Introduction

Cedar or limestone glades (Figure 12.1) are open areas of rock pavement, gravel, flagstone, and/or shallow soil in which occur natural, long-persisting (edaphic climax) plant communities dominated by herbaceous angiosperms and/or cryptogams (J. M. Baskin and Baskin 1985a; Quarterman, Burbanck and Shure 1993). They may, or may not, be surrounded by forest (Galloway 1919). Cedar glades may support low densities of woody plants, which become established in deep soil-filled cracks in the bedrock (e.g., Picklesimer 1927 [see J. M. Baskin and Baskin 1996a]; Quarterman 1950b). The dominant plants are C4 summer annual grasses; C3 winter annual, summer annual, and/or perennial herbaceous dicots; mosses (primarily Pleurochaete squarrosa); the cyanobacterium Nostoc commune; and crustose, foliose, and fruticose lichens (Quarterman 1948, 1950a, b; Finn 1968; Mahr and Mathis 1981; Somers et al. 1986; Drew 1991; Dubois 1993)

Historically, in the Central Basin the term cedar glades has referred to rocky limestone openings (“glades”) and the adjacent redcedar–redcedar/hardwood–hardwood forest complex, that is, Quarterman's (1989) glade complex or ecosystem (e.g., Safford 1851; Galloway 1919; Freeman 1933; Quarterman 1950b; Mahr and Mathis 1981). However, in the past 20–30 years botanical studies in cedar glades of the southeastern United States (e.g., Ware 1969; J. M. Baskin and Baskin 1985a; Somers et al. 1986; Quarterman, Burbanck and Shure 1993; J. M. Baskin, Webb and Baskin 1995) have used cedar glades (or limestone glades) in reference to the rocky openings only, that is, glades or open glades, sensu Quarterman 1950b), and this is how we use the term in the present chapter.

One of the greatest triumphs of modern medicine has been the introduction of a rational system of antimicrobial chemotherapy to combat infectious diseases. Since time immemorial, folk remedies have exploited moulds or mould extracts to treat infections. In the early days of microbiology, attempts were made to use extracts derived from fungal cultures to prevent surgical wound infection. Joseph Lister used cultures of his own urine to investigate the microbiology of air. He noted that if moulds were present in his cultures, the bacteria that were also there appeared non-motile and degenerate, whereas if bacteria grew without moulds, they were highly motile. Lister concluded that moulds produced a substance or substances that adversely affected the viability of bacteria. He then reasoned that culture filtrates obtained from moulds should prevent infection if used to irrigate surgical wounds. This practice started 60 years before Alexander Fleming described the antibacterial properties of penicillin, produced from a mould that he had originally misidentified.

The problem of producing sufficient antibiotic from mould cultures defeated both Lister and Fleming. Indeed, Fleming was slow to appreciate the clinical applications of his observations. He intended that penicillin should be used as a selective agent in laboratory media rather than to be administered to patients directly. It was not until the early days of the Second World War that an allied Anglo-American effort overcame the problem of large-scale production and penicillin therapy for human infection was properly initiated.

When we wrote Introductory Microbiology some very hard decisions had to be made concerning the contents of the book. We were constrained by the style of the Studies in Biology series to write a book of no more than 200 pages. In the end, we decided that students needed a description of what microorganisms were and how they can be safely manipulated before appreciating what they can do. We therefore took the decision to base our first book on these fundamental aspects of the subject. We were convinced at the time, however, that we could fill a second book with the material that we had omitted from the first. All we had to do was to persuade a publisher that students need to know about much more than we could include in that book.

Tim Benton, who edited our Introductory Microbiology, was so pleased with our proposal that he accepted our ideas and then promptly left Cambridge University Press to take up an academic career. We are not suggesting that this career change has any bearing on Tim's ability to make rational decisions or on the viability of our proposals. The project was handed on to Barnaby Willitts. He was very supportive throughout the writing of this book. As the deadline for submission arose, however, Barnaby left the press (and the country). The project was then handed to Maria Murphy. We owe all those who played a part in producing this book a debt of thanks.

Glancing through the contents of this book you could easily be forgiven for thinking that microbes were mostly malign, the cause of destruction, disease and death. Indeed, because of the vital importance of the control of infectious diseases, an enormous effort has been directed towards the medical applications of microbiology. Not even Louis Pasteur was lured into a study of microbiology with the intention of ridding the world of disease, as he later aspired to do. Rather, he was appointed to solve an economic and industrial problem threatening to ruin France.

Pasteur started his professional life as a chemist. As a young man, he had found that when polarised light is shone through solutions of organic compounds derived from living organisms the beam is either diverted to the left (laevo-rotatory) or to the right (dextro-rotatory). When organic compounds are synthesised in vitro, no such rotation is seen. He explained this phenomenon by showing that the L-molecules and the L-molecules were optical isomers. In nature typically only one isomeric form is produced or used by organisms. There is a notable exception to this. The bacterial cell wall contains peptidoglycan, a polymer incorporating sugars and both L- and L-amino acids. When organic chemicals are synthesised in test tubes, however, there is an equal chance that either isomer will be made. Because of the reputation gained from this work, in 1854 Pasteur was invited to the University of Lille to study the problem of beer spoilage.

Soil is a dynamic habitat for an enormous variety of life-forms. It gives a mechanical support to plants from which they extract nutrients. It shelters many animal types, from invertebrates such as worms and insects up to mammals like rabbits, moles, foxes and badgers. It also provides habitats colonised by a staggering variety of microorganisms. All these forms of life interact with one another and with the soil to create continually changing conditions. This allows an on-going evolution of soil habitats.

The activity of living organisms in soil helps to control its quality, depth, structure and properties. The climate, slope, locale and bedrock also contribute to the nature of soil in different locations. The interactions between these multiple factors are responsible for the variation of soil types. Consequently, the same fundamental soil structure in different locations may be found to support very different biological communities. These complex communities contribute significantly to the continuous cycling of nutrients across the globe.

What habitats are provided by soil?

Soil forms by the breakdown of bedrock material. Erosion of rocks may be the result of chemical, physical or biological activity, or combinations of the three factors. Dissolved carbon dioxide and other gases cause rain water to become slightly to moderately acid. This pH effect may cause the breakdown of rocks such as limestone. Physical or mechanical erosion can result from the action of wind or water, including ice erosion.

How do microbes cause disease and how do we defend ourselves from infection

The vast majority of microbes that humans encounter on a daily basis do no harm. Indeed, the microbes that constitute our commensal flora are, on balance, beneficial under most circumstances. Only a minority of microbes can interact with humans to cause disease. These are known as pathogens from the Greek word pathos, meaning ‘suffering’. Some pathogens cause mild illnesses: others are responsible for life-threatening infections. Some infections are chronic, developing slowly over many months or years: others may be rapidly fatal. Virulence is the term used to describe the degree to which an organism can cause disease. This term is derived from the Latin word virus, meaning a poison. Some authors do use the terms ‘pathogenicity’ and ‘virulence’ interchangeably. Other authors prefer to reserve the term ‘virulence’ for a quantitative description of the degree to which a microbe can damage its host.

Infections spread from a source known as the reservoir of infection. These may be human beings, as with Salmonella typhi, animals, as with Salmonella typhimurium, or the environment. Soil is the reservoir of infection for tetanus, caused by Clostridium tetani, and water for Legionnaire's disease, caused by Legionella pneumophila. The source of infection is the individual or location from which an infection is acquired.

How do microbes affect food?

An inevitable consequence of the start of agricultural practices that heralded the dawn of civilisation was the need to store crops from one season to the next. This brought with it the risk of microbial contamination and spoilage. The problems of food spoilage are, therefore, as old as civilisation. Not all spoilage, however, is detrimental. Fermentation, for example, can vastly improve the flavours of foods and can also turn an inedible food into a delicacy. The food processing industry has thus been exploiting microbes for centuries. Even so, it is only in the last 150 years or so that we have realised the contribution that microbes make to food production.

How are fungi used as food?

Probably the most familiar edible fungus is the mushroom. We have been eating mushrooms for centuries. The Romans valued mushrooms but were also very familiar with their potentially fatal effects. Sometimes they used this knowledge to great effect when someone important obstructed their ambitions. Agrippina murdered the emperor Claudius by feeding him mushrooms so her son Nero could succeed him as emperor. Nero then declared mushrooms the food of the gods, since it was mushrooms that had made Claudius a god. There is even a mushroom known as Caesar's mushroom (Amanita caesarea). This is a rather rare and highly prized specimen: a close relative of the death cap mushroom (Amanita phalloides).

What are mycorrhizas?

The name mycorrhiza is derived from two Greek words, mukes meaning a mushroom and rhiza, a root, illustrating a very important mutualistic interrelationship between plants and fungi. These partnerships have a long history. The fossil record shows that fungi and higher plants have lived in the close association of mycorrhizal relationships for at least 400 million years. The first recorded observations of mycorrhizal associations were made in the mid-nineteenth century. The numbers of plants that form mutualistic associations with fungi perhaps best illustrates the importance of mycorrhizal relationships. Over 80% of higher plants and ferns grow in association with a fungal partner. The range of higher plants affected include hard- and softwood trees, shrubs and other flowering plants as well as grasses.

The fungi that form mycorrhizal partnerships greatly extend the active surface area of the root system of plants. Fungi replace and extend the root system of the plant. The roots of trees that carry mycorrhizas are typically short and dichotomously branched. Unaffected roots are much longer. Orchids have evolved to such a degree that their mycorrhizal fungi have even replaced the plant root hairs. Plants that support mycorrhizas have much greater access to inorganic nutrients, particularly nitrates, phosphates and water. In return, the plant partner supplies its fungus with a source of organic nutrients and, in many cases, vitamins.

What constitutes the resident and transient flora of humans?

It has been estimated that the human body contains cells. Of these, 90% are not of human origin. They represent the microbes of our commensal flora. The term commensal is partly derived from the Latin word mensa, meaning table. Commensal organisms are considered to share their food from a common table; one that we provide as human hosts. Different anatomical sites are associated with a flora peculiar to each location.

During our time in the womb we live in a sterile environment, protected on one side by the placenta and on the other by the amniotic sac. From the moment of birth, however, we are subjected to a huge array of microbes. The first organisms that we as babies come across are those present in the birth canal. During birth we inhale, swallow and acquire on our surface a vast diversity of microbes as a result of contact with the new environment. This process will continue throughout our lifetime. If the organisms with which we come into contact find themselves in a suitable ecological niche, whether on an internal or an external surface, they will multiply and form complex communities. They will interact with each other and with their human host. This process requires the microbes to adhere to the host as an initial step in the colonisation process and then the microbes must multiply.

Water is essential for the maintenance of all life on Earth. It also acts as the vector for many diseases caused by bacteria, viruses, protozoa and worms. For water to be regarded as potable, i.e. of a quality fit and safe for drinking, it must be free from such pathogens. Furthermore, it must not contain any other noxious substances such as chemical hazards including pesticides, insecticides or herbicides, artificial fertilisers or heavy metal ions. Potable water should not have an unpleasant odour or taste.

What are water-borne diseases?

Among the bacterial infections that are spread by water are cholera, the enteric fevers and dysentery. Hepatitis A and poliovirus cause infections after drinking contaminated water. Amoebic dysentery is caused by the protozoan Entamoeba histolytica and is spread either by drinking contaminated water or by eating food such as fresh fruit, salad or raw vegetables that have been washed in contaminated water. Other protozoal diseases such as those caused by Giardia intestinalis (Giardia lamblia), Balantidium coli and Cryptosporidium species are spread in a similar fashion. Schistosomiasis, also known as bilharzia, is a water-borne infestation caused by worms of the genus Schistosoma.

Cholera

Cholera is a disease that has been known since ancient times. It was confined to the Indian sub-continent but between 1817 and 1923 there were six pandemics in which cholera spread from its original home across the world. It is now also endemic in South America as well as in Asia.

Introduction

Diatoms have great potential for studies of marine paleoecology and paleoceanography, especially in high latitudes and coastal regions. In these settings they are diverse and abundant, usually being the dominant group in the fossil assemblage. Elsewhere, their use may be limited by the relatively poor preservation of biogenic silica. The red clays of the central oceanic gyres contain no diatoms at all; most calcareous sediments contain only fragments of a few robust forms.

The poor preservation results from two interrelated conditions. (i) Diatoms as a group are at a competitive disadvantage in conditions of low nutrient supply. In addition to the universal requirement for nitrogen and phosphorus, they will be limited by availability of silicon, and trace metals such as iron may be limiting also (Martin & Gordon, 1988; Coale et al., 1996). Therefore, over large areas of the world ocean, diatoms are a minor component of the phytoplankton, and those taxa which are present are frequently very weaklysilicified. (ii) Seawater and sediment porewaters are usually undersaturated with respect to biogenic silica (Tréguer et al., 1995), so that dissolution of the frustules occurs rapidly, especially when pH is relatively high, as it often is in calcareous sediments. Preservation is good only in sediments with a high component of rock particles (ice-rafted detritus, coastal sediments, volcanic ash beds) or in siliceous (diatom) oozes, which result from a combination of high rates of diatom production and exclusion of other sediment components.

Introduction

Diatoms are an important and often dominant component of the benthic microalgal assemblage in estuarine and shallow coastal environments. This chapter will be concerned mainly with the motile diatom assemblages of intertidal sediments in these environments and secondarily with diatom assemblages epiphytic on submerged aquatic vegetation. Admiraal (1984) provided an excellent summary of the ecology of estuarine sediment-inhabiting diatoms. A variety of topics was covered, including distribution, effects of physicochemical factors, population growth, primary production, and interactions with herbivores. The focus of the present review will be considerably narrower as only those applied studies which have utilized structural (e.g., species diversity) and/or functional (e.g., primary production rates) attributes of benthic diatom assemblages will be considered. By applied is meant studies that treat benthic diatom assemblages as tools to address concerns about larger ecosystem problems such as cultural eutrophication of estuarine and shallow coastal environments. The three diatom-related research topics that will be reviewed in this chapter include eutrophication, sediment stability, and resuspension. These topics are important because of threats posed to estuarine and shallow coastal systems by increasing nutrient levels and reduced light transmission in the water column; both may significantly impact the role of algae and other primary producers in trophic dynamics and consequently affect ecosystem health. Relevant studies conducted in the Baltic Sea will not be included as they will be part of the chapter on applied studies of diatoms in brackish waters by Snoeijs (this volume).