The metaphor of dance is a very apt way to portray the unfolding and increasing complexity of plant-life on Earth. The dance of plants is the dance of plant form in space and time. From a reductionist point of view, the conversion of solar energy is what plants are really all about, either at the level of the individual, or the community, or even in the characteristics of the plant-life of a given region. Form, is the physical expression of the energy captured and transformed by plants, and it provides the basis for all ecological relationships. It is not surprising then that, broadly speaking, the plants of tropical regions that have access to the greatest input of radiant energy also have the greatest exuberance, while those of energy- and nutrient-limited environments, such as alpine moorlands and bogs, have a more restricted range of body plans.

Introduction

Ectomycorrhizal fungi (EMF) form symbioses with forest trees. These fungi are mainly basidiomycetes and ascomycetes and they probably evolved from saprotrophic fungi when organic matter began to accumulate in certain soils 200 million years ago (Cairney, 2000). The tree host benefits from the symbiosis through improved nutrient acquisition since the fungus explores the soil efficiently for nutrients (especially N and P) in return for host carbon (Smith & Read, 1997). Forest trees with ectomycorrhiza usually dominate in acidic soils with thick litter layers, with the associated EMF forming extensive external mycelia with a high capacity to take up nutrients from the soil. The fungi form mantles around the root tips with large storage capacities (Read, 1991). The trees invest large amounts of carbon in the ectomycorrhizal (EM) symbionts, especially under nutrient-poor conditions, with up to 20% of photosynthetic assimilates allocated to the mycorrhizal symbionts (Finlay & Söderström, 1992). This large carbon source for EMF gives them an advantage over non-symbiotic microorganisms in the soil ecosystem since these are usually carbon-limited (Aldén et al., 2001). The importance of current photosynthate for soil processes was recently demonstrated by Högberg et al. (2001), who girdled trees in northern Sweden and found a rapid reduction in soil respiration of more than 50% within 1–2 months. More precise calculations the second year after girdling demonstrated that 65% of total respiration was contributed by EM roots, their associated EMF and other rhizosphere microorganisms (Bhupinderpal-Singh et al., 2003).

Introduction

This chapter addresses the resource requirements for the assembly of photoautotrophic biomass. In addition to light and carbon, growth of phytoplankton consumes ‘nutrients’ and, equally, may often be constrained by their availability and fluxes. Put at the most basic level, every replication of a phytoplankton cell roundly demands the uptake and assimilation of a quota of (usually) inorganic nutrients similar to that in the mother cell, if her daughters are to have the similar composition. Ignoring skeletal biominerals for the moment, we may recall from Section 1.5.3 that, in addition to carbon, the living protoplast comprises at least 19 other elements. Some are needed in considerable abundance (hydrogen, oxygen, nitrogen), others in rather smaller amounts (phosphorus, sulphur, potassium, sodium, calcium, magnesium and chlorine), for the assembly and production of the organic matter of protoplasm. Others occur as vital traces in support of cellular metabolism (silicon, iron, manganese, molybdenum, copper, cobalt, zinc, boron, vanadium). However, it is less the amounts in which these elements are required that constrains growth than does the ease or otherwise with which they are obtained. It is the demand (D) relative to the supply (S) that is ultimately critical, bearing in mind that a measurable presence is not a measure of availability if the element in question is not both soluble and diffusible and, so, assimilable by cells.

There is a huge literature on this topic.

Introduction

The purpose of this chapter is to assess the role of phytoplankton in the pelagic ecosystems and other aquatic habitats. The earliest suppositions to the effect that phytoplankton is the ‘grass’ of aquatic food chains and that the production of the ultimate beneficiaries (fish, birds and mammals) is linked to primary productivity are reviewed in the context of carbon dynamics and energy flow. The outcome has a bearing upon the long-standing problem of phytoplankton overabundance and related quality issues in enriched systems, its alleged role in detracting from ecosystem health and the approaches to its control.

The chapter begins with an overview of the energetics and flow of primary product through pelagic ecosystems, especially seeking a reappraisal of the relationship between biomass and production.

Material transfers and energy flow in pelagic systems

One of the essential components of ecological systems is the network of consumers that exploit the investment of primary producers in reduced organic carbon compounds. Some of these are re-invested in consumer biomass but much of the food intake is oxidised for the controlled release of the stored energy in support of activities (foraging, flight, reproduction) that contribute to the survival and genomic preservation of the consumer species in question. In thermodynamic terms, the food web serves to dissipate as heat that part of the solar energy flux that was photosynthetically incorporated into chemical bonds (see p.355).

Introduction

There were times on our planet when the barren dryness of uninhabited continents sharply contrasted with the densely populated sea. The continental lithosphere was then essentially represented by rock surfaces of different types. Sedimentary rocks were rare, if not absent. As rock materials became exposed to the subaerial environment at the Earth's surface, they encountered a whole range of environmental challenges such as temperature fluctuations, water, unbuffered cosmic and solar irradiation and atmospheric gases and solids instead of dissolved species. These influences resulted in rocks undergoing alterations in material properties leading to erosion and breakdown into ever-smaller particles and constituent minerals, formation of sandy sediments, and mineral soils (Ehrlich, 1996). Primordial terrestrial environments can therefore be visualized as a freshly exposed and only slightly physically pre-weathered rock surface.

However, physical and chemical changes in rock-forming minerals even during the very first stages of the terrestrial evolution were accompanied by an initially slow but steady establishment and spread of living organisms. Life started to colonize rock surfaces during the Archean. The first settlers were undoubtedly biofilms and later mature microbial mats not unlike modern desert or intertidal stromatolithic systems (Costerton & Stoodley, 2003). Environmental and geochemical settings of these ancient subaerial habitats were probably very similar to the conditions of present-day deserts. Rock surface environments were then, and remain now, exceptionally hostile with respect to all conditions necessary for the maintenance of living systems.

Introduction

Fungi are adapted to a diverse array of freshwater ecosystems. In streams and rivers, flowing water provides a mechanism for downstream dispersal of fungal propagules. The dominant group of fungi in these habitats, aquatic hyphomycetes, have conidia that are morphologically adapted (tetraradiate and sigmoid) for attachment to their substrates (leaf litter and woody debris from riparian vegetation) in flowing water (Webster, 1959; Webster & Davey, 1984). In freshwater wetlands and lake littoral zones, production of emergent aquatic macrophytes is often extremely high, resulting in an abundance of plant material that eventually enters the detrital pool. The dead shoot material of these macrophytes (leaf blades, leaf sheaths and culms) often remains standing for long periods of time before collapsing to the sediments or water. This plant matter is colonized by fungi that are adapted for surviving the harsh conditions that prevail in the standing-dead environment (Kuehn et al., 1998). There are a number of other freshwater ecosystems where fungi are present and exhibit interesting adaptations, e.g. aero-aquatic fungi in woodland ponds, zoosporic organisms (Chytridiomycota and Oomycota) in a variety of habitats including the pelagic zones of lakes, and Trichomycetes that inhabit the guts of a variety of aquatic insects. Despite the well-known occurrence of these fungal groups in aquatic habitats, virtually nothing is known concerning their roles in biogeochemical processes. Overall, the contributions of fungi to biogeochemical cycles have been understudied in most freshwater ecosystems.

Introduction

This chapter considers the sinks and, more particularly, the dynamic rates of loss of formed cells from phytoplankton populations. Several processes are involved – hydromechanical transport, passive settlement and destruction by herbivores and parasites – which, separately or in concert, may greatly influence the structuring of communities and the outcome of competitive interactions among phytoplankton. Moreover, these same processes may contribute powerfully to the biogeochemical importance of pelagic communities, through their role in translocating bioproducts from one point of the planet's surface to another.

Before expanding upon these processes, however, the opportunity is taken to emphasise that the losses considered in this chapter are those that affect the dynamics of populations. The (sometimes very large) loss of photosynthate produced in excess of the cell's ability to incorporate in biomass is not considered here. The topic is covered in a different context in Chapter 3 (see especially Section 3.5.4). The emphasis is necessary as the term ‘loss rates’ was applied collectively to the dynamics of almost all measurable photosynthetic production that did not find its way into increased producer biomass (Jassby and Goldman, 1974a). It had been supposed by many workers at the time that the realised shortfall was attributable to grazing and sedimentation of biomass. However, with the demonstration that, very often, production in some systems was almost wholly and precisely compensated by simultaneous bulk loss rates (Forsberg, 1985), when the rates of grazing or sedimentation might only rarely explain the disappearance of the equivalent of the day's new product, it became clear that some further separation of the ‘losses’ was necessary, together with some refinement of the terminology.

Introduction: characterising growth

Whereas the previous two chapters have been directed towards the acquisition of resources (reduced carbon and the raw materials of biomass), the concern of the present one is the assembly of biomass and the dynamics of cell recruitment. Because most of the genera of phytoplankton either are unicellular or comprise relatively few-celled coenobia, the cell cycle occupies a central position in their ecology. Division of the cell, resulting in the replication of similar daughter cells, defines the generation. On the same basis, the completion of one full replication cycle, from the point of separation of one daughter from its parent to the time that it too divides into daughters, provides a fundamental time period, the generation time.

Moreover, provided that the daughters are, ultimately, sufficiently similar to the parent, the increase in numbers is a convenient analogue of the rate of growth in biomass. The rate of increase that is thus observed, in the field as in the laboratory, is very much the average of what is happening to all the cells present and is net of simultaneous failures and mortalities that may be occurring. The rate of increase in the natural population may well fall short of what most students understand to be its growth rate. It is, therefore, quite common for plankton biologists to emphasise ‘true growth rates’ and ‘net growth rates’.

Introduction

The following definition of geomicrobiology will provide a proper context for the discussion in this essay. Geomicrobiology is a study of the role that microbes have played in the geologic past from the time of their first appearance on the planet Earth about 4 eons ago to the present, and the role they are playing today and are likely to play in the future in some of the processes that are of fundamental importance to geology. The discussion will be restricted to current geomicrobial activities because being able to observe them directly, we know most about them. Geomicrobial activities in the geologic past have been deduced from the detection in the geologic record of (1) microbial fossils that morphologically resemble present-day microorganisms of geologic significance and (2) relevant biomarkers. Past geomicrobial activities have also been inferred from present-day geomicrobial activities that occur under conditions similar to those presumed to have existed in the geologic past. Molecular phylogeny is providing information that supports inferences about ancient geomicrobial activity.

Geomicrobial agents

Phylogenetic distribution

Although geomicrobial agents that are presently recognized include members of the domains Bacteria (Eubacteria) and Archaea in the Prokaryota and members of Algae, Protozoa and Fungi in the Eukaryota, the following discussion will emphasize mainly geomicrobial activities of members of the Bacteria, Archaea and Fungi.

Geomicrobial activities

Types of geomicrobial activities

Geomicrobial activities play a role in (1) mineral formation, (2) mineral degradation, (3) the cycling of organic and inorganic matter, (4) chemical and isotopic fractionation and (5) fossil-fuel genesis and degradation.

Introduction

The aims of this chapter are to develop an appreciation of the adaptive requirements of phytoplankton for pelagic life and to demonstrate the consequences of its embedding in the movements of the suspending water mass. The exploration begins by dismissing the simplistic notion that the essential requirement of plankton is to prevent or minimise the rate of sinking, in the sense that this will prolong its residence in the upper part of the water column. This would be a clear nonsense, were there no counteractive mechanism to ensure that organisms start out at the top of the water in the first instance. Moreover, slow sinking from the upper layers is of illusory respite if the downward passage to depths beyond the adequacy of penetrating light, whether that is 50 cm or 50 m beneath the water surface, is inevitable, unless there is some mechanism for the organism's return. Manifestly, it is not enough just to reduce the rate of irreversible sinking to qualify as a phytoplankter.

Prolonged residence in the upper insolated layers of the open water of lakes and seas (the photic zone) is, without doubt, a primary requirement of the individual phytoplankter, if it is to synthesise sufficient organic carbon to build the tissue of the next generation. The survival of the genetic stock and the seed population capable of providing the base of subsequent generations may also depend upon the survival of a relatively small number of extant individuals.

Introduction

Ecosystem ecologists have calculated carbon and nitrogen budgets for a variety of forest ecosystems. Despite a growing awareness of the importance of mycorrhizal fungi in nitrogen uptake, as carbon sinks for photosynthate and as conduits for carbon from plants to the below-ground community, few ecosystem ecologists have incorporated mycorrhizal fungi in their conceptual models of how forests function. Longstanding difficulties in assessing the presence and quantity of mycorrhizal fungi in soil, in identifying mycorrhizal fungi to species, and in assessing the mycorrhizal role in carbon and nitrogen cycling, have probably limited the willingness and ability of ecosystem ecologists to incorporate mycorrhizal fungi into their research. In particular, ecosystem models have not yet included mycorrhizal fungi, despite the key role of mycorrhizal fungi at the interface of plants, the soil and microbial communities below-ground.

In this review we will focus on ectomycorrhizal fungi that form symbioses with many of the dominant trees of temperate and boreal forests, particularly in trees of the Pinaceae, Fagaceae, Betulaceae and Salicaceae. Ectomycorrhizal fungi also form symbioses with many tropical trees, including the Dipterocarpaceae of southeast Asia and Eucalyptus of Australia. We will lay out the current state of knowledge of the functioning of ectomycorrhizal fungi in carbon and nitrogen cycling of forest ecosystems as inferred from field and laboratory studies. Finally, we will discuss progress in integrating mycorrhizal fungi into quantitative frameworks of forest ecosystem function.

Introduction

Man-made polymeric materials are ubiquitous in our everyday lives and have an enormous range of applications from man-made textiles to plastics, coatings, paints and additives. As a consequence, a vast array of man-made polymers accumulates in the environment and landfill waste sites where they cause considerable water and land pollution problems. Over the last few decades, plastics and plasticizers in particular, due to their wide production and distribution, have led to a large increased environmental burden (Bouwer, 1992). According to recent estimates, the annual production of plastics in the world exceeds more than 140 million tonnes per year (Shimao, 2001). Plastics possess a number of key characteristics including weight, inertness, flexibility and low production costs that make them widespread in many areas of human life. However, it is their inertness and durability, valuable during their use, that becomes a particular problem later during their disposal. Contrary to other synthetic chemicals and pesticides, synthetic polymers do not generally possess particular toxicological problems, unless supplied with protective agents such as biocides (Bentivegna & Piatkowski, 1998) or particular plasticizers, such as phthalates (Staples et al., 1997; Zeng et al., 2002). Plastics however contribute greatly to the amount of municipal solid waste (Palmisano & Pettigrew, 1992) and are an increasing problem due to improper disposal (Alexander, 1994). The UK alone consumed 4.7 million tonnes of plastics in 2002 with most of the material being used in packaging and the building/construction industries (Fig. 9.1).

This is the third book I have written on the subject of phytoplankton ecology. When I finished the first, The Ecology of Freshwater Phytoplankton (Reynolds, 1984a), I vowed that it would also be my last. I felt better about it once it was published but, as I recognised that science was moving on, I became increasingly frustrated about the growing datedness of its information. When an opportunity was presented to me, in the form of the 1994 Ecology Institute Prize, to write my second book on the ecology of plankton, Vegetation Processes in the Pelagic (Reynolds, 1997a), I was able to draw on the enormous strides that were being made towards understanding the part played by the biochemistry, physiology and population dynamics of plankton in the overall functioning of the great aquatic ecosystems. Any feeling of satisfaction that that exercise brought to me has also been overtaken by events of the last decade, which have seen new tools deployed to the greater amplification of knowledge and new facts uncovered to be threaded into the web of understanding of how the world works.

Of course, this is the way of science. There is no scientific text that can be closed with a sigh, ‘So that's it, then’. There are always more questions. I actually have rather more now than I had at the same stage of finishing the 1984 volume.

Introduction

Polycyclic aromatic hydrocarbons (PAHs) are a large group of toxic compounds (Fig. 8.1) that are components of coal and petroleum and are also produced during incomplete combustion of fuels. They are introduced into the environment via many routes, including fossil-fuel combustion, automobile and diesel engine exhausts, production of manufactured gas and coal tar, wood-preservation processes and waste incineration (Harvey, 1997; Pozzoli et al., 2004). Benzenoid PAHs are thermodynamically stable, with positive bond resonance energies (Aihara, 1996), and have vapour pressures of 2.8 × 10− 5 to 10.4 Pa (Sonnefeld et al., 1983). The aqueous solubility of PAHs ranges from 0.2 μg/l for indeno[1,2,3-cd]pyrene and 1.6 μg/l for benzo[a]pyrene to 31.7 mg/l for naphthalene (Lehto et al., 2003). Despite their low solubility, PAHs are widely distributed in the environment (Wilcke, 2000; Saltiene et al., 2002; Peachey, 2003; Pozzoli et al., 2004) and, as persistent organic pollutants, they are involved in biogeochemical cycling (Del Vento & Dachs, 2002; Jeon et al., 2003). The five-ring PAH, perylene, found in Jurassic sediments may even have originated from ancient fungi (Jiang et al., 2000).

Sixteen PAHs are on the lists of priority pollutants of the US Environmental Protection Agency and the European Union (Lehto et al., 2003); mixtures containing more than 50 individual PAHs have been found in sediments at hazardous waste sites (Brenner et al., 2002). Low-molecular-weight PAHs, with two or three rings, are the most volatile and usually the most abundant. High-molecular-weight PAHs, with four or more rings, are less volatile.

Introduction

This volume focuses primarily on the influence of free-living fungi in biogeochemistry. Lichens, fungi that exist in facultative or obligate symbiosis with one or more photosynthesizing partners, also play an important role in many biogeochemical processes. Pioneer colonizers of fresh rock outcrops, lichens were possibly one of the first life forms to occupy Earth's land surfaces. The unique lichen symbiosis formed between the fungal partner (mycobiont) and the photosynthesizing partner, an alga or cyanobacterium (photobiont), enables lichens to grow in all surface terrestrial environments. These include extreme environments where no other multicellular vegetation can survive, such as the dry Antarctic valleys (Nash, 1996). An estimated 6% of the Earth's land surface is covered by lichen-dominated vegetation.

Globally, lichens play an important biogeochemical role in the retention and distribution of nutrient (e.g. C, N) and trace elements (e.g. Knops et al., 1991; Garty et al., 1995), in soil formation processes (Ascaso et al., 1976; Jones, 1988) and in rock weathering (Hallbauer & Jahns, 1977; Wilson et al., 1981; Wessels & Schoeman, 1988; McCarroll & Viles, 1995; Barker et al., 1997; Lee & Parsons, 1999). Lichens tend to accumulate trace elements such as lead, copper and other heavy metals of environmental concern (see below), including radionuclides (Yliruokanen, 1975; Nieboer & Richardson, 1981; Beckett et al., 1982; Boileau et al., 1982, 1985a, b; Richardson et al., 1985; Fahselt et al., 1995; Haas et al., 1998; McLean et al., 1998; Jacquiot & Daillant, 1999; Purvis et al., 2004).

Introduction

In the pelagic, as in the great terrestrial ecosystems, space is occupied by numbers of organisms of various species forming distinct populations fulfilling differing roles. Of course, these assemblages of species reflect autecological aspects of preference and tolerance but they also show many synecological features of the mutual specific interactions and interdependences that characterise communities. The numbers of organisms, the relative abundances of the species, their biological traits and the functional roles that they fulfil all contribute to the observable community structure. In the plankton and in other biomes, the challenge to explain how these structures are put together, how they are then regulated and how they alter through time, falls within the understanding of community ecology.

This chapter considers the structure of phytoplankton assemblages among a broad range of pelagic systems, in the sea and among inland waters, seeking to identify general patterns and common behaviour. In the second main section (7.3), the processes that govern the assembly of communities and shape their structures are traced in detail. Because some of the terminology has been used uncritically in the literature, sometimes erroneously and often confusingly, their usage in the current work is explained in a separate text (Box 7.1).