The process of photosynthesis as carried out by the chloroplast is arguably the most important biochemical process that occurs on the planet. Whilst many organisms gain their energy and carbon molecules by consuming other organisms in a heterotrophic manner, ultimately the basis of all food chains is the energy and carbon which is accumulated by autotrophic organisms carrying out photosynthesis. All of these organisms either contain photosynthetic chloroplasts or are single-celled organisms, such as photosynthetic bacteria, which carry out photosynthesis themselves. Such photosynthetic organisms are autotrophic in that they obtain their energy directly from the light emitted from the sun, a result of nuclear fusion. The light energy is transduced into energy stored in molecular bonds, which is then used to drive a complex series of biochemical reactions, which enables the fixation of gaseous carbon dioxide (CO2) molecules from the air. This fixation process involves binding of the CO2 to simple phosphorylated sugar molecules located in the stroma of the chloroplast, which eventually give rise to related phosphorylated sugar molecules which are either exported or retained in the chloroplast and give rise to biochemical pathways which synthesise sucrose or starch. In this way, plants can grow and increase in biomass by accumulating carbon molecules from the atmosphere and subsequently they synthesise a myriad of large complex carbon-based molecules. Probably the most abundant of these is the polymer cellulose, composed of long chains of glucose molecules, which forms the basic structure of plant cell walls and comprises a significant proportion of global plant biomass.

During the development of the endosymbiotic relationship between the invading ‘plastid’ and the recipient prokaryotic cell through the course of evolution, many changes occurred to the invading ‘plastid’. As we have seen, one major change has been the extensive movement of genetic information from the plastid's own genome into the nuclear genome. As a result of these events, the cell is faced with a major problem; namely, how those proteins now encoded by the cell's nucleus get back into the correct place within the plastid in order to allow the plastid to function effectively. Since around 95% of the proteins that are present in the mature chloroplast in the cells of present-day plants are encoded by genes in the nucleus, this problem becomes significantly more than just routing the occasional protein and it constitutes a major flow of protein trafficking within the cell. Plastids import much more than proteins. In all cells, plastids play a major role in metabolic biochemistry and synthesise many important molecules, which are utilised in other parts of the cell (see Chapter 7). Thus a wide variety of molecules other than proteins are imported and exported by the plastid in its normal course of biochemical function. Foremost amongst these are the end products of photosynthesis as well as lipids, amino acids and various other intermediates in biochemical pathways.

A complication which has to be overcome in trafficking molecules into and out of the plastid is that the boundary of the plastid is a double membrane, composed of the outer envelope membrane and the inner envelope membrane, with a distinct compartment in between; the envelope lumen.

As we have seen in preceding chapters, the plastid plays a major role in the plant cell in carrying out photosynthesis and enabling the plant to increase in biomass as a result of carbon dioxide assimilation. In addition, the plastid also plays a crucial role in carrying out a variety of metabolic processes, which give rise to a myriad of different molecules, which are used both inside the plastid or are exported into the cytosol. As a result, the original endosymbiont that was taken up by an early eukaryotic cell has become so important to the functioning of the modern-day plant cell that it is generally considered that cells lacking plastids are non-functional and not viable. Thus the plastid is a prerequisite for plant cell function.

Furthermore, it is important to realise that a significant proportion of the plastids resident in the cells of a higher plant are not photosynthetic chloroplasts but other non-photosynthetic types such as leucoplasts, amyloplasts, root plastids or chromoplasts and that these plastids carry out many critical parts of cellular metabolism in these non-photosynthetic tissues which are essential to cell function. These plastids are generally termed non-green plastids.

Research on a diverse range of plastid metabolism has generated a huge amount of information about plastid biochemical pathways, the details of many of which are beyond the scope of this book. In this chapter, therefore, we will consider an overview of the main biochemical pathways that occur in plastids, especially those associated with the chloroplast.

Bryophytes have gained a lot of publicity in the past 10–15 years, at least among scientists. While there have always been those who for inexplicable reasons have had a particular fondness for bryophytes, in academic circles these organisms were generally viewed as just “poor relatives” of the more flashy and exciting angiosperms. The bryophytes include fewer species, of smaller stature, with more subdued colors, of less obvious ecological significance, and with apparently simpler and less exciting evolutionary stories to tell. That view has changed.

The three major groups of bryophytes – mosses, liverworts, and hornworts – comprise the earliest lineages of land plants derived from green algal ancestors. Although we still do not know with certainty which of the three lineages is the sister group to all other land plants, we do know that the earliest history of plants in terrestrial environments is inextricably bound to the history of bryophytes. If we wish to understand fundamental aspects of land plant structure and function, we should turn to the bryophytes for insights. These aspects include the origin and nature of three-dimensional plant growth from apical cells and meristems, the evolution of cellular mitotic mechanisms and machinery, the development of thick, water- and decomposition-resistant spore (and later pollen) walls, the molecular and biochemical mechanisms underlying desiccation tolerance, and plant genome structure, function, and evolution.

Introduction

Peatlands are unbalanced ecosystems where plant production exceeds decomposition of organic material. As a result, considerable quantities of organic material, or peat, accumulate over long periods of time: millennia. This organic material is composed primarily of plant fragments remaining after partial decomposition of the plants that at one time lived on the surface of the peatland. Decomposition occurs through the action of micro-organisms that have the ability to utilize dead plant components as sources of carbon for respiration (Thormann & Bayley 1997) in both the upper, aerobic peat column (the acrotelm) and the lower, anaerobic peat (the catotelm) (Ingram 1978, Clymo 1984, Wieder et al. 1990, Kuhry & Vitt 1996). Labile cell contents, cellulose, and hemicellulose are more readily available sources of carbon than recalcitrant fractions that contain lignin-like compounds, with these latter compounds being concentrated in peat by decomposition (Williams et al. 1998, Turetsky et al. 2000). The vascular plant-dominated, tree, shrub, and herb layers produce less biomass (Campbell et al. 2000) and decompose more readily than the bryophyte-dominated ground layer (Moore 1989). Surfaces of northern peatlands are almost always completely covered by a continuous mat of moss (National Wetlands Working Group 1988, Vitt 1990), and the large amount of biomass contained in this layer is composed of cell wall material that decomposes slowly. This slow decomposition, coupled with water-saturated, anaerobic conditions in the peat, cool climate, and a cool moist growing season conducive to bryophyte growth, allows organic matter to accumulate over large areas.

Introduction

Bryophytes do not appear to differ fundamentally from higher plants and green algae in their basic requirements for mineral macronutrients and trace elements. However, bryophytes differ significantly from vascular plants in pathways for nutrient acquisition and these may sometimes have far-reaching consequences for the ecosystems in which they grow. Owing to their specific modes of nutrient capture, bryophytes frequently accumulate chemicals to concentrations far exceeding those in the ambient environment. This property has led to the development of moss biomonitoring methods, which have taken hold firmly in the wider scientific community since the first edition of this book appeared.

As in the earlier edition, this chapter describes the special problems that bryophytes encounter in obtaining essential mineral nutrients, and in dealing with non-essential elements and compounds. Far more is known now than in the earlier edition about nitrogen deposition and utilization by bryophytes, and hence the chapter will focus on these aspects of mineral nutrition and substrate ecology.

The substratum on which a bryophyte grows can be a source of nutrients and other chemicals that may cause stresses. I have retained the useful distinction between “substrate”, used for the substance on which an enzyme or biochemical process works (as in Section 8.3.1), and “substratum”, used for the surface supporting a plant or lichen, although the etymological grounds for this are slight. Substratum specificity and chemical specialisms are considered in some detail but aspects involving competition and population dynamics are now largely covered in Chapter 10 by Rydin.

Introduction

Conservation biology is a fairly new, multidisciplinary science that has developed to deal with the crisis confronting biological diversity (Primack 1993). As a crisis discipline, conservation biology arose in response to an increasingly formulated political demand to face the dramatic loss of biodiversity and the need to take steps to anticipate, prevent, and reverse the trend (Heywood & Iriondo 2003). Subsequent ratification of the Convention on Biological Diversity at the United Nation conference held in Rio in 1992 by most of the world's governments has placed the subject of biodiversity firmly on the political agenda.

The past few years have witnessed a major evolution in our understanding of conservation. The increasing need for performing tools has rendered conservation biology a truly multidisciplinary science, feeding on a variety of other areas, including ecology, demography, population biology, population genetics, biogeography, landscape ecology, environmental management, and economics (Heywood & Iriondo 2003). Conservation interest has also been progressively enlarged to include a broad array of taxa that used to be completely overlooked. Cryptogams were, for example, the focus of only about 4% of published papers between 2000 and 2005 in leading conservation journals (Hylander & Jonsson 2007). The situation has been most recently changing and there has been an increasing awareness of the necessity to include cryptogams in general, and bryophytes in particular, in conservation programs (Hylander & Jonsson 2007).

Introduction

Bryophytes are on average some two orders of magnitude smaller than vascular plants, and this difference of scale brings in its train major differences in physiology, just as many of the differences in the structural organization and physiology of insects and vertebrates are similarly scale-driven. Surface area varies as the square, and volume and mass as the cube, of linear dimensions. Hence gravity is a major limiting factor for vertebrates or trees, but trivial for insects or bryophytes. Bryophytes in general have much larger areas for evaporation in proportion to plant mass than do vascular plants. Surface tension, which operates at linear interfaces, is of little significance at the scale of the vascular plant shoot but is a powerful force at the scale of many bryophyte structures. There are also major scale-related differences in the relation of bryophytes and vascular plants to their atmospheric environment. Vascular-plant leaves are typically deployed in the turbulent air well above the ground. The diffusion resistance of the thin laminar boundary layer is small, so the epidermis with its cuticle and stomata in effect marks the boundary between (relatively slow) diffusive mass transfer within the leaf and (much faster) turbulent mixing in the surrounding air. By contrast the small leaves of many bryophytes lie largely or wholly within the laminar boundary layer of the bryophyte carpet or cushion, or of the substratum on which it grows.

Introduction

There is a popular genre of politically incorrect jokes on the theme of “The World's Shortest Books” (of which the least offensive example is the title “Different Ways to Spell Bob”). Until recently, it would have been fair to surmise that the title of this chapter might have qualified with ease. Certainly, that would have been the view of many soi-disant “mainstream” plant developmental biologists, whose Arabidocentric view of the plant kingdom had tended to ignore any organism outside the angiosperms (and most within). Thankfully, this is no longer the case. It is now appreciated that an understanding of the evolution of gene function and of the roles of genes in the programming of developmental transitions (generically known as “Evo-Devo”) requires a comparative analysis of species representative of a wide range of diverse taxa. This has coincided with an explosion of molecular knowledge of at least one species of moss, Physcomitrella patens, the study of which is being facilitated by the complete sequencing of its genome. Consequently, we can expect to see a much greater interest in this species, and in mosses as a group of plants with their own unique features and fascination, developing within the wider plant science community. In this chapter I shall therefore concentrate on the recent discoveries made in Physcomitrella, and – more importantly – attempt to sketch out some of the challenges that lie ahead for researchers intending to make use of the burgeoning Physcomitrella resources.

Introduction

The three lineages of bryophytes, mosses, liverworts, and hornworts, compose successful groups of early embryophytes. The mosses are estimated to include some 12 700 species (Crosby et al. 2000), the liverworts approximately 6000–8000 extant species (Crandall-Stotler & Stotler 2000, Chapter 1, this volume), and the hornworts about 100–150 species (Chapter 3, this volume). Mosses are comparable in species richness to the monilophytes, which are estimated to include about 11 500 species (Pryer et al. 2004). Among the extant land plants, therefore, only the angiosperms are currently more species-rich than are the bryophytes.

It is often stated that bryophytes are most diverse in the tropics and fit the general pattern found in many groups of organisms, with increasing species richness toward the equator (Rosenzweig 1995). However, a quantitative analysis of latitudinal diversity patterns in the mosses failed to detect any such latitudinal gradient, except perhaps a weak one in the Americas (Shaw et al. 2005a). It appears that liverwort diversity is highest at moderate to high latitudes of the Southern Hemisphere, although one family, the Lejeuneaceae, is hyperdiverse in wet tropical forests of both the New and Old Worlds (Gradstein 1979).

The fossil record for mosses, liverworts, and hornworts is too incomplete to assess whether these groups were more or less diverse in the geological past (Miller 1984, Oostendorp 1987).

Introduction

With approximately 13 000 species, the Bryophyta compose the second most diverse phylum of land plants. Mosses share with the Marchantiophyta and Anthocerotophyta a haplodiplobiontic life cycle that marks the shift from the haploid-dominated life cycle of the algal ancestors of embryophytes to the sporophyte-dominated life cycle of vascular plants. The gametophyte is free-living, autotrophic, and almost always composed of a leafy stem. Following fertilization a sporophyte develops into an unbranched axis bearing a terminal spore-bearing capsule. The sporophyte remains physically attached to the gametophyte and is at least partially physiologically dependent on the maternal plant. Recent phylogenetic reconstructions suggest that three lineages of early land plants compose an evolutionary grade that spans the transition to land and the origin of plants with branched sporophytes (see Chapter 4). The Bryophyta seem to occupy an intermediate position: their origin predates the divergence of the ancestor to the hornworts and vascular plants but evolved from a common ancestor with liverworts (Qiu et al. 2006). The origin of the earliest land plants can be traced back to the Ordovician and maybe the Cambrian (Strother et al. 2004). Although unambiguous fossils of mosses have only been recovered from sediments dating from younger geological periods (Upper Carboniferous), divergence time estimates based on molecular phylogenies suggest that the origin of mosses dates back to the Ordovician (Newton et al. 2007) and thus that their unique evolutionary history spans at least 400 million years.

Introduction

Hornworts are a key lineage in unraveling the early diversification of land plants. An emerging, albeit surprising, consensus based on recent molecular phylogenies is that hornworts are the closest extant relatives of tracheophytes (Qiu et al. 2006). Prior to comprehensive molecular analyses, discrepant hypotheses positioned hornworts as either sister to all embryophytes except liverworts or the closest living relatives of green algae (Mishler et al. 1994, Qiu et al. 1998, Goffinet 2000, Renzaglia & Vaughn 2000). Morphological features are of little value in resolving the placement of hornworts within the green tree of life because this homogeneous group of approximately 150 species exhibits numerous developmental and structural peculiarities not found in any extant or fossil archegoniate. Until recently, hornworts were neglected at every level of study and thus even the diversity and the relationships within this group have remained obscure.

Virtually every aspect of hornwort evolution has been challenged and/or revised since the publication of the first edition of this book (Duff et al. 2004, 2007, Shaw & Renzaglia 2004, Cargill et al. 2005, Renzaglia et al. 2007). Phylogenetic hypotheses based on multigene sequences have revolutionized our concepts of interrelationships. New classification schemes have arisen from these analyses and continue to be fine-tuned as more taxa are sampled. Three new genera have been named, increasing the number of hornwort genera to 14, namely Leiosporoceros, Anthoceros, Sphaerosporoceros, Folioceros, Hattorioceros, Mesoceros, Paraphymatoceros, Notothylas, Phaeoceros, Phymatoceros, Phaeomegaceros, Megaceros, Dendroceros, and Nothoceros (Duff et al. 2007, Stotler et al. 2005).

Introduction

This is the era of whole-genome sequencing; molecular data are becoming available at a rate unanticipated even a few years ago. Sequencing projects in a number of countries have produced a growing number of fully sequenced organellar and nuclear genomes, providing computational biologists with tremendous opportunities, but also major challenges. The sheer amount of data is nearly overwhelming; comparative frameworks are needed. Comparative genomics was initially restricted to pairwise comparisons of genomes based on sequence similarity matching. The importance of taking a multispecies phylogenetic approach to systematically relating larger sets of genomes has only recently been realized.

Something can be learned about the function of genes by examining them in one organism, or by comparisons between two organisms. However, a much richer approach is to compare many organisms at once by using a phylogenetic approach, which lets us take advantage of the burgeoning number of phylogenetic comparative methods. A synthesis of phylogenetic systematics and molecular biology/genomics – two fields once estranged – is beginning to form a new field that could be called “phylogenomics” (Eisen 1998). We need to take advantage of the rich, multispecies approach provided by taking into account the history of life. Repeated, close sister-group comparisons between lineages differing in a critical phenotype (e.g. desiccation- or freezing-tolerance) can allow a quick narrowing of the search for genetic causes in a sort of natural experiment.