There have been many important recent developments in our knowledge of the breadth of prokaryote diversity, our understanding of the driving forces behind that diversity, and of its significance for our lives and for fundamental processes upon Earth. It has become clear that the microbes we know about are actually just the tip of a biological iceberg. In fact, the majority of microbes are unculturable on laboratory media at present. Much of our attention has been focused on pathogens, understanding their interaction with the host and how to prevent disease. However, there is a growing appreciation that without microbes fundamental ecological processes would not be balanced. For example, microbes in the ocean have a direct influence on the composition of the atmosphere we breathe.

A major advance in allowing us to understand the extent and nature of microbial diversity has been the development of genome sequencing. In parallel, there has been the development of tools to allow whole-genome comparisons. This has facilitated the study of microbial diversity and evolution, such as allowing the tracking of unculturable organisms, the study of organisms from extreme environments, and of medical and environmental bacteria and interactions between them. It has given us insights into the exchanges of genes between organisms, resulting in an understanding of the emergence of pathogens, a process which involves both gene acquisition and gene loss. Genomic comparison has helped to identify core genes, to the point where we can predict a minimal genome needed for life, which can be supplemented by the horizontal transfer of genomic islands, phenotypic innovation and catabolic pathway evolution.

The science of the environment encompasses a huge number of biological, chemical and physical disciplines. For several years, scientists have been interested in large-scale environmental processes/phenomena, such as soil formation, global warming and global elemental cycling. Until recently, the role and impact of micro-organisms on these ‘global’ environmental processes has been largely ignored or, at best, underestimated. However, there is growing awareness that important environmental transformations are catalysed, mediated and influenced by micro-organisms, and such knowledge is having an increasing influence on disciplines other than microbiology, such as geology and mineralogy. Geomicrobiology can be defined as the study of the role that microbes have played and are playing in processes of fundamental importance to geology. As such, it is a truly interdisciplinary subject area, necessitating input from physical, chemical and biological sciences, in particular combining the fields of environmental and molecular microbiology together with significant areas of mineralogy, geochemistry and hydrology. As a result, geomicrobiology is probably the most rapidly growing area of microbiology at present. It is timely that this topic should be the subject of a Plenary Symposium volume of the Society for General Microbiology (SGM) to emphasize and define this important area of microbiological interest, and help to promote exciting collaborations between microbiologists and other environmental and Earth scientists.

The study of biofilm has been embraced by the microbiological community as it recognizes the profound effect that attachment of cells and cell populations to surfaces has upon their physiology and combined metabolic potential. Particularly, growth of microbial cells as communities, associated with interfaces, has been found to more directly address the many problems and opportunities associated with micro-organisms than do planktonic mono-culture studies. Fifteen years ago, the term ‘biofilm’ was mentioned in the abstracts and titles of approximately one scientific publication per week. Today, such citations occur every few hours and the wealth of literature captured by this umbrella term has burgeoned. The term biofilm is no longer definitive; rather it is an epithet indicative of an organism's or community's relationship to its natural habitat. Biofilm research, particularly at the community level, does not lend itself to reductionist experiments. Rather, the more one approaches the perfect experiment then the less flexible and informative it sometimes becomes! Inevitably, as the complexity of the system is increased then the range of outcomes and their interpretation broaden. In selecting the contributions to this symposium volume, we have tried not only to reflect the dynamic nature of microbial communities but also to represent the wide range of diverse disciplines that have been brought to bear on this topic. We particularly hope that the book and symposium will kindle the ‘biofilm’ spirit in the young researcher.

We would like to thank all of the contributors for their input to both the meeting and to the book, and express our sincere gratitude to Melanie Scourfield of the Society for her efficient and gentle handling of the Editors in the production of this volume.

INTRODUCTION

It is increasingly evident that biofilms growing in a diverse range of medical, industrial and natural environments form a similarly diverse range of complex structures (Stoodley et al., 1999a). These structures often contain water channels which can increase the supply of nutrients to cells in the biofilm (deBeer & Stoodley, 1995) and prompted Costerton et al. (1995) to propose that the water channels may serve as a rudimentary circulatory system of benefit to the biofilm as a whole. This concept suggests that biofilm structure may be controlled, to some extent, by the organisms themselves and may be optimized for a certain set of environmental conditions. To date, most of the research on biofilm structure has been focused on the influence of external environmental factors such as surface chemistry and roughness, physical forces (that is, hydrodynamic shear) or nutrient conditions and the chemistry of the aqueous environment. However, there has been a recent increase in the number of researchers using molecular techniques to study the genetic regulation of biofilm formation and development. Davies et al. (1998) demonstrated that the structure of a Pseudomonas aeruginosa biofilm could be controlled through production of the cell signal (or pheromone) N-(3-oxododecanoyl)-L-homoserine lactone (OdDHL). In this paper, we will examine some of the research that has been conducted in our laboratories and those of others on the relative contribution of hydrodynamics, nutrients and cell signalling to the structure and behaviour of bacterial biofilms.

HYDRODYNAMICS

The hydrodynamic conditions of an aquatic environment will determine the transport rate of nutrients and planktonic cells to a surface, the shear stress acting on the biofilm and the rate of erosion of cells from the biofilm.

INTRODUCTION

This chapter reviews the broad area of biofilm detachment, the mechanisms of detachment and the methods used to study this important process. Two case studies are included: the first of these focuses on the control of clinical biofilms; the second case study examines detachment in the water industry.

Biofilms are dynamic structures found in a wide variety of both natural and man-made environments. Their formation has been well studied; for example, Characklis (1990) described eight different stages of biofilm accumulation (Table 1 and Fig. 1). There has been much research into the initial attachment of micro-organisms to surfaces, including the effect of electrostatic interactions and electrochemical forces (Bos et al., 1999). The physiological changes that attaching cells undergo have also been examined; for example, the production of surface appendages such as fimbriae (Austin et al., 1998). In contrast to the work undertaken on attachment, detachment has received little attention although many researchers regard it as a crucial stage of biofilm development (Stewart, 1993; Allison et al., 1999).

Bryers (1988) classified the detachment process into four separate groups: abrasion, grazing, erosion and sloughing. Detachment from the biofilm can be directly caused by the collision or rubbing together of surfaces on which the biofilm has developed, leading to abrasive detachment. Larger organisms feeding on the biofilm can indirectly cause detachment through grazing. Erosion and sloughing refer to physical or chemical processes, which indirectly affect the biofilm structure, leading to detachment. Erosion refers to the continual removal of cells or small groups of cells from the biofilm, whereas sloughing is the loss of discrete amounts of biofilm.

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

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

Biofilm formation is important in a wide variety of situations: for instance, colonization of pipe surfaces in the food and water industries, metal corrosion due to sulphate reducing bacteria in the shipping and oil industries, and in medicine associated with infections of various tissues (osteomeylitis and endocarditis), dental decay (Addy et al. 1992) and prosthetic implants (Dougherty 1988). Whereas biofilm formation in a chemostat is considered merely an operating nuisance (Bryers 1984), in industrial fermentors such fouling can cause physical damage by the production of metabolites at points on the surface. Biofilms may lead to reduced heat efficiency transfer and reduction in flow rates, and can also act as a resevoir for potential pathogens (Lappin-Scott & Costerton 1989).

Although biofilm formation is frequently associated with being harmful and detrimental, in many instances it can also be beneficial. Biofilms are used in wastewater treatment for the degradation of soluble organic or nitrogenous waste. In nature microbial decomposition of cellulose fibres requires prior attachment of cellulolytic bacteria and Rhizobium cells form biofilms on the roots of leguminous plants where nodules are formed to fix atmospheric nitrogen. Bar-Or (1990) stated the importance of biofilms in stabilizing soil either by acting as cementing agents or flocculating soil particles, thereby improving aeration and water percolation and allowing further microbial growth.

Biofilm formation is difficult to control. A number of authors have reported that biofilm bacteria (sessile) are more resistant to antimicrobial agents than suspended bacteria (planktonic) of the same species (Brown et al. 1988; Anwar et al. 1989). Most commercial biocides and antibiotics were developed and tested for their ability to kill planktonic bacteria (Chopra 1986; Gilbert et al. 1987).