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This chapter describes methods for studying forest dynamics. Topics covered include characterizing forest disturbance regimes, analysis of forest disturbance history, characterizing forest gaps, measuring light environments, measuring other aspects of microclimate, assessing the dynamics of tree populations, seed bank studies, and defining functional groups of species.

This chapter connects the soil biota to ecosystem structure and functioning and the concept of ecosystem services, i.e., the benefits people derive from ecosystems, and to the impact of land management and environmental drivers of change upon such phenomena. Carbon (C) transfer through organisms, via fixation and decomposition, is considered as the main integrating factor in ecosystem functioning, along with the associated cycling of nutrients. Functional groups of the soil biota, i.e., groups of organisms perceived as associated with certain ecosystem functions, which may be used for understanding of such C and nutrient transfers, are presented from two contrasting perspectives: a ‘soil biogeochemistry’ perspective on ecosystem functioning, which plays down the importance of functional group detail, vs. a ‘soil biology’ view, which considers such detail as a necessary perspective. Following recent developments in trait-based ecology, functional trait groups, based on organismal- and species-trait diversity, are proposed as more suitable than functional groups based on species diversity per se, in order to relate drivers of change to soil biota-mediated ecosystem functioning and services. Such knowledge is useful when extending fundamental understanding of ecosystem functioning to practical management for enhanced ecosystem services. This concept is then elaborated for agro-ecosystems and agricultural landscapes.

This chapter examines the life forms, functional traits, and functional groups of plants that predominate during different successional stages, and describes patterns and mechanisms of species turnover during succession. The high photosynthetic and growth capacity of plants that colonize early in succession enables these species to compete effectively for high levels of resource availability. But species with these “fast” traits lose their competitive edge later in succession, when establishment and survival depend more upon “slow” traits that reduce intrinsic rates of growth and enable long-term persistence in shaded understory. Changes in species composition during succession reflect a combination of initial floristic composition and relay floristics, in which species colonize sequentially in response to changing forest conditions. Tree recruitment during later stages of succession favors species that are more functionally and phylogenetically distinct than during earlier stages of succession as biotic interactions become increasingly important drivers of community assembly.

This chapter provides an overview of the three chapters in Section 1. Chapter 1.1 considers the soil as a habitat. Chapter 1.2 reviews the levels of biodiversity that occur belowground. Chapter 1.3 considers how the soil biota actually delivers ecosystem services. It also explores the contrasting ‘soil biogeochemistry’ and ‘soil biology’ perspectives of how ecosystems function, and reviews the functional group concept.

Ecological theory indicates that increasing the number of species, the number of interactions, and the strength of these interactions all tend to make communities less stable. Conversely, stability is enhanced by strong intraspecific density dependence, low connectivity, or weak trophic links. These theoretical predictions are borne out in many fish communities. Species diversity is an important metric for ecological communities. Organizing species into groups according to size, function, or diet composition can reduce the dimensionality of fish community models. Analyses of fish communities from around the world lend support to the prediction of strong compensation within functional groups, with weaker predator–prey links among groups. Size spectra describe the distribution of individuals across size classes irrespective of their species. Qualitative models can be used to assess the indirect effects of species on each other and the overall stability of the community.

Chapter 10 “Environmental DNA for functional diversity” discusses the potential of environmental DNA to assess functional diversity. It first focuses on DNA metabarcoding and discusses the extent to which this approach can be used and/or optimized to retrieve meaningful information on the functions of the target community. This knowledge usually involves coarsely defined functional groups (e.g., woody, leguminous, graminoid plants; shredders or decomposer soil organisms; pathogenicity or decomposition role of certain microorganisms). Chapter 10 then introduces metagenomics and metatranscriptomics approaches, their advantages, but also the challenges and solutions to appropriately sampling, sequencing these complex DNA/RNA populations. Chapter 10 finally presents several strategies and software to analyze metagenomes/metatranscriptomes, and discusses their pros and cons.

This chapter deals mainly with the feeding devices and foraging strategies of aquatic life stages. It first describes the kinds of food resources potentially available to aquatic insects, including animal prey, macrophytes, plankton and attached biofilms, and detritus. The rest of the chapter discusses various functional feeding groups (insects that consume similar food resources in a functionally similar way), including predators that are primarily carnivorous (engulfers, fluid feeders, and raptorial predators); parasites; shredders, chewers, and xylophages; algal piercers or bursters; grazers, collector-gatherers; filter feeders. The focus is on the feeding strategies, mechanisms, structures, and apparatuses used to capture food and transfer it into the mouth (e.g., mouthparts). Feeding usually involves the movements of multiple mouthparts, coordinated in a manner which results in food being acquired and then transported into the mouth. The aquatic medium puts constraints on the mechanics of feeding and the sequence of events is critical to successful foraging.

This chapter introduces the field of microbial ecology and some terms used in the rest of the book. Microbial ecology, which is the study of microbes in natural environments, is important for several reasons. Although most are beneficial, some microbes cause diseases of higher plants and animals in aquatic environments and on land. Microbes are also important because they are directly or indirectly responsible for the food we eat. They degrade pesticides and other pollutants contaminating natural environments. Finally, microbes are important in another ‘pollution’ problem: the increase in greenhouse gases such as carbon dioxide and methane in the atmosphere. Because microbes are crucial for many biogeochemical processes, the field of microbial ecology is crucial for understanding the effect of greenhouse gases on the biosphere and for predicting the impact of climate change on aquatic and terrestrial ecosystems. Even if the problem of climate change was solved, microbes would be fascinating to study because of the weird and wonderful things they do. The chapter ends by pointing out the difficulties in isolating and cultivating microbes in the lab. In many environments, 〈 1 per cent of all bacteria and probably other microbes can be grown in the lab. The cultivation problem has many ramifications for identifying especially viruses, bacteria, and archaea in natural environments and for connecting up taxonomic information with biogeochemical processes.

The pollination syndrome concept has underpinned much of floral biology for many years. The purpose of this chapter is to assess the usefulness of the concept in understanding flowers and flowering. The chapter begins by considering why and how the pollination syndrome concept has become so entrenched in the literature on flowering, and then assesses whether the key assumptions that underlie it are met. Finally it assesses the experimental evidence that pollination syndromes do exist, and the experimental evidence against them - those cases where the major pollinator in the native habitat is not that which the flower’s morphology would lead the observer to predict. This chapter also provides a brief overview of the relative importance of generalization and specialization in pollination ecology.

The goal of this chapter is to introduce the field of microbial ecology and some terms used in the rest of the book. Microbial ecology, which is the study of microbes in natural environments, is important for several reasons. Although most are beneficial, some microbes cause diseases of higher plants and animals in aquatic environments and on land. Microbes are also important because they are directly or indirectly responsible for the food we eat. They degrade pesticides and other pollutants contaminating natural environments. Finally, they are important in another “pollution” problem: the increase in greenhouse gases such as carbon dioxide and methane in the atmosphere. Because microbes are crucial for many biogeochemical processes, the field of microbial ecology is crucial for understanding the effect of greenhouse gases on the biosphere and for predicting the impact of climate change on aquatic and terrestrial ecosystems. Even if the problem of climate change were solved, microbes would be fascinating to study because of the weird and wonderful things they do. The chapter ends by pointing out the difficulties in isolating and cultivating microbes in the laboratory. In many environments, less than one percent of all bacteria and other microbes can be grown in the laboratory. The cultivation problem has many ramifications for identifying especially viruses, bacteria, and archaea in natural environments, and for connecting up taxonomic information with biogeochemical processes.

How the diversity of an ecological community affects its stability is an old and important question (Forbes, 1887; Elton, 1927; Nicholson, 1933). The science of ecology grew out of the study of natural history in the nineteenth century, when nature was viewed as wondrous, mysterious, complex, and largely in balance (even if murderous to experience from an individual’s point of view; Forbes, 1887). Whereas our current scientific view is more textured and guarded, the ‘balance of nature’ still permeates the popular press. Some vestiges also remain in the scientific literature. Over the last 100 years, conclusions about the relationship between ecological diversity and stability have varied wildly (May, 2001; Ives, 2005). The goal of this chapter is to show that these wildly varying conclusions are due largely to wildly varying definitions of both stability and diversity. To do this, I will take two tacks, one for stability and the other for diversity. For stability, I will give an abbreviated history of the changing definitions of stability, merging both empirical and theoretical studies. I make no pretence of being comprehensive, but will instead pick highlights that show how the definition of stability often changes from one study to the next. For diversity, I will present a theoretical model to illustrate how different ‘diversity effects’ on stability can be parsed out. This model shows in a concrete way how any theoretical study (and, for that matter, empirical study) necessarily makes a long list of assumptions to derive any conclusion about diversity and stability. The multiple definitions of stability, and the multiple roles of diversity, argue against any general relationship between stability and diversity. In the final section of the chapter, I will argue that understanding the relationship between diversity and stability requires the integration of theory and experiment. Theory is needed to define in unambiguous terms the meanings of stability and diversity. Experiments are needed to ground theory in reality. Unfortunately, rarely is this done. To present an abbreviated history of the changing definitions of stability, I will discuss theoretical and empirical studies side by side.