Why marine turtles?

Ectothermic species are fundamentally affected by environmental temperatures, which largely dictate their metabolic rate. In marine turtles, foraging behavior, migratory patterns, and ultimately breeding success may be modulated by the environment and influenced by climate change. This has the potential to have both positive and negative effects. The seven species of marine turtles broadly occupy three foraging niches (planktivory, herbivory, and omnivory) and occur in almost every non-polar ocean basin in the world, from shallow coastal seas to open ocean habitats. The effects of climate change to marine turtles likely will be wide ranging and of direct relevance to other marine animals in these varied habitats. Marine turtles are a fascinating “canary in the coal mine” with which to study the effects of climate change in marine habitats, and there has been an exponential increase in interest in the effects of climate change on them in the last decade (Poloczanska et al., 2009; Hamann et al., 2010; Hawkes et al., 2010). Marine turtles are also generally considered charismatic, making them ideal subjects with which to raise awareness of climate change effects to biodiversity and to increase support for effective management and conservation of marine environments.

In explaining the relation between temperature and chemical reactions in his Etude de Dynamique Chemique in 1884, Jacobus van’t Hoff built a conceptual bridge between the concepts of thermodynamics, which had emerged in cogent fashion during the second half of the nineteenth century, and chemical equilibrium, which had emerged from studies on reversible reactions earlier in that century. In the quote above from his Nobel Prize lecture, van’t Hoff refers to the concept of exothermic reactions as being the “favored” outcome of a chemical interaction, which we now understand to be predicted by thermodynamic laws. Chemical transformations within the earth system must follow the same thermodynamic laws that were presented in the last chapter and to which van’t Hoff alluded in the statement above. In this chapter, we will build on those thermodynamic laws in order to establish a foundation for the more detailed considerations of biochemistry and metabolism. More specifically, we will delve into the theory underlying chemical reactions, their sensitivity to temperature, and their biochemical association with protein catalysts.

Prior to 1900 most meteorologists recognized that atmospheric temperature decreased with height and they assumed that this decrease was continuous. Late in the nineteenth century, however, the French meteorologist Leon Philippe Teisserenc de Bort used hydrogen balloons with precisely calibrated thermometers to demonstrate that while temperature did indeed decrease with height to approximately 8–12 km, above that height the temperature remained constant, or even increased slightly. Teisserenc de Bort referred to the atmosphere above 8–12 km as the “isothermal zone.” Later, studies by the German meteorologist Richard Assmann confirmed the observations of Teisserenc de Bort, and even extended them to note that the so-called “isothermal zone” was actually a zone with consistent temperature increase as a function of height. This condition of warmer air above cooler air is now referred to as an “inversion,” thus distinguishing it from the more commonly observed pattern of decreased temperature with height. In later writings, during the early twentieth century, Teisserenc de Bort postulated the existence of two atmospheric layers separated by the inversion – the troposphere, literally translated from the Greek word “tropein,” which means to turnover, and the stratosphere, literally translated from the Latin word “stratificationem,” which means to form into layers. Since his writings on this subject, the temperature inversion observed by Teisserenc de Bort has become known as the tropopause, the region separating the troposphere from the stratosphere. The discoveries of Teisserenc de Bort were not only important for our understanding of the physical arrangement of the atmosphere, but by focusing on atmospheric turnover in the troposphere, they laid the foundation for our current understanding of surface-atmosphere transport and even more general aspects of atmospheric physics.

Plants not only exchange inorganic C with the atmosphere, but also organic C in the form of a broad range of biogenic volatile organic compounds (BVOCs). The magnitude of the global BVOC flux is small compared to the global photosynthetic CO2 flux: ~ 2 Pg of C contained in annual BVOC emissions (including CH4 and CO) compared to global gross primary productivity, which is ~ 120 Pg of CO2. However, the BVOC flux is critical to understanding chemical reactions that occur in the atmosphere, especially those that produce important oxidant compounds, such as ozone, those that determine the oxidation rate of important greenhouse gases, such as methane, and those that determine the production of organic aerosol particles, which affect the earth’s radiation budget. Scientists did not recognize that the emission of compounds from vegetation could have such an important impact on atmospheric chemistry until the mid 1960s when researchers such as Rei Rasmussen and Fritz Went began collecting air samples in remote locations, far from the influences of urban pollution. This effort to describe the volatile chemical “fingerprints” of natural ecosystems revealed the presence of a large outward flux of reactive compounds that had previously been unidentified. For example, as reflected in the quote above, careful analysis using gas chromatography revealed the presence of reactive isoprene and other terpenes in an oak forest, which would have been undiscovered if left to detection by the human nose alone. Once these observations started to accumulate, it became clear that biogenic sources of reactive compounds were even more important than anthropogenic sources in their potential to catalyze oxidative photochemistry and, in many cases, control the overall oxidative capacity of the troposphere.

Most of the net transport of mass and energy between an ecosystem and the atmosphere occurs through the turbulent wind. As discussed in the last two chapters, turbulence varies greatly in its properties depending on where and when it occurs, but it also exhibits coherency and organization in its motions. Both the variable and coherent aspects of turbulence are induced by features of the earth’s surface; especially by topographic features, such as the location of hills, mountains, and valleys, and canopy characteristics such as depth and roughness. From a theoretical perspective, it had been reasoned since the groundbreaking work in 1954 by Andrei Monin and Alexander Obukhov that near-surface shear forces, in the neutral surface layer above a horizontally homogeneous land surface, could not sustain vertical divergence in the momentum flux. This led to the inevitable conclusion that surface fluxes must be conserved as a function of height in the surface layer, which in turn led to the concept of a “constant flux layer.” In the late 1950s and early 1960s several research groups took up the aim of validating these theoretical predictions – an aim that required careful observations above flat, simple terrain. The initial experiments conducted in Kansas (and later in Minnesota) in the late 1960s did indeed validate the predictions and this validation has withstood numerous subsequent tests and debates. As referenced in the paper cited above from Kaimal and Wyngaard, after more than 30 years of testing, the tenets of these early experiments are still widely accepted and used.

Preface

This book is about interactions – those that occur between the terrestrial biosphere and the atmosphere. Understanding biosphere-atmosphere interactions is a core activity within the discipline of earth system sciences. Many of the most pressing environmental challenges that face society (e.g., the anthropogenic forcing of climate change, urban pollution, the production of sustainable energy sources, and stratospheric ozone depletion), and their remedies, can be traced to biosphere-atmosphere interactions within the earth system. Traditionally, biosphere-atmosphere interactions have been studied within a broad range of conventional disciplines, including biology, the atmospheric and geological sciences, and engineering. In this book we take an integrated, interdisciplinary perspective; one that weaves together concepts and theory from all of the traditional disciplines, and organizes them into a framework that we hope will catalyze a new, synergistic approach to teaching university courses in the earth system sciences.

As we wrote the initial outline for the book, we recognized that the interdisciplinary perspective we sought, in a subtle way, had already emerged; it simply had not been formally collated into a synthetic format. For the past several years, biologists have been attending meetings and workshops traditionally associated with meteorology and geochemistry and conversely meteorologists and geochemists have been attending biology meetings. As a result, newly defined and integrative disciplines have already appeared with names such as “biometeorology,” “bioclimatology,” and “ecohydrology.” Thus, the foundations for the book had already been laid. We simply needed to find the common elements and concepts that permeated these emerging disciplines and pull them together into a single treatment.

This quote from a general discussion paper by Raupach and Finnigan is actually the title of the paper, and it succinctly summarizes one of the underlying compromises that must be made when developing models of earth system processes – convenience versus accuracy. Models are necessary for allowing us to proceed from observations to generalizations, and therefore from descriptions to projections. However, a model, by necessity, is an imperfect representation of a process. In earlier chapters we addressed the nature of models that have been developed at the biochemical and leaf scales. Here, we address models describing the turbulent exchanges between canopies or landscapes and the atmosphere.

If models are accurate in their depiction of transport processes, the area-specific turbulent flux that is predicted at the scale of a whole canopy should converge with the integral spanning all leaf diffusive fluxes determined within the canopy. Given this constraint, one could argue that knowledge of turbulence and its representation in a model is not necessary to determine surface-atmosphere fluxes; one need only determine the integral sum of diffusive fluxes in the underlying leaves. This type of bottom-up model, however, in which diffusive fluxes are simply summed to give a canopy flux, is incapable of describing how those fluxes distribute their respective scalar entities across the space within and above the canopy, and thus how variance in scalar concentration gradients can affect diffusive source or sink activity. In essence, modeled fluxes are uncoupled from dynamics in their associated concentration gradients. In order to dynamically link fluxes to gradients, atmospheric transport must be considered; mass or energy must be dispersed to or from the immediate vicinity of sources and sinks. One of the primary challenges facing modelers seeking to describe dynamic flux systems at the canopy scale is the inclusion of accurate scalar dispersion algorithms.

The observation that a mixture of gas molecules of different masses does not behave as expected when subjected to gravity was systematically described by Thomas Graham early in the nineteenth century. Rather than sorting according to their masses, Graham observed that a true mixture was achieved. It was clear that a force must exist to oppose gravity and facilitate the intermingling of gases, but what could be the nature of that force? Even earlier, in 1827, Robert Brown had used a microscope to observe that pollen grains suspended in water exhibit random patterns of motion. Brown reasoned that these motions must be caused by randomly arranged forces in the molecular realm, but once again the nature of such forces was not apparent. It was not until several decades later that Albert Einstein, working on issues concerned with thermal and kinetic energy, provided a theoretical explanation. Einstein reasoned that the thermal energy contained within microscopic bodies is transformed into kinetic energy providing a means for velocity. In the case of Graham’s gases we can use Einstein’s theory to explain how suspended molecules collide with one another in “random walks,” providing the potential for an upward force vector that opposes gravity and sustains a random mixture. In the case of Brown’s pollen grains we can use the theory to explain the perpetual motion of water molecules with random collisions occurring between molecules and grains, forcing the grains to vibrate and move through the water. We now understand that Einstein’s theories on energy and motion explain one of the fundamental processes by which mass is transported at the microscopic scale – molecular diffusion.

Creating a computer model for processes as complex as photosynthesis, photorespiration, and dark respiration has proven to be an exceptional challenge. The various feedbacks that are engaged within the processes at specific metabolic steps, and that are triggered by specific sets of conditions, render the numerical modeling framework most applicable. Within the numerical framework, processes can be modeled as a series of sequential biochemical reactions, which can then be integrated across finite time intervals to produce pathway fluxes. While numerical solutions have their advantages, the path to the ultimate outcome tends to be less transparent than the alternative, an analytical solution. Numerical models are seldom amenable to complete mathematical closure, requiring that approximations be made to close the numerical iteration and reach a stable, steady-state, solution. An analytical solution is not constructed from sequential, time-dependent steps, but rather represents a closed set of equations (i.e., no variables left to approximation) that fully accounts for all components of a process or problem. For processes as complex as metabolic pathways, however, analytical solutions are difficult. Thus, even for this approach, researchers have sought approximations and simplifications that must be accommodated in order to achieve a stable, steady-state solution. The danger of relying on such approximations, as stated in the quote above by Graham Farquhar, a noted analyst in the field of photosynthetic modeling, is that these simplifications tend be forgotten and the analytical models migrate with time toward uncritical acceptance.

In one of his influential essays on the nature of the biosphere, which subsequently laid the foundation for modern biogeochemistry, Vladimir Vernadsky quoted his geology teacher, Vasily Dokuchayev, in a manner that made clear Dokuchayev’s view that soil is uniquely influenced by the organisms that live within; it lies at the interface between geology and biology. Roots and microorganisms exchange material with the soil and in doing so influence its chemical composition and physical structure. The interactions between the biological and geological components of soil ultimately determine how it interacts with the atmosphere. Soil is the medium through which terrestrial plants gain access to most mineral elements of the geosphere (carbon being the principal exception), and to liquid water from the hydrosphere, both of which exert major controls over the capacity for plants to exchange CO2, H2O, and energy with the atmosphere. Microbial activities in soil carry out the recycling of organic matter, returning carbon to the atmosphere, thus closing the terrestrial carbon cycle. Certain types of bacteria, in symbiotic relations with plant roots, or free-living in soil and water, facilitate the fixation of N2 from the atmosphere. Chemolithotrophic microorganisms in soil oxidize inorganic compounds to generate energy that is subsequently used to drive the autotrophic assimilation of carbon and at the same time produce volatile trace gases (including nitrogen oxides and N2) that are emitted to the atmosphere. Any concentrated consideration of ecosystem-atmosphere exchange must include soil processes in order to fully comprehend the relevant mass and energy fluxes.

We begin this chapter with an introduction to the decomposition of soil organic matter – a principal source of soil respiration and the process responsible for recycling nutrients between dead and living biomass. We then take up the topic of transport mechanisms for the exchange of mass between soils and the atmosphere, once again focusing on the flux of CO2 from soil respiration. Finally, in a series of sections we consider recent observations and models that focus on biological controls over the exchanges of CH4 and NOx between soils and the atmosphere. Cumulatively, these trace gases represent major contributions to the terrestrial carbon and nitrogen budgets, as well as to the reactive photochemistry and energy partitioning that occurs in the atmosphere.

Leaves provide the infrastructure within which solar photons and CO2 are channeled to photosynthetic mesophyll cells to support gross primary productivity, and from which absorbed energy is partitioned into latent and sensible heat loss. Both the internal environment and surface features of a leaf are the products of modification through natural selection to produce a form and function that provides advantages toward carbon and energy assimilation, and ultimately growth. For example, the structural arrangement of leaf cells affects the organized dispersion of the solar photon flux and the density and function of stomata affect the diffusive uptake of atmospheric CO2 and its relationship to H2O loss. As indicated in the quotes from two famous architects that we cite above, the concept that “form is married to function” is perpetuated across generations of multiple disciplines; it is not limited to the biological sciences. It is a fundamental philosophical relation. In fact, some of the earliest intellectual pursuits of this relation were conducted by very broad thinkers; practitioners of literature, music, and the visual arts. Johann Wolfgang von Goethe, best known for his literary works, spent many hours in discussions with Alexander von Humboldt, the “founder” of the discipline of phytogeography, discussing the concept that plant form could be used to discern plant-climate relations; discussions that no doubt influenced Humboldt’s theories on the determinants of vegetation distribution across the globe. There is no requisite sequence by which “form mandates function” or “function mandates form”; evolutionary modification occurs to both anatomy and physiology, maintaining both within a coordinated set of resource use parameters. Leaf form and function must be viewed as integrative, and the coupled nature of form and function must be viewed, in and of itself, as a target of natural selection.

Closure of the water budget for an ecosystem requires that precipitation and flows of water from neighboring ecosystems be returned to the atmosphere through evapotranspiration, transferred to storage pools, or allowed to flow out of the system. Transfer and storage of water creates capacitance in the liquid phase of the water cycle and delays the inevitable return of water vapor to the atmosphere, but a globally balanced water cycle requires that the molar equivalent of precipitated water be accounted for in the fractions stored in surface and subsurface reservoirs, plus that evaporated back to the atmosphere. Recognizing that in terrestrial ecosystems a large fraction of precipitation is returned to the atmosphere through leaf transpiration, plants occur at an important interface between the liquid and vapor phases of the water cycle. Water moves from soil into plants through viscous flow in the liquid phase, as it is “pulled” by thermodynamic forces through roots, vascular tissues, and leaf mesophyll cells, following negative pressure (tension) gradients. Tension develops in the conduction tissues as water is evaporated faster from leaves than can be replaced by flow from the soil. Physical continuity within capillary “threads” of the ascending water column is maintained by cohesive and adhesive forces that are facilitated by the electrostatic polarity of water molecules. In the vicinity of stomata, water is evaporated to the atmosphere. In the atmosphere, water is carried in the vapor phase to and from leaf and soil surfaces through diffusion near the surfaces and turbulent air motions in the well-mixed atmosphere. Given the continuous nature of these water transfer paths, and their serial relation to one another, it was recognized early in the study of plant-water relations that the “whole plant” must be considered at the center of an integrated and articulated soil-plant-atmosphere continuum, or SPAC.