Diatoms are being used increasingly in a wide range of applications, and the number of diatomists and their publications continues to increase rapidly. Although several books have dealt with various aspects of diatom biology, ecology, and taxonomy, the first edition of this volume, published over a decade ago, was the first to summarize the many applications and uses of diatoms. However, many new and exciting papers have been published in the intervening years. This, coupled with the fact that research on environmental and earth science applications of diatoms has continued at a frenetic pace, prompted us to undertake a major revision of our first edition.

Our overall goal was to collate a series of review chapters that would cover most of the key applications and uses of diatoms in the environmental and earth sciences. Due to space limitations, we could not include all types of applications, but we hope to have covered the main ones. Moreover, many of the chapters could easily have been double in size, and in fact several chapters could have been expanded to the size of books. Nonetheless, we hope material has been reviewed in sufficient breadth and detail to make this a valuable reference book for a wide spectrum of scientists, managers, and other users.

Marine diatoms as indicators of modern environment change

A substantial part of the ocean's primary productivity is provided by diatoms (Tréguer et al., 1995). In general, they are the dominant primary producers in temperate and cold areas, and are very abundant in the recently upwelled waters of Eastern Boundary Currents and in diverging surface currents where nutrients are brought to the surface (Nelson et al., 1995, and references therein). On an annual basis, the relative contribution of diatoms to primary productivity is highly variable: Nelson et al. (1995) and Tréguer et al. (1995) proposed upper limits of 35% in oligotrophic areas and up to 75% in coastal upwelling areas and other nutrient-rich systems. Regardless of the area, the general trend is for an increase in the relative abundance of diatoms in the phytoplankton together with primary productivity (Ragueneau et al., 2000). As a general statement we may say that diatoms are the dominant primary producers in a number of oceanographic settings that offer both the required high-nutrient and turbulence conditions (e.g. coastal upwelling areas, equatorial divergences, ice-edges, river plumes; Ragueneau et al., 2000). In contrast, small, non-siliceous pico- and nanoplankton are of great importance to total productivity in oligotrophic regions (Tréguer et al., 1995, and references therein).

Introduction

The legal process has used scientific procedures for many years in its various deliberations. Some of these, for instance DNA profiling of body fluids, are now essential and routine practice. The use of diatoms in forensic science is naturally much smaller, but in certain types of investigation, diatom taxonomy and ecology play a significant role. A diatomist may be able to provide investigations with evidence, which will enable the court to reach its verdict, and may be used by either the prosecution or the defence. Below we summarize some of the major applications of diatoms to forensic science.

Drowning

The most frequent application of diatoms in forensic science is in diagnosis of death by drowning. Drowning is a very common accidental cause of death, and thousands die each year in this fashion. The majority of these individuals die in circumstances that are not contentious, where there are witnesses, or strong indications of suicide, such as a note. Where circumstances surrounding an individual's death are less clear, it is often important to be as certain as possible of how death occurred.

Where a body is fresh, the pathologist may have little difficulty in reaching a verdict of drowning. However, the histopathological signs of drowning are often transient and overlaid by the grosser effects of decomposition. Additionally, in cases where an individual has been severely injured before being immersed in water, it is obviously important to determine whether death is due to these injuries or because of drowning.

Coral reef communities as diatom habitats

Coral reefs, well known for their tremendous biodiversity and beauty (Veron, 2000; Spalding et al., 2001), are the most complex ecosystems in the sea, and are often compared to rainforests, both because of the large numbers of organisms (estimates in both cases based on larger organisms and extrapolated wildly to small animals and microorganisms!) and because corals, like rainforest trees, create the structure and habitat for the wealth of other organisms. Coral reefs are formed by a highly successful yet environmentally sensitive symbiotic association between animals (cnidarians; scleractinian corals) and protists (dinoflagellate algae; zooxanthellae in the genus Symbiodinium). The term coral is generally used to denote the holobiont, i.e. both partners in the symbiosis. On a healthy coral reef, macroalgae are generally sparse and coral cover is high, but the balance can be tipped to communities dominated by fleshy algae by nutrient inputs that promote algal growth in the otherwise oligotrophic waters, or by reduction of normally high grazing pressure (Littler & Littler, 1984).

Coral reefs are vital resources for millions of humans in tropical, especially developing countries, who depend on them for fisheries (Cesar, 2000; Sadovy, 2005; Vincent, 2006), tourism income (Brander et al., 2007), storm protection (UNEP-WCMC, 2006), and sometimes structural materials (Berg et al., 1998; Mallik, 1999). Biodiversity of coral reefs is also recognized for its pharmacological potential (Adey, 2000).

Introduction

Water-level changes result from a variety of geological, biological, and/or climatic processes. Many of these changes occur over long periods; others may be rapid or result from catastrophic events. In aquatic environments, diatoms are highly sensitive indicator organisms and their microfossils, deposited in lake sediments, can be used to infer environmental changes (Smol, 2008). Unambiguous diatom signals can be reconstructed from lakes isolated from marine or brackish waters (e.g. Fritz et al., this volume; Horton & Sawai, this volume). However, in freshwater systems lake-level changes are often recorded as increases in planktonic (free-floating) diatoms – although as discussed below, interpretation of this signal should be supported by additional evidence.

In the Laurentian Great Lakes region of North America (e.g. Finkelstein & Davis, 2006; Wolfe et al., 2000; Wolin, 1996) and the North Sea and Baltic regions of Europe (e.g. Digerfeldt, 1998), freshwater lake levels are commonly affected by geological processes of isostatic rebound, subsidence, and outlet incision following glaciation, and lake isolation by coastal-sediment transport (e.g. Karrow & Calkin, 1985; Larsen & Schaetzl, 2001; Lewis et al., 2008).

Biological processes, such as vegetation succession, can alter drainage patterns and groundwater flow, which in turn affect water levels. As vegetation develops following glaciation, surface runoff patterns change and this can moderate water levels on a seasonal or short-term basis. Natural deposition processes of internal (autochthonous) plant and animal remains, and mineral and organic inputs from the catchment (allochthonous) result in a shallower lake over time (Wetzel, 2001).

Introduction

We define ancient lakes as those that contain sedimentary records that span timescales since at least the last interglacial (c. 128 ka before present (BP)). We use this definition because by far the majority of diatom applications and reconstructions are undertaken on lakes that have formed since the end of the last glaciation (Termination 1). Ancient lakes are commonly found within grabens in active rift zones. Important examples include lakes Baikal (Russia), Biwa (Japan), Hövsgöl (Mongolia), Kivu (Democratic Republic of Congo, Rwanda), Malawi (Malawi, Mozambique, Tanzania), Ohrid (Albania and Macedonia) and Prespa (Greece, Albania and Macedonia), Tanganyika (Burundi, Congo, Tanzania), Titicaca (Bolivia, Peru), Tule (USA), and Victoria (Kenya, Tanzania, Uganda). These extant lakes contain sedimentary archives that often span at least the full Quaternary period (c. 2.6 million years (Ma)). Other ancient lakes with significantly long sedimentary archives include those associated with volcanic activity, e.g. Lake Albano (Italy), karst landscapes, e.g. Ioannina (Greece), and meteorite-impact craters such as El'gygytgyn (Russia), Pingualuit (Canada), Bosumtwi (Ghana), and Tswaing (formerly known as the Pretoria Salt Pan) (South Africa).

Diatom records from ancient lakes provide potentially powerful insights into mechanisms of environmental change over glacial–interglacial (G–IG) timescales, with most studies focusing on interpretation of paleoclimate records. However, records from ancient lakes can also provide useful insights into ecology and evolution of diatoms over long timescales (Khursevich et al. 2001).

Introduction

Wetlands comprise about 6% of the Earth's surface, but their ecological importance may be disproportionately higher (Batzer and Sharitz, 2006). Existing at the interface between terrestrial and aquatic landscapes, wetlands can support more species and greater productivity than adjacent communities because they are at the confluence of species pools and resources (Gopal et al., 2000; Wetzel, 2006). They are, therefore, important contributors to global biodiversity and their highly active biological communities modify nutrient and gas concentrations and soil-forming processes at a variety of scales. Organic wetlands (peatlands) store an estimated 450 gigatonnes of carbon (Gt C), equivalent to ∼20% of carbon in the terrestrial biosphere (Gorham, 1991; Maltby and Immirzi, 1993; Roulet, 2000) and almost equivalent to the entire global atmospheric carbon pool (Charman, 2002). The economic value of services that all wetland types provide to humans are reported to be higher than other ecosystems (Costanza et al., 1997) because they can be harvested for food, regulate availability and quality of fresh water, and protect neighboring landscapes from flooding.

Despite their importance, wetlands are being lost at an alarming rate. Almost half of the wetlands in the United States were drained or filled by 1970 (Tiner, 1984) and globally they are amongst the most threatened ecosystems on the planet. Threats come in the form of land loss and habitat degradation resulting from drainage for agricultural purposes, conversion for urban expansion, and flooding to create reservoirs for water storage or power generation.

Introduction

The application of diatoms in paleoenvironmental studies has largely focused on tracking past changes in water chemistry (e.g. nutrients, salinity, pH) and habitat features (e.g. lake ice or macrophytes). When used in conjunction with other paleolimnological proxies, however, diatoms can be used to infer past changes in vertebrate populations or harvests such as fish, birds, and whales. This research is particularly insightful because the fossil record of these vertebrates is fragmented and sparsely distributed. Time series of inferred animal population dynamics also provide the much-needed long-term data required to develop sustainable management plans for these often ecologically sensitive and sometimes commercially harvested taxa (e.g. Selbie et al., 2007).

Many studies that are included in this review are focused on population dynamics of migratory animals. A common thread across these studies is that large densities of migratory animals can introduce substantial nutrient loads to lakes. If the animal population is, at any time, contributing the largest source of nutrients to a study lake, then fluctuations in nutrients can be correlated to the animal's population size. Given that diatom community composition is strongly influenced by nutrient status (see Hall and Smol, this volume), the diatoms are then indirect indicators of animal population dynamics. A second field of study included in this review is focused on changes in non-anadromous fish populations. There have been numerous studies showing that fish kills, fish introductions, or human manipulations of fish community structure can influence primary producers and/or water quality.

Introduction

Atmospheric temperature records from central Greenland and Antarctic ice cores reveal a dramatic shift between the Late Pleistocene and the Holocene in terms of estimates and amplitudes of temperature change. Following recovery of these long, high-resolution ice cores in the early 1990s, initially it was believed that this shift into the Holocene involved a change from low mean temperatures with large, rapid oscillations on decadal to millennial timescales, to high mean temperatures with relatively little variability. More recently, other records from different regions of the world, together with our increased understanding of external climate forcings and feedbacks, have shown that this ice-core-derived picture of Holocene climate stability is not the case (Maslin et al., 2001; Wanner et al., 2008). Holocene climate variability appears to exhibit relatively regular patterns of change. However, these patterns of change are complex; not all changes are observed globally or synchronously (Mayewski et al., 2004). And, although the oscillations in climate during the Holocene are of lower amplitudes than those of the Late Pleistocene, they are of sufficient magnitude to cause significant perturbations to our contemporary climate and to have had an impact on human civilizations.

The primary goal of this chapter is to present a detailed view of the contribution of diatom analysis from marine sedimentary records to our understanding of climatic and environmental change during the Holocene. This chapter will provide a link between other chapters in this book that deal with diatoms as indicators of recent changes in oceanographic condition (Romero and Armand, this volume) and diatoms as indicators of paleoceanographic events (Jordan and Stickley, this volume).

Introduction

Research involving diatom assemblages, both modern and fossil, has expanded enormously in recent decades. Because many of the questions asked in such research are quantitative in character (e.g. what was the lake-water pH at AD 1850, what are the major environmental gradients determining the modern diatom assemblages in a set of lakes on the Isle of Skye), there has been a similar development and application of numerical methods appropriate for the quantitative analysis of diatom assemblage data.

Despite diatom ecology and paleoecology being over 100 years old, the relevant statistical methods for assessing the inherent uncertainties associated with diatom counts were only relatively recently developed (in the context of pollen counting) by Mosimann (1965). The application of multivariate data analytical techniques such as cluster analysis, principal components analysis, and correspondence analysis to diatom assemblage data began in the early 1970s. With the upsurge of interest in the mid 1980s in diatom ecology and paleoecology in response to research on the causes of surface-water acidification in Europe and North America, the development and application of data analytical techniques such as canonical correspondence analysis (ter Braak, 1985, 1986) and weighted-averaging regression and calibration (ter Braak & van Dam, 1989) in diatom research expanded greatly (Birks, 1998). Such techniques are now widely used items in the diatomist's tool-kit (Smol et al., 2011 and chapters in this volume).

Introduction

Assessments of environmental conditions in rivers and streams using diatoms have a long history in which two basic conceptual approaches emerged. First, based on the work of Kolkwitz and Marsson (1908), autecological indices were developed to infer levels of pollution based on the species composition of assemblages and the ecological preferences and tolerances of taxa (e.g. Butcher, 1947; Fjerdingstad, 1950; Zelinka and Marvan, 1961; Lowe 1974; Lange-Bertalot, 1979). Second, Patrick's early monitoring studies (Patrick, 1949; Patrick et al., 1954; Patrick and Strawbridge, 1963) relied primarily on diatom diversity as a general indicator of river health (i.e. ecological integrity), because species composition of assemblages varied seasonally and species diversity varied less. The conceptual differences in these two approaches really address two different goals for environmental assessments, one inferring pollution levels and the other determining biodiversity, a more valued ecological attribute (Stevenson, 2006). Thus, the concepts and tools for assessing ecosystem health and diagnosing causes of impairment in aquatic habitats, particularly rivers and streams, were established and developed between ∼50 and 100 years ago.

Today, diatoms are being used to assess ecological conditions in streams and rivers around the world (Asai, 1996; Kelly et al., 1998; Wu, 1999; Lobo et al., 2004; Wang et al., 2005; Chessman et al., 2007; Taylor et al., 2007; Porter et al., 2008). They have become valuable elements in large-scale national and international assessment programs of the United States and Europe (e.g. Kelly et al. 2009a).

Introduction

The degree to which diatoms move across the Earth by natural processes is debatable (Finlay et al., 2002; Vyverman et al., 2007), but the inadvertent spread of diatoms in a globalized human society is apparent. In this chapter, we examine documentation of diatom introductions and their implications for aquatic ecosystems. For many organisms, especially larger ones, the ecologic, economic, and social impact of species introductions, or invasions, is relatively well known (Pimental et al., 2000). On the other hand, recognition of the microscopic trespasses of diatom species and their impact on ecosystems in new geographic areas is generally far less noticed.

A species is considered to be “non-native” if it is located in a region outside of its native geographic range. Non-native species are also referred to as introduced, non-indigenous, exotic, alien, or invasive. While some non-native species cause little harm, others cause severe ecosystem damage. The use of terminology, particularly the adoption of military words to describe species geographic distributions, elicits emotional reactions that influence scientific and popular responses (Larson et al., 2005). We recognize that much of the current literature employs these military metaphors, but we seek to promote an ecological perspective.

Even among well-known organisms, such as the common reed (Phragmites australis (Cav.) Trin. ex Steud.) growing near Lake Superior, the distinction between native and non-native status may be unclear (Willis and Birks, 2006). The biogeographic distribution of diatoms, and microscopic organisms in general, is currently under debate.

The preceding chapters provide a summary of the major advances (and challenges) related to the application of diatoms to environmental and earth-science issues. A simple comparison between the content and diversity of chapters published in the first edition of this book in 1999 and the current volume should provide considerable satisfaction to practitioners and users of these data. Although many challenges remain, progress has clearly been made on many fronts. Nonetheless, and at the risk of ending the book on a pessimistic note, we re-iterate below some of our concerns about the lack of progress and resources dedicated to some of the more basic and fundamental issues related to diatoms.

In the previous edition of this book, we were so bold as to attempt an assessment of future directions in diatom research applications. It seems appropriate, and perhaps humbling, to assess those prognostications and their implications for future directions. Our (1999) statement that “It is very clear that a good deal of effort needs to be devoted to the formalities of taxonomy and nomenclature, which have been sadly neglected for the past century” remains virtually unchanged today. In fact, our enthusiasm for the “great strides (that) have been made very recently in the alpha level taxonomy of diatoms” has proven to be rather naive. Significant increases in taxonomic resolution have certainly been made, partially through application of objective techniques, such as cladistic analysis and numerical shape analysis, but perhaps more importantly through simple, but more thorough, exploration of a much wider range of regions and habitats.