SUMMARY

1. Habitat modification and fragmentation of remaining pristine areas in the tropics is occurring at a speed that threatens to compromise any serious attempt to assess their value in the biosphere, and catalogue their true biological diversity.

2. Knowledge about the functional significance of soil biodiversity has been strongly influenced by emphasis on temperate climates and by focusing on particular processes of significance to high-input, intensive agriculture. We do not know how robust our methodologies and our concepts are when applied to low-input systems.

3. Links between diversity and function are clearer for functions that are relatively specific, such as the roles of ecosystem engineers, or specific nutrient transformations compared with generalist functions, such as decomposition, micrograzing, predation and antibiosis.

4. Substantial redundancy exists in relation to general functions that could be important for functional stability.

5. When considering the legume–rhizobium symbiosis as a specific case, rhizobial diversity based on molecular phylogeny is only weakly correlated with specific functions such as ability to form nodules (infectiveness), to fix N2 (effectiveness) and to survive in the soil (adaptation).

6. Major challenges for the future include developing tools for managing soil biodiversity through manipulation of above-ground vegetation and soil amendments, and understanding the effects of scale to design land use systems for optimal future conservation of the biodiversity of tropical soils.

Introduction

If the soil is said to be the ‘poor man's rainforest’ in terms of the bewildering biodiversity it harbours (Usher 1985), then what status should the soil in the tropical rainforest be assigned?

SUMMARY

1. The microbial world is tremendously diverse. This fact was established in the early days of microbiology and is supported by ever increasing lists of 16S rDNA sequences and more recently by whole genome comparisons.

2. It is now time to divert attention from lists of organisms – even though these lists are undoubtedly incomplete – to questions such as the evolutionary and ecological causes of diversity; the ecological factors maintaining diversity and the significance of diversity in terms of ecosystem function.

3. Recognising the inherent difficulties of addressing these questions within the soil environment we have chosen to use experimental populations of bacteria maintained in simple laboratory environments. These populations have allowed us to reduce complexity to the point where insights into mechanistic processes become possible and have permitted rigorous empirical tests of fundamental ecological and evolutionary concepts.

4. Particularly significant has been clear demonstrations of the importance of ecological opportunity and competition in driving diversification of microbial populations. In addition, it has been possible to show how productivity, disturbance and predation can shape patterns of diversity by affecting the outcome of competition and how the observed patterns of diversity depend upon environmental complexity.

5. Most recently we have begun to explore the consequences of microbial diversity in terms of ecosystem properties and have been able to show, at a mechanistic level, how diversity, productivity and invasibility are connected.

Introduction

Recent technological advances have confirmed a long-held suspicion that soils are biologically diverse.

SUMMARY

1. The mycelia of fungal communities in soil and plant litter are strongly structured by soil horizon and resource availability. Resource quality is important in determining species composition and a certain degree of ‘host’ specificity exists. In soil fungal communities, a few taxa occur much more frequently than the large number of rare ones. The taxa detected are highly dependent on the techniques used. Therefore, it is necessary to cross-reference the information obtained from different methods.

2. Fungal communities in soil and plant litter are enormously diverse taxonomically, with possibly hundreds of species present in a particular soil horizon. There is still much work to be carried out at the local scale to detect the mycelia of fungi and identify them, together with estimating fungal species richness. Without these initial taxonomic studies, it is impossible subsequently to relate mycelial location and function to species diversity.

3. Scattered data exist about functional diversity of fungi in soil and plant litter, and there is still far to go before specific fungal decomposer functions are satisfactorily described, especially in the natural environment. Again, a combination of methods is needed. The results of functional tests, especially for ‘key’ species, should be related to community structure.

4. Are all the possibly hundreds of fungal species present on decomposing plant litter necessary to maintain decomposition rates? There is some evidence for functional redundancy because frequently isolated species have been found to have the same specific enzyme capabilities for decomposition as occasional ones. The idiosyncratic hypothesis may also be supported. The existence of ‘keystone’ species, on which the maintenance of whole ecosystems may rely, suggests that decomposition rate is dependent more on fungal species composition, and its functional repertoire, rather than on simply richness alone.

SUMMARY

1. This chapter examines the vast diversity of organisms that live in the soil and discusses the various factors that regulate its spatial and temporal patterning.

2. There is a dearth of information available on the diversity of soil biota, especially at the species level, but existing data provide little support for the idea that the same forces that regulate patterns of diversity above-ground (i.e. productivity and disturbance) control patterns of biodiversity below-ground, or that regional-scale patterns of soil biodiversity show similar trends to those that occur above-ground.

3. We argue that patterning of soil biodiversity is related primarily to the heterogeneous nature, or patchiness, of the soil environment at different spatial and temporal scales, and that this heterogeneity provides unrivalled potential for niche partitioning, or resource and habitat specialisation, leading to avoidance of competition and hence co-existence of species.

4. We highlight the challenge for soil ecologists to identify the hierarchy of controls on soil biological diversity that operate at different spatial and temporal scales, and to determine the role of spatio-temporal patterning of soil biodiversity as a driver of above-ground community assembly and productivity.

Introduction

The Earth hosts a bewildering diversity of organisms that are distributed in a wide variety of spatial and temporal patterns across, and within, the Earth's ecosystems. Making sense of these complex patterns of diversity, and understanding the dominant forces that control them, has been a major theme of community ecology (Huston 1994).

SUMMARY

1. Soils support a taxonomically and physiologically diverse biota widely regarded as more extensive than that of any other group of organisms. However, the limits of this diversity and its importance in delivering soil function remain unclear.

2. The last 20 years have seen renewed interest in soil microbiology and in the application of molecular methods to explore what is there and how it changes over time or in response to environmental stimuli. For the first time microbiologists have been able to open the microbial ‘black box’ in soils.

3. The justification often given for opening this ‘black box’ is that the diversity of the contents therein is vitally important to the maintenance and sustainability of the biosphere. However, despite almost 20 years of detailed sifting through the box contents, there is little evidence to support this, suggesting that many of the thousands of microorganisms in soils are functionally redundant and that many of the major functions of the microbial biomass are unaffected by its exact species composition.

4. This chapter looks at some of the approaches used to open the microbial ‘black box’ and discusses whether we are any closer to understanding the relationship between diversity and function in soils.

Introduction

Soils are an important natural resource and have a key role in the biosphere with most of the annual carbon and nutrient fluxes occurring in the top 5–10 cm of the soil profile.

SUMMARY

1. Soils have hardly featured in nature conservation thinking. Criteria have been developed for selecting networks of important Earth science sites, but these have not included criteria for soils.

2. Above ground, nature conservation has focused on communities of plants and the animals that they support, and criteria have been developed for selecting the ‘best’ sites. There has been scant attention to the soils on which those plant communities depend.

3. Although species rich, soils do not contain the charismatic species that have been favoured by conservationists. There is no giant panda, corncrake or lady's slipper orchid.

4. Both the increasing concentration on biodiversity and ‘the ecosystem approach’ are shifting thinking in relation to soils. Despite limited taxonomic knowledge, some attention is being paid to fungi (e.g. the waxcaps, Hygrocybe spp.) and the larger soil-inhabiting invertebrates (e.g. the mole cricket, Gryllotalpa gryllotalpa, and earthworms). The ‘ecosystem approach’ is forcing a more holistic view, focusing on the function of terrestrial ecosystems.

5. Soils are intimately involved in many ecosystem processes that contribute to the sustainable use of the planet's land resources. The contribution of soils and their biota to sustainable development will ultimately be far more important than the protection of either individual soil types or individual species.

Introduction

Although it is true that nature conservationists have generally neglected soils, there is one notable exception, that relating to peat soils (e.g. Heathwaite & Göttlich 1990).

SUMMARY

1. Globally accelerating rates of species loss make it imperative that relationships between biodiversity and ecosystem function are analysed, yet resolution of these interactions has presented one of the most intractable challenges in ecological research.

2. Because biodiversity in soil is considerably greater than that above ground, and the identities and functions of many soil microorganisms are uncharacterised, the difficulties involved in establishing diversity–function relationships in the below-ground environment are compounded.

3. For some keystone groups of soil microorganisms, prominent among which are the mycorrhizal fungi, diversity–function relationships are starting to be elucidated. Mycorrhizal symbionts are present in virtually all terrestrial ecosystems where they are major components of the soil microbial biomass.

4. There is increasing evidence that mycorrhizal diversity is of central importance in agro-ecosystem functioning, and that intensification of agriculture and forestry, combined with air and soil pollution, is reducing their diversity and compromising their functioning. Two lines of evidence support the case that mycorrhizal diversity is of major functional significance, namely (1) that mycorrhizal associations are multi-functional and exhibit complementarity, assisting plants in nutrient acquisition, mediating carbon transfer between plants and protecting their roots from pathogens; and (2) that on the basis of emerging evidence of a combination of high specificity and dependency in many mycorrhizal associations, especially those involving myco-heterotrophic plants, it is hypothesised that the extent of functional ‘redundancy’ is low.

Introduction

It is now recognised that the accelerating rates of species extinctions, which are arising from progressive intensification of land use, pose a global threat to biodiversity (Pimm et al. 1995).

SUMMARY

1. Molecular biological methods have provided new insights into the true extent of bacterial diversity in soil, and here we focus on their application in tandem with soil process measurements.

2. Data from a field experiment are used to illustrate the impact of perturbation on the total bacterial community as well as those functional groups responsible for nitrification, denitrification, methanogenesis and methane oxidation. Increasing the organic matter by about 20% by sewage sludge addition had no statistically significant effect on soil respiration rates, and although methanogenesis and methane oxidation were both stimulated, the effect was short lived and variable. We argue that the methane transformations are particularly dependent on unevenly distributed microsite activity, unlike nitrification/denitrification rates, which were stimulated by liming and organic matter addition in a manner that was both reproducible and persistent. The genetic diversity of the ammonia-oxidising bacteria concomitantly decreased, implying classical selection or enrichment of competitive species upon perturbation.

3. Effects on the diversity of the soil bacterial flora quickly disappeared with time, and we argue that seasonal variation, and particularly its effect on plant growth, has a greater impact on the dynamics of bacterial populations in soil than single time-point perturbations aimed at stimulating general biological activity. However, time course experiments revealed that the bacterial diversity in untreated soils was more stable, as the 16S rRNA gene profiles were more stable than those that developed in disturbed soils.

4. […]

SUMMARY

1. Microorganisms play an essential role in modulating the fluxes of organic carbon and nutrients in soil. However, their diversity and functional significance are largely unknown. Recent technical developments in molecular, chemotaxonomic and physiological techniques complement traditional techniques and can now enable us to investigate the linkage between rhizosphere carbon flow, microbial diversity and soil function.

2. Reporter gene systems provide an important method for resolution of rhizosphere carbon flow. Their greatest advantage is that they can be used in situ without uncoupling the plant–microbial interaction vital to maintaining both quantity and quality of carbon flow.

3. Any consideration of rhizosphere carbon flow and soil microbial diversity should not only include substrate carbon flow and trophic interactions, but also the role of signal molecules, especially in terms of controlling rhizosphere community structure, diversity and function.

4. Little is known of carbon flow in natural systems. Ecosystem function and, specifically, carbon-cycling pathways can be determined by lipid analysis or nucleic acid stable isotope probing (SIP) using 13C incorporated into microbial biomass. The ability to ascertain which components of the biomass are being enriched in root-derived carbon enables an understanding of how rhizosphere carbon drives microbial diversity.

5. Changes in 16S rDNA sequence diversity and relative abundance provide indications of which organisms are responding to changing conditions and SIP analysis of mRNA allows for assessment of their activity, and thus may be used to follow changes in the microbial community during rhizosphere development.

SUMMARY

1. This chapter deals with the impact of the soil's physical habitat on the operation of soil microbes.

2. The importance of the spatial and temporal nature of soil structural heterogeneity is emphasised.

3. The moisture characteristic is revealed as having a pre-eminent impact on soil biology.

4. The sensory ecology of nematodes is described in relation to the chemotaxis process.

Introduction

All terrestrial life lives and moves in the context of a more or less physically structured environment. The antelopes have their veldt, the mountain goats their crevasses, the rabbits their warrens and soil microbes their dark recesses of soil structure. How each individual, population and community operates is defined to a large extent by the physical landscape in which they live, which serves to partition substrate, mates, predators, water, gases and so forth. Geography, even the microgeography of the soil, sorts and drives the species in earth and on Earth.

Much has been published in relation to the so-called aggregate sizes and the presence of microorganisms. For example, Vargas and Hattori (1986) are convinced that there is order in soil, with bacteria living in the centre of aggregates more often than on the surface. Linn and Doran (1984) link the direct influence of soil structure to changes in microbial activity and community structure at the field scale. Work from The Netherlands has produced conclusive proof that the structure of soil, and the attendant moisture, are controlling factors in predator–prey interactions between bacteria and protozoa (e.g. Kuikman et al. 1989; Postma ' van Veen 1990), an area that Young et al. (1994) and Young and Crawford (2001) revisited with respect to the impact of structure on substrate location and accessibility.

SUMMARY

1. Comparative field research, backed up by field and laboratory experimentation, on the effects of stress on communities is necessary to increase insight into the relationships, if any, between stress, (soil) biodiversity and ecosystem functioning.

2. Such insight is needed as a complement to ecotoxicological research on the effects of contaminants on species populations so as to broaden the base for environmental policies and legislation.

3. From a synthesis of research on reversed succession of plants, nematodes and insects in the Drentse A grasslands in the northern Netherlands, we infer that knowledge of life-history strategies at various levels of taxonomic detail is an important key to understanding stress effects on natural communities.

4. We observe that different approaches in research of stress on communities and ecosystems are beginning to converge in taking life-history strategies into account.

Introduction

Ecosystem structure and functioning are governed by three classes of driving variables: the physical environment, resource quality and organisms (Swift et al. 1979). Stress effects on organisms may result from biotic interactions or from changes of the physical environment and resource quality. Stress can be defined to occur when the organisms within an ecosystem are chronically confronted with abiotic conditions, resource quality conditions, new species or abundance of existing species (especially herbivores, predators or parasites) near or beyond the range of their ecological amplitude (Grime et al. 1988), and when physiological adaptation to such changes is absent (Calow & Forbes 1998).

SUMMARY

1. In the classical view of nitrogen cycling, the processes that involve nitrogen inputs and outputs (e.g. fixation, denitrification) are physiologically ‘narrow’ and so should be sensitive to microbial community composition, while internal turn-over (i.e. mineralisation, immobilisation) involves ‘aggregate’ processes that should be insensitive to microbial community composition.

2. A newly developing view of nitrogen cycling, however, identifies several ways in which mineralisation and immobilisation can be ‘disaggregated’ into individual components that may be sensitive to microbial community composition. Two of these are extracellular enzyme and microsite phenomena.

3. Exoenzymes are critical in driving decomposition, and hence mineralisation/immobilisation. Different classes of enzymes are produced by different groups of microorganisms. Additionally, the kinetics of exoenzymes may regulate microbial carbon and nitrogen limitation and hence community composition.

4. Microsite phenomena appear to regulate system-level nitrogen cycling (e.g. the occurrence of nitrification in nitrogen-poor soils), yet these effects scale non-linearly to the whole system. Different organisms may live and function in different types of microsites.

5. This new view of the nitrogen cycle provides an intellectual structure for developing research linking microbial populations and the nitrogen cycling processes they carry out.

Introduction

Since the days of Winogradsky and Beijerink in the late nineteenth century, nitrogen cycling has been at the centre of soil microbiology. Since then, we have largely deciphered the microbial physiology of the important nitrogen cycling processes and have identified some of the important microbial groups involved in them.