacteria would allow these primitive organisms to colonize a permissive habitat and persist therein. Biofilm formation would allow these sessile organisms to trap and retain scarce organic compounds and to develop a focused attack on complex or refractory nutrients whose processing required time and/or the cooperation of one or more bacterial species. Biofilm formation would also change the microenvironment at the colonized surface in a colonized habitat and render its inhabitants less susceptible to hostile chemical, physical, or even biological (e.g. bacteriophage) factors. Each colonized habitat would become a stable crucible of genetic adaption and physiological cooperativity that would flourish in its own location but would also shed its component organisms as planktonic cells so that, if they survived, they could establish a similar integrated biofilm community in any permissive habitat downstream.

Introduction

Cholangitis consists of bacterial infection of bile in the biliary system. The syndrome of acute cholangitis has been well recognized since Charcot (1877) described the classical triad of pain, fever and jaundice in these patients. It is an important cause of abdominal emergency cases and septicaemia with a high rate of morbidity and mortality (Li et al. 1985; French et al. 1990). Biliary obstruction, due to gallstones obstructing the bile ducts, or to benign or malignant stricture of the biliary tract, is an essential element in the development of cholangitis. In the past decade, endoscopic drainage by biliary stenting has become a standard procedure in palliation for inoperable biliary malignancies and some cases of large biliary stones causing obstructive jaundice. Unfortunately, there is an increased incidence of cholangitis related to the blockage of the biliary stents with the use of this technique (Huibregtse et al. 1986; Cotton 1990). Some studies have revealed that the pathogenesis of pigment gallstones (Stewart et al. 1987; Leung et al. 1988), and the blockage of the biliary stents (Leung et al. 1988; Speer et al. 1988) are closely related to the formation of bacterial biofilms in which the glycocalyx enclosed microcolonies coalesce to form an adherent structure (Jacques et al. 1987). This chapter reviews the present knowledge of the microbial ecology of the biliary system, formation of bacterial biofilm from bacterial infection within this system, the pathogenesis of brown biliary pigment stone and blockage of the biliary stent.

Biofilms and the physiology of microorganisms within them

Microbiologists have been accustomed until recently to think of microbes as homogeneous cultures grown in well mixed containers ranging in size from shake flasks to large industrial continuously stirred tank reactors. The investigative tool of choice has been the chemostat which is homogeneous not only in spatial terms but, when operating at a steady state, in time as well.

The only other traditional badge of the microbiologist is the colony. This is much more representative of the natural ecosystem since it is a microbiological aggregate dominated by diffusion gradients. For example oxygen only penetrates about 25–35 μm into a rapidly growing young colony (Wimpenny & Coombs 1983).

Microbial ecosystems are generally spatially heterogeneous implying that solutes move down concentration gradients between sources and sinks. Such gradients are found over a huge range of dimensions, from nanometres for pH gradients around clay lattices to hundreds of metres in the case of oxygen gradients in the Black Sea. These scale factors are illustrated, generally for oxygen, in Table 5.1.

Biofilms have been defined in many different ways; however, perhaps the simplest view is that it is a microbial aggregate that forms at phase interfaces. The most common biofilms appear at solid–water interfaces epitomized by the epilithon that forms on submerged rocks in streams and other water bodies. Generally such biofilm development follows a fairly standard life history. Clean surfaces become coated with a conditioning film consisting of organic molecules, for example proteins or polysaccharides. A little later individual cells attach to the surface, first loosely and reversibly and then firmly and irreversibly.

Introduction

Traditional microbiological investigations have focused on the culture and analysis of pure cell lines of bacteria, in either batch or chemostat culture. However, it has been clearly established that in nature, disease and industry, the majority of bacteria exist attached to surfaces within biofilms (Costerton et al. 1978, 1987; Lappin-Scott & Costerton 1989; Characklis et al. 1990a). Furthermore, it has also been established that the bacteria which exist in biofilms, termed sessile bacteria, are inherently different from bacteria existing in the planktonic state. In the sessile state, bacteria may express different genes, alter their morphologies, grow at different rates, or produce extracellular polymers in large amounts (Costerton et al. 1978; Wright et al. 1988; Gilbert et al. 1990; Dagostino et al. 1991; McCarter et al. 1992). One significant consequence of sessile growth is that biofilm bacteria are more resistant to medical and industrial control strategies than their planktonic counterparts (Brown et al. 1988; Nichols 1989; Eng et al. 1991; Blenkinsopp et al. 1992).

The development of complex attached and aggregated communities is also important for the survival and reproductive success of microorganisms. These communities have been considered to act as reservoirs for diverse species, sites of specific limited niches, and protective refuges from competition, predation or harsh environmental conditions, allowing otherwise poor competitors to survive. Integration into a biofilm or bioaggregate may be regarded as a survival strategy beyond that of maximizing or increasing the growth rate.

Introduction

The rhizosphere

The rhizosphere encloses the zone of soil around a plant root in which the plant root exerts an influence on the growth and distribution of microorganisms. An important source of microbial growth limiting nutrients are the products of rhizodeposition, which include exudates, secretions, lysates and gases (Whipps & Lynch 1985). The increase in the specific growth rate of microorganisms in response to increased organic carbon input has been shown to result in a 5 to 10-fold increase in the number of bacteria when compared with that of the population in the bulk soil (Rouatt et al. 1960; Rovira & Davey 1974). Rhizosphere microorganisms largely depend on root products for their carbon and energy supply (Merckx et al. 1986), and maximum microbial population density occurs at the root surface or rhizoplane (Clarke 1949). This is a consequence of the presence of the highest concentration of growth limiting nutrient at the rhizoplane. Rhizosphere microorganisms do not form a continuous layer on the root surface, but occur in microcolonies (Newman & Bowen 1974; Rovira & Campbell 1975). This microbial cover has been estimated to be below 10% (Rovira et al. 1974; Bowen & Rovira 1976; Bowen & Theodorou 1979). The concentrations of growth limiting nutrient and microbial numbers decrease as a function of radial distance from the root, and under optimal conditions, with adequate growth limiting nutrient supply, the total bacterial numbers would be limited by space. Chemotaxis towards plant root exudates and extracts is a well established phenomenon (Morris et al. 1992), enabling motile bacteria to migrate towards the root through chemotaxis. Non-motile bacteria accumulate in response to an elevated specific growth rate.

The primary concept of this series of books is to produce volumes covering the integration of plant and microbial biology in modern biotechnological science. Illustrations abound: for example, the development of plant molecular biology has been heavily dependent on the use of microbial vectors, and the growth of plant cells in culture has largely dawn on microbial fermentation technology. In both of these cases the understanding of microbial processes is now benefitting from the enormous investments made in plant biotechnology. It is interesting to note that many educational institutions are also beginning to see things in this way and are integrating departments previously separated by artificial boundaries.

Many definitions have been proposed for biotechnology but the only one which has specifically defined environmental biotechnology is that of the European Federation of Biotechnology as The specific application of biotechnology to the management of environmental problems, including waste treatment, pollution control and integration with nonbiological technologies. The study of microbial biofilms is clearly an excellent illustration of environmental biotechnology. The manipulation and control of biofilms is of great interest to industries, including agriculture, chemicals and healthcare.

One of the leaders in the study of biofilms has been Bill Costerton, especially in his early studies when he produced superb electron micrographs to demonstrate the fascinating microbial assemblages which developed in biofilms. However, he rapidly proceeded to demonstrate important physiological functions which occured in these interesting layers. In 1986, Hilary Lappin-Scott joined him to work partly in Cambridge and partly in Calgary on the biofilms associated with oil wells, so starting a long and productive association.

Introduction

Urinary tract infections (UTI) of the lower urinary tract are a common problem causing significant morbidity in females and males (Nickel 1990). Most of the causal organisms are Gram negative bacilli such as Escherichia coli and Proteus mirabilis, or Gram positive Enterococcus and Streptococcus spp., which have their reservoir in the gastrointestinal tract. The other major source of UTI pathogens is direct transmission through sexual activity. These organisms first colonize the introitus and the periurethral area before entering the bladder or prostate. There is an indigenous population of Gram positive, acid producing lactobacilli in this environment which under normal circumstances appears to enhance the urinary defence mechanisms and inhibit the successful progression of the enterics into the urethra and bladder (Chan et al. 1985; Reid et al. 1987, 1990a). When the balance between enteric uropathogens and host defences is upset, uropathogens are able to ascend through the urethra into the bladder, the prostate (in males) and less often into the kidneys where they colonize and cause infection. Usually only the bladder is infected giving rise to simple, uncomplicated acute cystitis. This condition is readily treated by several standard antibiotic regimes (Nickel 1990). Problems arise when this infection spreads from the bladder into other organs such as the kidneys (pyelonephritis) or prostate (prostatitis), or induces the formation of calculi (struvite urolithiasis: McLean et al. 1988, 1992). In these cases, significant tissue damage may occur, possibly causing permanent damage to renal function, which can be life threatening.

Introduction

Wastewater treatment is an essential component of our social order, for without it we soon find our communities suffering from waterborne disease, and our ecosystems suffering unwanted change. For over a century wastewater treatment systems have been designed to increase microbial growth in order to remove organic carbon and other nutrients, while limiting the release of suspended solids into receiving waters. Optimizing design parameters for these goals has been a successful strategy for many conventional wastewaters. However, in the past two decades we have confronted an increasing variety of non-conventional wastewaters in the form of chemical and industrial process effluents and landfill leachates. Legislation has been enacted in many countries that specifies the levels of toxic organic and inorganic chemicals that may be released into the environment. For example, in Canada the provinces of British Columbia, Ontario and Quebec have enacted strict regulations dealing with the discharge of chlorinated organics in pulp mill wastewaters. The long term cost to Canadian industry of this legislation plus proposed new regulations further limiting the chronic toxicity of wastewater discharges will be in the billions of dollars. These costs are already exerting pressure on the industries concerned to solve toxicity problems in the most efficient way possible.

There are three components to a successful toxic wastewater treatment process: knowledge of the nature of the toxic chemicals, an understanding of the concentrations of these chemicals that affect target organisms in receiving waters, and knowledge of the conditions required for growth of toxin degrading microorganisms in the treatment system. The first two of these have been placed on a sound scientific footing using the techniques of analytical chemistry and toxicology.

Introduction

Biofilms possess a number of distinctive characteristics that both define their inherent interest as biological systems worthy of study, and determine their very considerable practical importance in a wide range of environmental, industrial and medical processes. For example, in most natural ecosystems they are comprised not of individual organisms growing in axenic culture, but rather of mixed communities of species with differing but complementary metabolic capabilities. Such consortia demonstrate structural as well as functional organization giving rise to localized microenvironments, each with a particular combination of organisms and physicochemical conditions. The ubiquity of bacterial biofilms extends to their normal association with metal substrata in such situations as ships' hulls and marine structures, water and petroleum transmission lines, and a wide range of process equipment.

In biocorrosion, biofilms are of central importance to the processes involved, with the following individual features of their structure and function assuming particular significance. (i) The substratum on which the biofilm is built may also become a substrate in respect of acting as a source of metabolic energy (H2 oxidation). (ii) Heterogeneities in the horizontal dimension (colonial growth or patchiness) can establish localized electrochemical corrosion cells through the creation of oxygen concentration or differential aeration cells. (iii) The most significant vertical heterogeneity arises from the development of anaerobic regions at the base of the biofilm which can support the growth of sulphate reducing bacteria (SRB). (iv) The extracellular-polymeric substances, which constitute the main mass of the biofilm and underpin the maintenance of these heterogeneities and microenvironments, can also influence corrosion more directly by metal binding and/or retention of corrosion products.

Introduction

In order to examine whether or not the flora of the healthy adult female urogenital tract has any role in protecting a host from infection, and thereby performing a probiotic function, we must first outline the formation, composition and fluctuations of the flora. This is not a simple task as factors such as age and hormonal status influence the type and quantity of organisms present. In simple terms, the establishment of the flora can be seen to follow the path outlined in Fig. 17.1. This figure is based upon epidemiological studies of the urogenital flora (Reid et al. 1990b, c; Sadhu et al. 1989) and a theory for maintenance and causation of infection.

The primary colonizers comprise organisms such as lactobacilli, Gram positive cocci and diphtheroids which have dominated the flora from puberty. In general, the secondary colonizers can comprise a number of species, including potential pathogenic coliforms, Escherichia coli, coagulase negative staphylococci, Klebsiella, Proteus sp. and other Gram positive and Gram negative bacteria. Depending upon the virulence of these secondary colonizers, the host may be able to maintain an infection free state or succumb to the pathogens which then infect the bladder or vagina.

Morphological and structural analyses of the urogenital flora adherent to the epithelia have shown the presence of many distinct organisms, often interacting and coaggregating, in micro colonies or diffuse patterns on the cells (Sadhu et al. 1989; Reid et al. 1990c). Figure 17.2 illustrates this adherence, primarily dominated by Lactobacillus species. The presence of glycocalyx material intertwined between the cells is evident.

In vitro studies have to some extent mimicked this coaggregation or cooperativity between lactobacilli and other urogenital organisms, including potential pathogens.