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Photosynthesis — both anoxygenic and oxygenic — allows access to new sources of energy. Oxygenic photosynthesis has the potential to create an oxygen-rich atmosphere and so allow aerobic respiration, which yields much higher amounts of energy than anaerobic respiration. The amount of oxygen added to the atmosphere is intimately linked to the burial of organic matter in sediments, therefore marine phytoplankton are crucially important in maintaining the levels of atmospheric oxygen on Earth. Anoxygenic photosynthesis will have a positive Gaian effect by providing an important source of energy. Oxygenic photosynthesis is more problematical; as with anoxygenic photosynthesis it provides an energy source, but the oxygen given off is likely to be toxic to organisms evolved in anoxic conditions. It is currently impossible to know if we should expect most biospheres to evolve oxygenic photosynthesis. However, improvements in telescope technology should allow us to look for oxygen-rich atmospheres around distant Earth-like planets.

First life-forms appeared at least as early as 3.5 billion years ago in the form of prokaryotes. Some of these species developed oxygenic photosynthesis, which resulted in the presence of oxygen gas in the atmosphere. Later, eukaryotes appeared and diversified through mutation and gene duplication (including mutation and duplication of master genes), which led to the rewiring of entire gene networks. The chapter shows that there is no fundamental difference between macroevolution and microevolution. It shows that making artificial life in the lab as well as transgenic life-forms would be impossible if the Intelligent Design scenario were correct. Indeed, ID posits that living systems were holistically designed and thus cannot be constructed in a piecemeal fashion.

The phytoplankton comprises a diverse array of photosynthetic organisms. The majority of polar lakes are classified as ultra-oligotrophic based on maximum chlorophyll concentrations. However, few lakes have been studied seasonally to determine the annual peak in biomass, thus trophic status is probably underestimated; intensively-studied lakes are mostly oligotrophic. The seasonal progression of primary production is initiated and ended by the large seasonal changes in solar radiation. A springtime peak occurs in most polar lakes, with subsequent enhancement or restraint by changes in light, nutrient availability or losses from grazing, disease, washout, and sedimentation. Comparisons between Arctic and Antarctic lakes imply that there may be differences in biodiversity, lake trophic status, and primary production that can improve understanding of the how polar lake phytoplankton are influenced by climate, nutrient supply, biotic interactions, and their own capacity to acclimate to their environment.

The benthic component of lakes, ponds, rivers, and streams is often rich in biodiversity as well as biomass. The main communities in the benthic habitat are microbial mats, aquatic mosses, and green algal felts that inhabit both running and lentic waters. The substantial primary production in these benthic autotrophic communities, together with their reduced losses of assimilated carbon because of the low temperatures, low degradation rates, and minimal grazing pressure, can result in luxuriant growth and accumulation of these photosynthetic elements. This chapter describes the types of communities typically found in non-marine benthic habitats. A review of the primary production rates that have been measured under different circumstances is also presented, drawing on information from the literature as well as unpublished data. The chapter concludes by exploring why the benthic component (phytobenthos) often dominates over planktonic communities (phytoplankton) in polar aquatic ecosystems.

In symbiotic associations, there is great variation in ecological outcomes shaped by the underlying coevolutionary process. Endophytic fungi of grasses have been shown to affect host growth and reproduction, photosynthetic physiology, abiotic stress tolerance, and competitive ability. Although positive effects of endophytes on host growth in several grass-endophyte systems have been described, many studies have been done mostly on a limited set of species growing in controlled environments. Effects of endophytes on host sexual reproduction range from parasitic castration (e.g., sexual Epichloë endophytes which cause choke disease) to improved seed production (e.g. asexual Neotyphodium endophytes in tall fescue). Vertical transmission within seeds occurs in asexual endophytes and may favor the evolution of mutualistic symbioses. Most reports of improved tolerance of abiotic stresses, such as low soil water and/or minerals shown by infected hosts, have involved tall fescue or perennial ryegrass. The grass-endophyte interaction could represent an adaptive symbiosis in relation to at least some environmental stresses. Effects of elevated atmospheric CO₂ on grass-endophyte interactions have not been clearly demonstrated. Although past workers have sometimes shown that endophytes increased the competitive ability of their hosts, recent analyses have not supported the contention that endophytes significantly improve host competitive ability.

Priestley's observations and experiments enabled others to interpret nature in a new way. This chapter reviews these observations and experiments covering electrostatics, optics, pneumatic chemistry, and photosynthesis. It then considers the ways recent historians have interpreted Priestley's scientific activities in the context of his theological, educational, and political activities. Finally, the chapter re-examines the question of Priestley's attitude towards Lavoisier and his continuing support for a phlogistic world view.

This chapter focuses on internally generated changes due to evolutionary inventions of new forms life. These evolutionary inventions include the evolution of oxygen-yielding photosynthesis and the colonization of land by the first forests. Oxygen-dependent photosynthesis and respiration evolved to take advantage of the appearance of oxygen in the biosphere, while anaerobes crashed from preeminence to relative obscurity. Meanwhile, land plants evolved to adapt to the low carbon dioxide and low temperatures that earlier generations had produced, and enormous insects thrived temporarily to take advantage of the transiently abundant oxygen, only to disappear again when oxygen levels subsequently subsided. Eventually, new types of fungi evolved to make use of the new food source. Ultimately, these internally generated events produced some changes that generally improved the global environment for life, but also some that tended to spoil it.

The diversity in size, shape, and growth requirements of different plants produces an astonishing array of features to see — from hairs, thorns, and waxes to tilting responses towards sunlight (phototaxis) and rapid responses to touch (sensitive plants). Widely differing growth forms also occur, including life styles associated with photosynthesis, parasitism, and carnivory, as well as the mining and galling effects of insects. This chapter describes a few of the many intriguing features of plants, including descriptions of the above characteristics as well as lenticels, plant patches, variegated leaves, and poison plants.

This chapter considers the challenge of improving crop resource-use efficiency using biotechnology or traditional plant breeding. It argues that some of biotechnology's stated goals, such as more efficient use of water by crops, are unlikely to be achieved without tradeoffs. After providing an overview of crop genetic improvement via traditional plant breeding or biotechnology, the chapter discusses the importance of greater resource-use efficiency and increasing yield potential. It then explains how natural selection has improved the efficiency of photosynthesis as well as water-use efficiency and how tradeoffs limit biotechnology improvement of crop water use. It also assesses the potential of genetic engineering to improve nutrient-use efficiency and asserts that near-term benefits of biotechnology have been exaggerated. The chapter concludes with a review of biotechnology's possible benefits and risks.

This chapter discusses how seagrasses adapt to their environment. Topics covered include growth and structure, photosynthesis and respiration, salinity, nutrients, reproduction, propagule dispersal, and how seagrasses change their environment.

This chapter reviews current knowledge of the process and measurement of microplankton respiration in marine surface waters. The principal approaches are outlined and their potentials and limitations discussed. A global database, containing 1,662 observations has been compiled and analysed for the spatial and temporal distribution of surface water respiration. The database is tiny compared to that of photosynthesis and biased with respect to season, latitude, community structure, and depth. Measurements and models show that the major portions of respiration lies in that attributable to bacteria (12-59%) and to algae (8-70%). The mean of the volumetric rates of respiration in the upper 10 m of the open ocean is 3.3±0.15 mmol O₂/m³-d and that of depth-integrated open-ocean respiration 116±8.5 mmol O₂/m²-d. A global estimate of 13.5 Pmol O₂/a is derived from the mean depth-integrated rate, which significantly exceeds contemporary estimates of ocean plankton production (2.3-4.3 Pmol O₂/a).

This chapter provides a general background on the synthesis of chemical biomarkers and their association with key metabolic pathways in organisms, as related to differences in cellular structure and function across the three domains of life. It discusses photosynthesis, the dominant pathway by which biomass is synthesized. It also presents information about chemoautotrophic and microbial heterotrophic processes. The holistic view of biosynthetic pathways of chemical biomarkers provides a roadmap for other chapters in the book, where more specific details on chemical pathways are presented for each of the respective biomarker groups. While other organic geochemistry books have generally introduced the concepts of chemical biomarkers in the context of physical and chemical gradients found in natural ecosystems (e.g., anaerobic, aerobic), this book begins by examining biosynthetic pathways at the cellular level of differentiation.

This chapter discusses the evolution of oxygen-producing organisms by considering the evolution and assembly of its basic constituent parts. It focuses on the following key questions: (1) What is the evolutionary history of chlorophyll? (2) What are the evolutionary histories of photosystem I and photosystem II (PSII)? (3) What is the origin of the oxygen-evolving complex in PSII? And finally, (4) what is the evolutionary history of Rubisco? In addressing these, the chapter seeks to understand the complex path leading to the evolution of oxygenic photosynthesis on Earth. This event was one of the major transforming events in the history of life. With no oxygenic photosynthesis, there would be no oxygen in the atmosphere; there would also be no plants, no animals, and nobody to tell this story.

This chapter discusses the importance of cyanobacteria. The evolution of cyanobacteria brought the biological production of oxygen to Earth for the first time. This led, in turn, to the eventual accumulation of oxygen in the atmosphere and to the widespread evolution of oxygen-utilizing organisms. However, the importance of cyanobacteria goes beyond this. Cyanobacteria were the first photosynthetic organisms on Earth to use water as a source of electrons. Unlike the sulfide, Fe²⁺, and H₂ used by anoxygenic phototrophic organisms, water is almost everywhere on the planet surface. This means that biological production on Earth was no longer limited by the electron source (water in this case), but rather by nutrients and other trace constituents making up the cells. In the end, the use of water in photosynthesis resulted in an increase in rates of primary production on Earth by probably somewhere between a factor of ten to a thousand. For the first time, life on Earth became truly plentiful. With the evolution of cyanobacteria, Earth was on its way to becoming a green planet.

This concluding chapter evaluates the Gaia hypothesis. Based on the evidence studied in this book, the chapter argues that the Gaia hypothesis is not a reasonable picture of how Earth and life interact with each other. There is no single body of facts or line of unimpeachable reasoning that sways the debate conclusively in favor of Gaia. The lack of any established bottom-up mechanism that can explain how Gaia is produced also weighs against it. No one has been able to explain convincingly how Gaia could emerge out of evolutionary or ecological dynamics. It is therefore perhaps not surprising that major evolutionary advances, such as the evolution of oxygenic photosynthesis, or the first foresting of the land by sizeable trees, have been associated with environmental catastrophes.

Some of the most interesting adaptations of plants to their environments are shown by desert plants. One need only think of the cacti of North and Central America, Welwitschia mirabilis of the Namib, and the Mesembryanthemaceae of the Karoo to realise that deserts contain a uniquely-adapted flora. Geophytes and other plants with special storage organs may be considered to be pre-adapted to desert conditions, while trees and shrubs with deep root systems are able to exploit deep aquifers in an otherwise dry environment. Many annual plants do not have clear morphological or physiological adaptations to the desert environment but thrive there by germinating immediately after the infrequent rains, and completing their life cycles before the onset of the summer heat. This chapter examines the various ways in which mesic plants have been able to exploit resource variability in order to survive in extreme desert environments.