The three separate excerpts quoted above from the classic book on plant canopies and their radiation regime by the biophysicist, Juhan Ross, underscore three aspects of past studies of the solar radiant flux at the canopy scale. First, description of the architecture of plant canopies is a central activity of researchers interested in controls over plant productivity and its relation to climate. Second, the relation of canopy architecture to the distribution of solar radiation within the canopy is complex. Third, in large part due to that complexity, researchers have sought ways to simplify descriptions of canopy structure and radiative transfer using statistical models. In this chapter we will use these three fundamental tenets as the context within which to explore canopy structure and its relation to the capture of solar radiation.

Processes in the atmosphere have long had the power to capture human imagination and determine the fate of major historical events. Wind and atmospheric transport produced the “pure and white clouds” described in the poetry of Keats and are responsible for the dust storms that blinded armies during the Napoleonic wars. In our own lives we experience and depend on wind every day. It affects how airplanes fly, the efficiency of automobile travel, and our ability to predict weather. Wind is air with velocity. Given that mass multiplied by velocity is a measure of momentum, wind can also be referred to as air with momentum. Through its velocity the wind is coupled to “forces” that drive or resist its flow, such as pressure and friction, respectively. Instabilities in the atmospheric flow develop as these forces work against one another, causing gustiness, or more formally, turbulence. Turbulence reflects departures in the velocity vectors of the wind from their mean values. Turbulence represents a variance about the mean velocity. Turbulent departures from the mean wind flow are complex and not currently subject to precise mathematical description, as stated in the humorous quip reprinted above from the renowned atmospheric physicist, Theodore von Kármán. The transport of mass, energy, and momentum in the atmosphere occur through both the mean and turbulent components of the wind. Thus, in order to understand atmospheric transport, we must develop an understanding of the wind.

Of the 98 naturally occurring elements on earth, 18 are known to be radioactive, meaning that they exhibit time-dependent decay to lighter elements, and 80 are known to be stable. Of those 80 stable elements, 54 are known to exhibit isotopic variation, meaning that atoms within the same elemental category have different atomic masses due to variations in neutron number (Section 3.5). Given the dependency of diffusive flux on atomic mass, molecules of the same compound, but composed of different isotopes, will diffuse at different rates and thus segregate into isotopic fractions over time. Analysis of isotopic fractionation provides researchers with one of their most valuable tools for understanding rates of diffusive flux, enzyme-substrate interactions, interactions among metabolic pathways, and the sources and sinks of compounds used for various biogeochemical processes, even extending beyond those defined solely by diffusion. Of particular importance have been analyses of the isotopic composition of CO2 and H2O, given that C, H, and O are among those 54 elements that exhibit stable isotope variation.

The playful statement written by Josiah Gibbs, who claimed identity as both a mathematician and physicist, provides some truth in jest. Mathematical treatments carry an elegance and beauty that can be appreciated within the abstract world of pure contemplation. However, descriptions of physical processes must be anchored within the allowable states and transitions defined by thermodynamics. As we begin to focus on the specific processes that drive biosphere-atmosphere fluxes we will return to the concept of flux that was established in the last chapter, but now we will construct a physiochemical foundation beneath that concept. Fluxes of scalars and vectors are driven by states of thermodynamic disequilibrium. A flux of mass or energy represents work that is done at the expense of internal energy that is derived from a state of thermodynamic disequilibrium. Thus, as we open this chapter we will develop the thermodynamic context for energy and work, and we will discuss their roles as underlying drivers of biogeochemical fluxes. This will require us to spend some time on the fundamental laws of thermodynamics, the concept of equilibrium, and the various forms of energy that drive biogeochemical processes. One of the concepts we will develop in some detail is the biogeochemical context of potential energy. Potential energy is how we define the capacity for components in a natural system to do work. Potential energy exists in a thermodynamic system that is in a state of disequilibrium; in contrast, a system that is at equilibrium lacks potential energy, and therefore lacks the capacity to generate work on its surroundings or on other systems.

Energy flows from the sun to the earth where some fraction is absorbed by plant surfaces. Plants use some of that energy to drive primary production, but that is a small fraction of the total absorbed energy. Most of the absorbed energy is redistributed back to the surroundings. Following the laws of thermodynamics, energy can be transformed, transferred, or stored, but not destroyed. Thus, energy input from the surroundings must be balanced by an equal and constant output or be stored within the plant’s mass. The requirement for a full accounting of energy transfers and storage, and thus reconciliation of the plant’s energy budget, has been recognized for several decades as an important perspective from which to study biophysics and the evolutionary adaptation of plants to their environment. The “environment” of a plant consists of all scales between the sun and earth; though we may isolate certain components to prioritize the factors that determine energy exchange. The quotes above, by Klaus Raschke and David Gates, two of the pioneers in the field of plant-atmosphere biophysics state in very clear terms, the continuum of space that describes the “environment” with which a plant must exchange energy, and the necessity of “energy accounting” as a means to understand plant function and adaptation.

The inspiration referenced in Donald Cram’s Nobel Prize lecture results from a sense of awe at the intricate control and complex design reflected in cellular genetics and metabolism. An understanding of metabolism is requisite to prediction of the exchange of many trace gases between organisms and the atmosphere. Metabolism has evolved as a complex web of intersecting biochemical pathways. Control over the flux of metabolites through these pathways requires that they be channeled in the proper direction, partitioned to alternative reactions at pathway intersections, and processed at the proper rate. Metabolic complexity includes network integration, adaptable control, and feedback, which in turn produce non-linear dependencies in the coupling of flux to the cellular environment. In recent decades a new framework, called systems biology, has emerged from the fields of metabolic biology and biochemistry to provide new approaches to describing the quantitative complexity of metabolic networks. Systems biology borrows heavily from concepts in the fields of engineering and mathematics, especially those involved with control theory and network integration. New fields of inquiry have emerged from systems biology, carrying names like genomics, transcriptomics, metabolomics, and fluxomics (Sweetlove and Fernie 2005, Steuer 2007).

The quote by Paul Jarvis, which he offered in a synopsis paper concerning leaf diffusive resistances, contains implicit reference to the fact that controls over plant-atmosphere fluxes reflect not only the processes that drive the exchanges of H2O and CO2, but also past evolutionary modification of the leaf form and function. Thus, an understanding of fluxes at the plant and leaf scales requires perspectives on adaptation, in addition to biophysical processes. In fact, recognition that leaf and plant function can be best explained when both of these principles are integrated into a common framework has served as the intellectual cornerstone for the discipline of plant physiological ecology for over four decades. In this chapter we develop this integration with regard to the specific case of leaf processes and their underlying diffusive fluxes. In the next chapter, we will consider explicitly the process of adaptation with regard to leaf function, and the concept of adaptation as an organizing principle from which we can predict patterns of covariance between environmental change and traits that control leaf-atmosphere gas exchanges. Although we will focus on the leaf scale in both chapters, we will also begin to introduce concepts associated with atmospheric pressure gradients, turbulent transport, and eddy diffusivity, all of which will be valuable as we move into future chapters.

Sherwood Rowland’s comment at the banquet held to honor receipt, along with Paul Crutzen and Mario Molina, of the 1995 Nobel Prize in Chemistry, places the atmosphere at the center of some of the most influential scientific discoveries to have been made during human history. Within Rowland’s comment we can recognize Thales of Miletus who in the sixth century BC struggled to understand the different states of water and the process of evaporation, Lavoisier in the late eighteenth century discerning the exchange of oxygen between organisms and the atmosphere, and Arrhenius in the early part of the twentieth century calculating the relation between the carbon dioxide content of the atmosphere and the earth’s surface temperature. The importance of the atmosphere in the history of natural philosophy is clearly underscored by these seminal studies. Within all of these studies, however, is the undeniable influence of the earth’s surface and in particular the earth’s biosphere, on the chemical composition and dynamics of the atmosphere. The two are linked in a type of “co-dependency” in which processes and change can only be understood through studies that include both biotic and abiotic systems. The requisite nature of the nexus between the biotic and abiotic domains of the earth system is recognizable, albeit in extreme form, in the controversial concept of “Gaian homeostasis” laid out by James Lovelock and Lynn Margulis in 1974. While we (the authors) do not, in its entirety, endorse the tenets of a Gaian earth, we do recognize the value of this concept in defining the biosphere and atmosphere as coupled and interdependent systems. It is this interdependency, and the processes that maintain it, that will be the focus of this book.

Introduction

There is a major planet-wide experiment under way. Anthropogenic changes to the atmosphere–biosphere system mean that all ecosystems on Earth are now affected by our activities. While outright deforestation is physically obvious, other subtler processes, such as hunting and surface fires, also affect forests in ways that are less evident to the casual observer (cf. Estes et al. 2011; Lewis, Malhi & Phillips 2004a; Malhi & Phillips 2004). Similarly, anthropogenic atmospheric change is intensifying. By the end of the century, carbon dioxide concentrations may reach levels unprecedented for at least 20 million years (e.g. Retallack 2001) and climates may move beyond Quaternary envelopes (Meehl et al. 2007). Moreover, the rate of change in these basic ecological drivers may be unprecedented in the evolutionary span of most species on Earth today. Additionally, these atmospheric changes are coinciding with the greatest global upheaval in vegetation cover and species’ distributions since at least the last mass extinction at ~65 million years ago (Ellis et al. 2011). Collectively, the evidence points to conditions with no clear past analogue. We have entered the Anthropocene, a new geological epoch dominated by human action (Crutzen 2002; Steffen et al. 2011).

In this chapter we focus on the changes occurring within remaining tropical forests. Most forest vegetation carbon stocks lie within the tropics. Tropical forests store 460 billion tonnes of carbon in their biomass and soil (Pan et al. 2011), equivalent to more than half the total atmospheric stock, and annually process 40 billion tonnes (Beer et al. 2010). They have other planetary influences via the hydrological cycle, and emit aerosols and trace gases, and they are also characterised by their exceptional variety and diversity of life.

Introduction

The widespread loss and degradation of native forests is now recognised as a major environmental issue, even a crisis (Spilsbury 2010). During the first decade of the twenty-first century, global forest area declined by around 13 million ha yr−1 (FAO 2010). However, such estimates based on national statistics are uncertain (Grainger 2008); Hansen et al. (2010) report a substantially higher annual forest loss of approximately 20 million ha yr−1 for 2000–2005, based on analysis of satellite imagery.

The Food and Agriculture Organization (FAO 2010) also report that during the decade 2000–2010, the area of undisturbed primary forest declined by an estimated 4.2 million ha yr−1 (or 0.4% annually), largely because of the introduction of selective logging and other forms of human disturbance. Accurate data on the extent of forest degradation at the global scale are difficult to obtain (Gibbs et al. 2007), but an indication of its impact is provided by a recent estimate of the amount of carbon stored in forest vegetation. Over the period 1990–2005, global forest carbon stocks declined, in percentage terms, by almost double the decline in forest area (UNEP 2007). Given the current emphasis of global forest policy initiatives on both deforestation and forest degradation, particularly in the context of the UN REDD+ programme, there is an urgent need not only for improved forest monitoring (Baker et al. 2010; Gibbs et al. 2007; Grainger 2008; Sasaki & Putz 2009), but for a deeper understanding of the processes responsible for forest degradation and their potential impacts on forest biodiversity.

Introduction

Whether in the temperate zone or tropics, tree species composition and forest productivity are strongly associated with soil characteristics (e.g. Figure 11.1). Although these community- and ecosystem-level processes necessarily arise from variation in individual tree performance, the influences of specific soil resources on particular tree demographic processes have yet to be fully elucidated (Kobe 1996).

It is important, for several reasons, to understand how soil resources govern tree performance. First, and perhaps most salient to the theme of this volume, human activity exerts a potentially strong effect on soil resource availability through atmospheric deposition of nitrogen (N) (Figure 11.2), which accelerates soil acidification and the leaching of phosphorus (P) and base cations (calcium (Ca), magnesium (Mg), and potassium (K)) (Izuta et al. 2004; Matson et al. 1999; Perakis et al. 2006). Inorganic N deposition takes two major forms: nitrate (NO3–) from the combustion of fossil fuels and ammonium (NH4+) from agricultural activity. Background levels of N deposition are typically <1 kgN ha–1 yr–1, as measured in remote non-industrialised areas of the world (Hedin et al. 1995). In North America, N deposition can be more than 20 kgN ha–1 yr–1 (Gradowski & Thomas 2008; Weathers et al. 2006). Levels in Europe are much higher, with maximum levels reaching at least 43.5 kgN ha–1 yr–1recently (Stevens et al. 2011) and 75 kgN ha–1 yr–1 in the 1990s (Dise & Wright 1995). Atmospheric deposition of N is not exclusively a temperate issue, and levels of N deposition are expected to increase in the tropics with further industrial and agricultural development (Matson et al. 1999). Even though soil N levels are higher in tropical than temperate forests, additional inputs of N through deposition could lead to lower plant diversity and increased bulk carbon storage, as well as losses of base cations and P (Cusack et al. 2011; Lu et al. 2010; Matson et al. 1999).

Introduction

Forests provide a range of goods and services upon which humanity depends, from local (e.g. flood prevention) to global (e.g. carbon sequestration). Yet some 13 Mha of forest is lost each year, mostly in the tropics (Canadell & Raupach 2008). Considerable political, media and scientific attention has focused on this forest destruction and fragmentation and its implications for livelihoods, biodiversity and ecosystem services. However, human influences on forests now go beyond deforestation and degradation, to changing the states of atmosphere and climates and altering biogeochemical cycles, which in turn bear heavily on the functioning and composition of forest ecosystems. A range of disciplines are required to chart such change, understand how it works and predict where it is going. They span a broad range of scales from photosynthetic machinery in leaves, to the dynamics of forests across wide regions, to global atmospheric circulation. Integration of these multiple strands and scales of investigation has only recently begun, and this volume makes an important contribution to weaving them together into a more cohesive, albeit still incomplete, picture.

The story is told in three parts, beginning with a collection of perspectives on the global environmental drivers of forest change, the complexity of their interaction and effects, and important feedbacks. The second section concentrates on species-level traits and trade-offs, and how these explain the composition and dynamics of forests in a changing world. Finally, a number of approaches and tools are presented for measuring forest change and forecasting its future direction.

Introduction

The planet was once much more forested. As human populations have grown, the forests have been cleared to make way for crops and livestock. This conversion from forest to agriculture started in Neolithic times (Brown 1997) but accelerated during the European colonisation of North America and other territories. Since the 1970s, it has continued apace in the tropics. The need to produce food is not the only cause of deforestation: humans have always used timber as fuel and as a raw material for construction. They will continue to do so, whilst new threats are likely to emerge: for example, in recent years tropical forests and woodlands have been cleared to make way for biofuel crops and plantations. These changes are causing widespread concern, as they may bring short-term benefits at the expense of the sustained provision of ecosystem goods and services (Foley et al. 2007).

Since 1990 the world’s forests have shrunk from 28.6% to 27.6% of the land surface, with substantial shrinkage in the tropics and slight expansion in the temperate regions (calculated from FAO 2011). Overall, we expect to see a continuation of this trend as human populations continue to expand and economic development proceeds.