The genome is relatively small and will be sequenced soon

The chromosomes of Dictyostelium are at the limit of light microscopic detection, and although seven are generally observed, the physical and genetic maps of the genome reveal only six chromosomes. Originally, the genome size was determined to be about 50 megabases (Mb) (Firtel and Bonner, 1972; Sussman and Rayner, 1971), about 1% of the size of the human genome, and about 11–12 times that of E. coli. More recent estimates yield a genome size of 34 Mb (Cox et al., 1990; Kuspa and Loomis, 1996).

One of the curiosities of the genome is its extreme AT-richness, especially in intergenic regions and introns. The stop codon is nearly always TAA. Coding sequences are skewed to an AT bias – when the third position of a codon can be an A or a T, it usually is. Overall, the base composition is 77% AT, while in coding sequences A and T constitute about 65% (Firtel and Bonner, 1972; Kimmel and Firtel, 1982; Sussman and Rayner, 1971). Other organisms such as Plasmodia falciparum are also exceptionally AT-rich, though what led to this AT-richness is unknown.

There is another strange element in the genome – coding sequences tend to have long repeats of the triplet AAC (Kimmel and Firtel, 1985; Shaw et al., 1989). The AAC repeats are present in all three reading frames, leading to long stretches of asparagine, glutamine, or threonine in the deduced proteins (Shaw et al., 1989).

Dictyostelium discoideum is the most studied species of the social amoebae, which are also known as the cellular slime molds. All of these organisms live in the soil and feed on bacteria, living a solitary life until the bacteria are consumed. The onset of starvation forces a major revision in the life cycle, and the amoebae respond by collecting into aggregates which transform into an organism that undergoes cell differentiation and morphogenesis. The result is a fruiting body consisting of a ball of resistant spores suspended on a stalk. D. discoideum and similar species have evolved strategies to survive in the harsh environment of the soil. A close examination of these strategies raises questions at all levels of biology: How do the amoebae sense starvation and other stresses, and how do they respond? How do they communicate with each other and how do they move? What mechanisms of signal transduction do they use, and how do those resemble the mechanisms of more complex organisms? How did the extraordinary cooperativity of development evolve? Rather than forcing the reader who has no experience with these organisms into details immediately, this chapter will provide a short glossary of terms and an overview of development, first in D. discoideum, and then in a few related species.

The developmental cycle begins when the amoebae consume all of their prey. If they do nothing to protect themselves, they will die from starvation.

Embryonic cells are spared some of the tasks that confront soil amoebae. Multicellular organisms are protected from direct contact with the environment because they are part of a large mass with specialized external epithelia. The plasma membrane of soil amoebae offers none of the protection of a multicellular organism. Every time it rains, the osmotic shock to the cells will be severe, because rainwater is essentially distilled water and like other single-celled organisms, D. discoideum and its relatives must be equipped to handle sudden changes in osmolarity. Other conditions, for example hyperosmotic mud, lead to hypertonic shock, for which the cells also have adaptive mechanisms. The internal membranes and organelles resemble those of higher organisms. Many of the membrane compartments of the amoebae can be marked by fusing the green fluorescent protein (GFP) gene to genes that code for appropriately targeted proteins. This useful property is illustrated in Plate 1.

The plasma membrane

The plasma membrane must be capable of movement on a variety of surfaces that constitute the matrix of the soil, whether the cellulose of decayed leaves, minerals, decaying vegetable matter, or films of bacterial growth. These cells must have substrate adhesion systems that are more versatile than those of embryonic cells, which move on a defined extracellular matrix. The amoebae eat all manner of bacteria and yeasts, and even undertake the occasional act of cannibalism, so several mechanisms of cell recognition must be deployed on the membranes.

Introduction

The rapidly expanding scientific knowledge on seagrasses has led to a growing awareness that seagrasses are a valuable coastal resource. Where seagrasses abound, humans benefit directly and indirectly from the presence of this marine vegetation. At the same time, it has also become evident that seagrasses are a vulnerable resource, easily lost in coastal areas facing environmental changes. Declines of seagrasses are reported world-wide, and in many cases anthropogenic factors are suspected to be responsible for these declines. In this chapter the relations between seagrasses and humans are addressed. Particular attention will be given to the various stresses on seagrasses resulting from human activities. Knowledge of the processes that lead to seagrass decline is obviously the key to remedial measures targeting the re-establishment or protection of seagrass systems.

The value of seagrasses to humans

The value of seagrasses, as perceived by humans, changes in time and place. In the past, seagrasses have been valued because the plants yielded material for various practical purposes. This direct use of seagrasses has a long history that continues, although on a very modest scale, until today. Seventeenth and eighteenth century Spanish colonial documents indicate that the seeds of Zostera marina were a major food resource of the Seri Indians living along the Gulf of California. The Seri harvested the carbohydrate-rich seeds to obtain flour that was used in different dishes (Felger et al., 1980). In the north-west Pacific, roots and leaf bases of eelgrass were eaten (Turner & Bell, 1973).

Introduction

In the previous chapter we discussed the ways seagrasses obtained carbon, nitrogen and phosphorus from the environment, elements that are vital for their structure and functioning. As tissues die, these elements are again lost from the plants, although resorption processes may somewhat mitigate the loss rates. The plants thus have a direct influence on the dynamics of chemical elements in their environment. Uptake by, and loss of, elements from the living plants are only two aspects of the fluxes of matter in seagrass systems. In this chapter we will focus on the various processes determining these fluxes, with particular attention to those relevant to the dynamics of carbon, nitrogen and phosphorus. A variety of processes, biological, physical and chemical, plays a role in shaping the dynamics of these elements, but they share one feature in common: directly or indirectly they are influenced or even determined by the presence of the key species in the system, the seagrasses. Primary production and mineralization are two major processes driving the carbon and nutrient dynamics within the seagrass system, these processes coinciding with fixation and release of inorganic compounds, respectively. Inorganic nitrogen- and phosphorus-containing compounds released during mineralization can be captured again for the production of plant biomass. Although much of the plant biomass dies without being eaten by herbivores and is directly processed by the decomposer community, some of it is consumed by herbivores.

Introduction

The few members of the angiosperm flora that have succeeded in adapting to submersed life in the sea share a common architecture, all species being clonal, rhizomatous plants. This clonal nature has been interpreted as a necessary adaptation for angiosperm growth in the high-energy marine environment (Sculthorpe, 1967). A consequence of the clonal nature of the seagrasses is that they display a highly ordered growth programme (Tomlinson, 1974), developed through the regular addition of the basic set of modules. Thus, a general understanding of the design of seagrasses will provide insight into their growth patterns (Patriquin, 1973, 1975; Tomlinson, 1974; Sand-Jensen, 1975; Duarte & Sand-Jensen, 1990; Duarte et al., 1994). Although the repertoire of architecture and associated growth programmes that seagrasses display is certainly narrow, they contain sufficient plasticity to yield order-of-magnitude variability in the clonal growth between individual shoots of seagrass species (Marbà & Duarte, 1998), as well as in their reproduction and dispersal. Even within a species, the plasticity of its growth programme and architecture allows the plants to cope with stress and heterogeneity in the environment, as has been extensively documented for land plants. This plasticity is also a central trait in the ecology of seagrasses.

In this chapter we provide a description of the basic architecture of seagrasses, the growth patterns resulting from their design, and their plasticity in growth characteristics to cope with stress and resource heterogeneity.

Introduction

The meadows formed by seagrasses have characteristics that make them a suitable habitat for many species of animals. The high primary productivity of the seagrasses, augmented with that of epiphytic and benthic algae, ensures an abundant supply of organic matter that can be used as the basic energy source for more or less complicated food webs. Moreover, the three-dimensional structure of the vegetation, with its network of roots and rhizomes and often dense leaf canopy, offers hiding places that protect against predation, and also provides substrate for attachment. The vegetation structure, furthermore, confers physical and chemical qualities to the environment that may attract fauna: currents within the canopy are reduced, the sediment is stabilized and often fine grained, and irradiance conditions are modified. In this chapter we will first take a closer look at the general abundance and species richness of the fauna associated with seagrass meadows, before turning to the faunal groups that have received major attention, i.e. fishes, crustaceans and molluscs. The association of sea cows and turtles with seagrass beds will also be discussed. The significance of seagrass meadows as a habitat and foraging area is a recurrent theme in these sections. In the final part of the chapter, the ways in which the fauna affect the functioning of the seagrasses will be addressed.

Abundance and diversity

The fauna of seagrass meadows are heterogeneous assemblages of animals belonging to a variety of taxa, with many different ecological characteristics.

Introduction

Seagrasses comprise <0.02% of the angiosperm flora, representing a surprisingly small number of species (about 50, Table 1.1) compared with any other group of marine organisms. The limited species membership of the seagrass flora has directed some (still limited) efforts to the study of their origin and their evolution in an attempt to account for this phenomenon. A second path of research has tried to find clues for the paucity of species by studying the stress factors constraining angiosperm life in the sea. This second approach has driven much effort towards the analysis of seagrass distribution and the definition of the habitat requirements of seagrasses. The attention these issues have received extends beyond scholarly concerns, for seagrasses are, despite their limited diversity, important contributors to coastal marine ecosystems, both locally and at the global scale. In this chapter we shall provide an overview of the origin, evolution and present diversity of extant seagrasses, and describe their present distribution and the basic requirements that delimit their possible habitats. The definition of how seagrass distribution is regulated leads, in turn, to the assessment of their global extent and, from this, to the evaluation of the role seagrasses play on the global ocean ecosystem.

The seagrass flora

Seagrasses are generally assigned to two families, Potamogetonaceae and Hydrocharitaceae, encompassing 12 genera of angiosperms containing about 50 species (Table 1.1).

Introduction

Seagrass meadows often appear to the casual observer as static landscapes. However, seagrass meadows are subject to intense dynamics involving the continuous loss and replacement of shoots in the population, which, when in balance, maintain a dynamic equilibrium. Such apparent steady-state conditions can be maintained over extended time periods, leading to long-lived seagrass meadows, such as some Posidonia oceanica meadows, which possibly may persist for > 4000 years in the Mediterranean (e.g. Mateo et al., 1997), and Zostera marina meadows exceeding a millennium in age (Reusch et al., 1999).

The equilibrium maintaining seagrass meadows is, however, often upset, leading to a regression of seagrass meadows, whereby large meadows can be totally lost over a few years (see Chapter 7). In fact, seagrass decline is now a common phenomenon throughout the world (Short & Wyllie-Echeverria, 1996), to the point that the law in various countries now protects seagrass meadows. However, effective protection of seagrass meadows requires an understanding of the regulation of seagrass losses and gains. This is currently the bottleneck to the development of reliable forecasts on the future status of seagrass meadows. Examination of the dynamics of genetic individuals (genets) and patches within the meadow requires knowledge of the life cycles of seagrasses. Seagrass life cycles are similar to those of clonal herbs on land, except that they are entirely confined to the marine realm. However, dispersal processes are remarkably different in the underwater marine environment compared with land.

Introduction

As outlined in the first chapter, seagrasses are the only angiosperms that are adapted to a marine submerged existence. Basic requirements for growth are similar for terrestrial angiosperms and seagrasses alike. Life in the marine realm, however, implies exposure to environmental conditions that are considerably different in many respects from those in terrestrial habitats, imposing constraints on the availability of some resources, or calling for specific adaptations to acquire others. In this chapter we will focus on environmental resources imperative for growth in seagrasses, i.e. light, inorganic carbon and nutrients, and on the plant properties relevant to their acquisition and use.

Light

Availability

Photosynthesis provides plants with chemically fixed energy and with carbon skeletons for the variety of biosynthetic processes associated with plant growth and functioning. The penetration of light through natural waters, however, is at least three orders of magnitude less than through air. Light intensity thus rapidly decreases with water depth, and even in clear ocean water virtually no photosynthetically active radiation (PAR; wavelength 350 or 400 to 700 nm) can penetrate beyond a depth of 200 m. Apart from absorption by pure water, particulate and soluble substances also each contribute to the total attenuation of light in the water column. The intensity of absorption varies with the wavelength; the absorption of pure water, for instance, begins to rise as wavelength increases above 550 nm (Fig. 4.1; Kirk, 1983).

Only a few decades ago, seagrass ecology was a virtually non-existent field within marine ecology. In the past 30 years or so, this situation has drastically changed. As a recent analysis of published papers by one of us (CMD; Aquatic Botany 65: 7–20) indicates, current publication rates on seagrass ecology in the international scientific literature are at a level of approximately 100 papers per year, and these rates are still increasing. The growing awareness of the role that seagrasses play in ecology, and in the regulation of the biogeochemical cycles of the coastal zones worldwide, undoubtedly does much to stimulate this ongoing expansion of research efforts. The increase in the number of studies also implies that the community of researchers that enters the field of seagrass studies is growing. Besides the scientists, there is also an expanding community of professionals working in governmental and non-governmental organizations in countries all over the world, which in the context of coastal management or conservation issues are actively involved in seagrass matters.

This book is intended to provide an introduction to the field of seagrass ecology. In the first place it is designed for students and for scientists who enter an area as yet unfamiliar to them. In the second place, we hope that the book will also serve as a source of information for those involved in management and conservation of coastal areas that harbour seagrasses.

Primitive ovulate plants and their precursors (Progymnospermopsida)

The class Progymnospermopsida contains only fossil plants. The concept of progymnospermy, a stage at which plants with conifer-like anatomy and morphology were still reproducing by spores, followed the surprising discovery that certain well-preserved trees of the Upper Devonian bore frond-like sprays of branches, some of which bore clusters of sporangia. Callixylon, the first progymnosperm to be recognized, provides a splendid example of this stage of evolution (Fig. 8.1a). The trunks reached a diameter of 1.5m (5 ft) and a length of 8m (26ft) or more. Permineralized remains reveal fine details of the anatomy. A central pith was surrounded by mesarch primary xylem. Outside this lay a considerable thickness of well-developed secondary xylem traversed by narrow rays. The pits in the radial walls of the tracheids were frequently grouped, the groups aligned horizontally and in register with tracheids in the rays. Dense wood of this kind, also characteristic of modern conifers, is termed pycnoxylic.

Although Callixylon was known for many years as the trunk of a late Devonian tree, only much later were discovered specimens in organic connection with frond-like branches. These branches were already known as Archaeopteris and had been assumed to be the fronds of ferns. Archaeopteris is known both sterile and fertile (Fig. 8.1b). The sporangia were spindle-shaped, up to 3.5mm (0.14in.) in length, and occasionally with stomata in the epidermis.

Algae containing chlorophylls a and c

Although chlorophyll a is always present in the algae to be considered in this chapter, the amount of chlorophyll c is sometimes small. Chlorophyll b is always absent (but see Dinophyta, p. 95).

The “a+c” algae show a number of organizational trends resembling those seen in the Chlorophyta. There are also features not represented in living Chlorophyta, but possibly present at some stage in their evolutionary history. The chlorophyll c-containing algae are sometimes referred to collectively as the “chromophyte algae”. The first four divisions considered here constitute the “heterokont algae” (Table. 2.1), and have a number of basic features in common, relating principally to the flagella and chloroplasts. Besides (where two are present) the inequality and difference in ornamentation of the flagella, the chloroplast is typically surrounded (in addition to its normal envelope) by a fold of endoplasmic reticulum. This “chloroplast endoplasmic reticulum” is part of the general endoplasmic system, connected with the outer membrane of the nuclear envelope. It is not, however, confined to the heterokonts, but is found also in the Haptophyta (p. 93) and Cryptophyta (p. 96), not regarded as closely allied to the heterokont algae.

CHRYSOPHYTA

Habitat Aquatic (mainly freshwater), often common in plankton.

Pigments Chlorophylls a, c;β-carotene; fucoxanthin conspicuous, but other xanthophylls also present.

General features of the bryophytes

The mosses and liverworts, although morphologically somewhat dissimilar, are classified together as the Bryophyta. Because of their distinctive features they are treated as a division of the plant kingdom, of a rank equal to that of the algal groups and the Tracheophyta (Table 1.2). There are about 25000 species of bryophytes in all. Three classes are recognized, namely Marchantiopsida, Anthocerotopsida and Bryopsida. They represent the simplest of the archegoniate plants and form a single division with the following characteristics:

BRYOPHYTA

Habitat Mainly terrestrial.

Plastid pigments Chlorophylls a, b;β-carotene; xanthophyll (lutein).

Food reserves Starch, to a lesser extent fats and oils.

Cell wall components Cellulose, hemicelluloses.

Reproduction Heteromorphic life cycle, the gametophytic phase normally the more conspicuous, and the sporophytic determinate and partly dependent upon it. Sex organs with a jacket of sterile cells, the egg cells enclosed singly in flask-shaped archegonia. Zooidogamous, spermatozoids with two whiplash flagella. Embryogeny exoscopic. Sporophyte producing non-motile, cutinized spores, in some species with heavily thickened and sculptured walls, usually all of one size (homospory). Vegetative propagation of the gametophyte by fragmentation or specialized gemmae.

Growth forms of gametophyte Thallus flattened, with some internal gametophyte differentiation, or consisting of a main axis with leafy appendages.

Although the simplest terrestrial plants, the bryophytes in some parts of the world form a conspicuous component of the vegetation.