INTRODUCTION

Both basic and applied science issues drive our interests in the microbiology of the deep terrestrial subsurface. As an environment that is disconnected from the Earth's surface, the deep subsurface is less subject to variations in temperature and light and, in unsaturated zones, to intense gradients across interfaces created at the microscale level. These characteristics dictate an average growth rate that is very slow, up to thousands of years per cell division (Kieft & Brockman, 2001), and an ecosystem where change occurs over very long time scales (Fredrickson & Onstott, 2001). Thus, the subsurface is one of the most extreme environments on Earth, and identifying what limits life in the subsurface has value as a model for life on other planets (Chapelle et al., 2002; Nealson & Cox, 2002). The inadvertent release of contaminants from industrial processing plants and storage tanks, as well as the possibility of permanently depositing nuclear wastes deep below the Earth's surface (Pedersen, 2001), raise questions about how microbial activities might exacerbate or mitigate contamination problems in the subsurface.

The terrestrial subsurface is the habitat for diverse microbial communities that, together with the oceanic subsurface, may be the habitat for the largest proportion of Earth's biomass (Whitman et al., 1998). As subsurfaces are characterized by a range of physical and chemical properties, from fully aerated sedimentary shallow aquifers to deep igneous rocks devoid of oxygen and elevated in temperatures, their microbial communities are equally varied (Fredrickson & Fletcher, 2001).

INTRODUCTION

Methane is an important link within the global carbon cycle and has become a major focus for scientific investigations over the last decades, especially since the discovery of large deposits of methane hydrates in continental margins. The majority of recent methane production is biogenic, i.e. produced either by thermogenic transformation of organic material or by methanogenesis as the final step in fermentation of organic matter carried out by methanogenic archaea in anoxic habitats (Reeburgh, 1996). There are also abiotic sources of methane, e.g. at mid-oceanic ridges, where serpentinization takes place. In marine environments, the bulk of the methane is produced in shelf and upper continental-margin sediments, which receive large amounts of organic matter from deposition (Reeburgh, 1996). As methane builds up, it migrates upwards and may reach the sediment surface. Here, its ebullition and oxidation can lead to the formation of complex geostructures, such as pockmarks or carbonate chimneys and platforms, as well as large-scale topographies, such as mud volcanoes and carbonate mounds (Ivanov et al., 1991; Milkov, 2000). In most of the deeper continental margin and the abyssal plain sediments, methane production is low, as only 1-5 % of the surface primary production reaches the bathyal and abyssal seabed, due to degradation processes in the water column (Gage & Tyler, 1996).

INTRODUCTION

This chapter will consider biogeochemical cycling in the coastal zone. This is defined as that area of estuarine and coastal, relatively shallow water where there is strong benthic-pelagic linkage and exchange between the water column and the underlying sediment. In deeper water this connection becomes increasingly tenuous as the exchange between the euphotic zone and the benthic layer declines. Longhurst et al. (1995) recognized the coastal boundary domain, divided into 22 provinces, as often bounded by a shelf-break front, and included coastal upwelling regions. The coastal zone generally exhibits high rates of primary production compared with the open ocean (Table 1), and there is the greatest impact from inputs from the land to the coastal sea through estuaries. Estuaries and coastal seas are highly heterotrophic systems which are net exporters of CO2 to the atmosphere due to the mineralization and recycling of both autochthonous and allochthonous organic matter (Borges, 2005).

PHYSICO-CHEMICAL DIFFERENCES BETWEEN LATITUDINAL REGIONS

The physical-biological interactions that influence marine phytoplankton production have been reviewed by Daly & Smith (1993). Because of the spherical shape of the Earth, more solar energy falls per unit area of surface in equatorial regions than at the poles (Fig. 1a), and the incidence of light at the equator is vertical to the surface, but oblique at the poles. Furthermore, the distance radiation travels through the atmosphere is longer at the poles, thus reducing the irradiation incident at the poles compared with equatorial regions.

INTRODUCTION

Although it has been known for over a century that micro-organisms have the potential to reduce metals, more recent observations showing that a diversity of specialist bacteria and archaea can use such activities to conserve energy for growth under anaerobic conditions have opened up new and fascinating areas of research with potentially exciting practical applications (Lloyd, 2003). Micro-organisms have also evolved metal-resistance processes that often incorporate changes in the oxidation state of toxic metals. Several such resistance mechanisms, which do not support anaerobic growth, have been studied in detail by using the tools of molecular biology. Three obvious examples include resistance to Hg(II), As(V) and Ag(II) (Bruins et al., 2000). The molecular bases of respiratory metal-reduction processes have not, however, been studied in such fine detail, although rapid advances are expected in this area with the imminent availability of complete genome sequences for key metal-reducing bacteria, in combination with genomic, proteomic and metabolomic tools. This research is being driven forward both by the need to understand the fundamental basis of a range of biogeochemical cycles, and also by the possibility of harnessing such activities for a range of biotechnological applications. These include the bioremediation of metal-contaminated land and water (Lloyd & Lovley, 2001), the oxidation of xenobiotics under anaerobic conditions (Lovley & Anderson, 2000), metal recovery in combination with the formation of novel biocatalysts (Yong et al., 2002a) and even the generation of electricity from sediments (Bond et al., 2002).

INTRODUCTION

Whilst chemolithoautotrophic micro-organisms are found in nearly every environment on Earth, they are more abundant in dark habitats where competition by photosynthetic organisms is eliminated. Caves, particularly, represent dark but accessible subsurface habitats where the importance of microbial chemolithoautotrophy to biogeochemical and geological processes can be examined directly. At Lower Kane Cave, WY, USA, hydrogen sulfide-rich springs provide a rich energy source for chemolithoautotrophic micro-organisms, supporting a surprisingly complex consortium of micro-organisms, dominated by sulfur-oxidizing bacteria. Several evolutionary lineages within the class ‘Epsilonproteobacteria’ dominate the biovolume of subaqueous microbial mats, and these microbes support the cave ecosystem through chemolithoautotrophic carbon fixation. The anaerobic interior of the cave microbial mats is a habitat for anaerobic metabolic guilds, dominated by sulfate-reducing and -fermenting bacteria. Biological controls of speleogenesis had not been considered previously and it was found that cycling of carbon and sulfur through the different microbial groups directly affects sulfuric acid speleogenesis and accelerates limestone dissolution. This new recognition of the contribution of microbial processes to geological processes provides a better understanding of the causal factors for porosity development in sulfidic groundwater systems.

Karst landscapes form where soluble carbonate rocks dissolve by chemical solution (karstification), resulting in numerous geomorphic features, including caves and subterranean-conduit drainage systems (e.g. White, 1988; Ford & Williams, 1989). This has traditionally been viewed as an abiotic, chemical process that occurs near the water table, with biologically produced CO2 as the principal reactive component.

INTRODUCTION

This chapter is intended to provide a brief overview of the key concepts underlying the emerging area of environmental microbial metal geochemistry, rather than an exhaustive synthesis. The reader is referred to the following more comprehensive reviews on the biogeochemistry of metals (Warren & Haack, 2001), metal-mineral reactions (Brown & Parks, 2001), emerging molecular-level geochemical techniques (O'Day, 1999; Brown & Sturchio, 2002) and a recent synthesis of how genetic expression in the environment can underpin geochemical reactions (Croal et al., 2004). The relevance of micro-organisms to metal behaviour arises from the overlap of the biosphere with the geosphere and the transformations that occur because of their interactions. Microorganisms have evolved in intimate association with the rocks, soils and waters (i.e. geosphere) in which they find themselves. In order to grow and survive, they have adapted to these environments and use the inorganic components to drive their metabolic machinery; the myriad functional pathways by which they do so ensure that they influence a number of key elemental cycles in the process. As a consequence, many important geochemical processes are ultimately shaped by life, rather than strict geochemical equilibria, a fact that is increasingly recognized as strict geochemical principles fail to constrain observed environmental behaviour.

Trace-metal behaviour in the environment is of increasing global concern as water and soil contamination with these toxic substances continues and the detrimental effects on ecosystems and human health emerge.

INTRODUCTION

Primary productivity in the ocean amounts to the net assimilation of CO2 equivalent to about 50 Pg (petagram, i.e. 1015 g) C year–1, while on land this is approximately 60 Pg C year-1 (Field et al., 1998). Almost all of this primary productivity involves photosynthesis, and in the ocean it occurs only in the top few hundred metres, even in waters with the smallest light attenuation (Falkowski & Raven, 1997). About 1 Pg C of marine primary productivity involves benthic organisms, i.e. those growing on the substratum (Field et al., 1998), in the very small fraction of the ocean which is close enough to the surface to permit adequate photosynthetically active radiation (PAR) to allow photolithotrophic growth. This depth at which photosynthetic growth is just possible varies in time and space, and defines the bottom of the euphotic zone (Falkowski & Raven, 1997). The remaining ∼49 Pg C is assimilated by phytoplankton in the water column (Field et al., 1998). This chapter will concentrate on the planktonic realm, while acknowledging the importance of marine benthic primary producers and their interactions with micro-organisms (e.g. Dudley et al., 2001; Raven et al., 2002; Raven & Taylor, 2003; Cooke et al., 2004; Walker et al., 2004).

The global net primary productivity of the oceans is less than that on land, despite about 70 % of the Earth being covered in ocean and primary productivity over considerable areas of land being limited by water supply.

INTRODUCTION

A fungal component of the marine biota was only recognized as recently as 1944 (Barghoorn & Linder, 1944), and it was not until the 1960s that studies commenced to assess the extent and diversity of fungi in marine systems. Since this time, considerable effort has been exerted to uncover marine fungal diversity, with high decadal discovery indices in the 1970s and 80s (Hawksworth, 1991), resulting in around 1000 fungal species known today from marine environments. Nevertheless, it is hardly surprising that, with the extent of marine environments globally, we probably have a very incomplete view of fungal diversity, together with their frequency and function in these ecosystems. The objective of this review is to assess the extent of our present knowledge and to highlight future directions to further elucidate their biology and ecology.

THE NATURE OF MARINE ENVIRONMENTS

Marine ecosystems are globally extensive, and account for around 70 % of global surface area. They can be defined generally as aquatic systems influenced by substantial concentrations of salts, particularly sodium chloride, from existing oceanic systems. Seas and oceans divide between regions bordering and influenced by terrestrial regions and the open ocean, which is strongly zoned through the water column. These broad boundaries are illustrated in Fig. 1, which also details linkages between marine compartments.

INTRODUCTION

The most important perceived environmental roles of fungi are as decomposer organisms, plant pathogens and symbionts (mycorrhizas, lichens), and in the maintenance of soil structure through their filamentous growth habit and production of exopolymers. However, a broader appreciation of fungi as agents of biogeochemical change is lacking and, apart from obvious connections with the carbon cycle, they are frequently neglected within broader microbiological and geochemical research contexts. While the profound geochemical activities of bacteria and archaea receive considerable attention, especially in relation to carbon-limited and/or anaerobic environments (see elsewhere in this volume), in aerobic environments fungi are of great importance, especially when considering rock surfaces, soil and the plant root-soil interface (Gadd, 2005a). For example, mycorrhizal fungi are associated with ∼ 80 % of plant species and are involved in major mineral transformations and redistributions of inorganic nutrients, e.g. essential metals and phosphate, as well as carbon flow. Free-living fungi have major roles in the decomposition of plant and other organic materials, including xenobiotics, as well as mineral solubilization (Gadd, 2004). Lichens (a symbiosis between an alga or cyanobacterium and a fungus) are one of the commonest members of the microbial consortia inhabiting exposed subaerial rock substrates, and play fundamental roles in early stages of rock colonization and mineral soil formation.

INTRODUCTION

The contribution of micro-organisms to amorphous silica precipitation in modern geothermal hot-spring environments has been the topic of intense study in the last three to four decades. Here, we present a review on the field and laboratory studies that have specifically addressed bacterial silicification, with a special focus on cyanobacterial silicification. Studies related to the biogenic silicification processes in diatoms, radiolarians and sponges are not discussed, despite the fact that, in the modern oceans (which are undersaturated with respect to silica), the diagenetic ‘ripening’ of such biogenic silica controls the global silica cycle (Dixit et al., 2001). It is well-known that the amorphous silica in these organisms (particularly in size, shape and orientation) is controlled primarily by the templating functions of glycoproteins and polypeptides (e.g. silaffin and silicatein). For information on these issues, we refer the reader to the extensive reviews by Simpson & Volcani (1981), Kröger et al. (1997, 2000), Baeuerlein (2000), Perry & Keeling-Tucker (2000), Hildebrand & Wetherbee (2003) and Perry (2003). In addition, in terrestrial environments, a large pool of amorphous silica is cycled through higher plants (grasses and trees) that are believed to use silicification as a protection mechanism against pathogens and insects. Information on these processes can be found in the papers by Chen & Lewin (1969), Sangster & Hodson (1986) and Perry & Fraser (1991).

INTRODUCTION

Metabolic diversity is used here as a physiological or ecological concept referring to the metabolic repertoire available to any group of organisms: in this case, microbes. At least for now, metabolic diversity is conceptually distinct from genetic diversity, although one imagines that, as both concepts are understood in greater depth, the relationships between them will become clear. The metabolic repertoire encompasses, for the most part, the entire range of redox-related energy sources that are available on our planet, from photochemistry to organic and inorganic redox chemistry. Earthly microbes have ‘learned’ to harvest the energy of nearly every useful and abundant redox couple, revealing a nutritional versatility that to some extent could be used to describe what the planet has to offer energetically. To turn this around, one can imagine that, if energy sources were defined for Earth, one might well predict what kinds of metabolism should have evolved to exploit them and, in fact, for the most part, this would lead to the correct answer. Metabolic diversity is further accentuated by various symbioses, syntrophisms and community interactions (intracellular, intercellular and interpopulation), leading to the establishment of communities with seemingly new and unexpected abilities. The functional diversity of the prokaryotic world is thus expressed in terms of its redox chemistry and, with regard to geobiology, this redox chemistry/metabolic connection defines a wide variety of relevant reactions, many of which involve phase changes of the interacting molecules (i.e. between solid, liquid and gas phase).

The science of the environment encompasses a huge number of biological, chemical and physical disciplines. For several years, scientists have been interested in large-scale environmental processes/phenomena, such as soil formation, global warming and global elemental cycling. Until recently, the role and impact of micro-organisms on these ‘global’ environmental processes has been largely ignored or, at best, underestimated. However, there is growing awareness that important environmental transformations are catalysed, mediated and influenced by micro-organisms, and such knowledge is having an increasing influence on disciplines other than microbiology, such as geology and mineralogy. Geomicrobiology can be defined as the study of the role that microbes have played and are playing in processes of fundamental importance to geology. As such, it is a truly interdisciplinary subject area, necessitating input from physical, chemical and biological sciences, in particular combining the fields of environmental and molecular microbiology together with significant areas of mineralogy, geochemistry and hydrology. As a result, geomicrobiology is probably the most rapidly growing area of microbiology at present. It is timely that this topic should be the subject of a Plenary Symposium volume of the Society for General Microbiology (SGM) to emphasize and define this important area of microbiological interest, and help to promote exciting collaborations between microbiologists and other environmental and Earth scientists.

INTRODUCTION

Exploration of the microbial world started slowly about 350 years ago, when van Leeuwenhoek and his contemporaries first focused their microscopes on extremely small living things. It is only during the last 20 years, however, that exploration of the world of intraterrestrial microbes has gathered momentum. Previously, it had generally been assumed that persistent life could not exist deep underground, out of reach of the sun and a photosynthetic ecosystem base. In the mid-1980s, scientists started to drill deep holes, from hundreds to a thousand metres deep, in both hard and sedimentary bedrock, and up came microbes in numbers equivalent to those found in many surface ecosystems. The world of intraterrestrial microbes had been discovered.

Intraterrestrial ecosystems have been reviewed elsewhere and the content of those reports need not be repeated here (Ghiorse & Wilson, 1988; Pedersen, 1993a, 2000; Bachofen, 1997; Bachofen et al., 1998; Fredrickson & Fletcher, 2001; Amend & Teske, 2005). Instead, this chapter will focus on characteristics that distinguish the intraterrestrial from the terrestrial world.

Most ecosystem environments have specific, distinguishing characteristics. The environments of intraterrestrial microbial ecosystems occupy a special position, differing substantially in many respects from those of most surface-based ecosystems. In many ways, underground ecosystems must be approached quite differently from the way in which those on the surface would be approached.

INTRODUCTION

Prokaryotes are the Earth's smallest life form and, yet, have the largest surface area : volume ratio of all cells (Beveridge, 1988, 1989a). They are also the most ancient form of life and have persisted on Earth for at least 3.6 × 109 years, even in some of the most extreme environments imaginable, such as the deep subsurface. Most of these early primitive (and today's modern) natural environments possess reasonably high amounts of metal ions that are capable of precipitation under suitable pH or redox conditions. Deep-seated in such geochemical situations is the likelihood of suitable interfaces that lower the local free energy, so that interfacial metal precipitation is promoted. Bacteria, being minute and having highly reactive surfaces (interfaces), are exquisitely efficient environmental particles for metal-ion adsorption and mineral nucleation. Metal ions interact with available reactive groups (or ligands) on the bacterial surface and precipitates grow as environmental counter-ions interact with more and more metal at the site (Beveridge & Murray, 1976, 1980; Beveridge et al., 1982; Ferris & Beveridge, 1986; Fortin et al., 1998). Once formed, these precipitates are under the influence of natural geochemical and additional microbially mediated conditions (Lee & Beveridge, 2001) that instigate the development of fine-grain minerals, usually via dehydration, so that crystalline phases are eventually developed (Beveridge et al., 1983). These minerals commence as so-called ‘nano-mineral phases’ and grow with time to become larger and larger.

MINERALS, MATS, PEARLS AND VEILS: A PANOPLY OF GIANT SULFUR BACTERIA

The biogeochemical cycling of sulfur has been at the heart of microbial ecology since the mid-19th century. This is due, at least in part, to the striking forms of many of the organisms involved in the transformation of reduced sulfur species. Giant sulfur bacteria were among the earliest micro-organisms to capture the interest of microbiologists exploring the links between geochemical cycling of the elements and the microbiota responsible. Consequently, giant sulfur bacteria were among the first bacteria described. Organisms resembling Beggiatoa (‘ Oscillatoria alba’) were described as early as 1803 (Vaucher, 1803), but were included in the genus Beggiatoa some time later (Trevisan, 1842). Thiothrix (Rabenhorst, 1865; Winogradsky, 1888), Achromatium (Schewiakoff, 1893) and Thioploca (Lauterborn, 1907) were all described by the early 20th century and Winogradsky (1887, 1888) had already formulated the principles of lithotrophic growth based on sulfide oxidation, from his work on Beggiatoa species. Surprisingly for such conspicuous organisms, novel giant sulfur bacteria are still being described (Guerrero et al., 1999; Schulz et al., 1999).

Achromatium

Bacteria of the genus Achromatium are remarkable. Cells of up to 125 μm in length have been reported (Babenzien et al., 2005; Head et al., 2000a) and, in addition to characteristic sulfur globules that become visible on treatment of the cells with dilute acid, their large oval cells are typically filled with enormous inclusions of calcium carbonate (Fig. 1).

INTRODUCTION

In 1903, the explorer Robert Scott was one of the first humans ever to see the dry valleys of Antarctica. He called them ‘valley(s) of the dead’ in which ‘we have seen no sign of life, … not even a moss or lichen’. A century later, we know that the soils and rocks are home to many microscopic organisms that Scott could not have seen.

The dry valleys are part of the small percentage of the land surface of the Antarctic continent that is ice-free, amounting to about 4000 km2, and thus have rock and soil surfaces that can be colonized by terrestrial organisms. They are an ancient polar desert, perhaps as much as 2 million years old, located in Victoria Land between about 77 and 79° south (Fig. 1). The valleys are in a precipitation shadow caused by the Transantarctic Mountains, which rise over 4000 m. The Antarctic dry valleys are now recognized as one of the harshest terrestrial environments on Earth, characterized by summer maximum temperatures that rarely exceed 0 °C and only a few tens of millimetres of precipitation, most of which falls as snow and is ablated by strong winds carrying dry air from the polar plateau - potential evaporation far exceeds precipitation (Fig. 1).