Understanding Microbially Active Biogeochemical Environments

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Publisher Summary

Microbial life accounts for the vast majority of all metabolic and genetic diversity on Earth, and encompasses an overwhelming majority of the Earth's total biomass. Microorganisms survive in almost all environments where it is thermodynamically favorable for them to do so, and niches once considered to be uninhabitable (for example, hot and cold deserts, hot springs, hypersaline environments, and deep subsurface) are now known to harbor thriving microbial communities. Although knowledge of microbial diversity in geologic systems is evolving, and methods to study diversity are improving, there is still little understanding of the complexity of global geomicrobiological processes or the relationship between biodiversity and biogeochemical function. Perhaps the greatest challenge facing geomicrobiology is linking phylogeny with function, as the most widespread molecular methods, which are based on ribosomal gene analysis, provide extensive information about the taxa present in an environment, however little insight into the functional role of each phylogenetic group. This chapter is intended to give an overview of the latest findings in the field of geomicrobiology and to provide a discussion on the influence of microbial populations and activities on geologic habitats.

Introduction

Microbial life accounts for the vast majority of all metabolic and genetic diversity on Earth, and encompasses an overwhelming majority of the Earth's total biomass. Microorganisms survive in almost all environments where it is thermodynamically favorable for them to do so, and niches once considered to be uninhabitable (e.g., hot and cold deserts, hot springs, hypersaline environments, and deep subsurface) are now known to harbor thriving microbial communities (Edwards 2000, Nercessian 2003, Schippers 2005, Smith 2006). Within this wide range of habitats, all major groups of microorganisms are represented, including cyanobacteria, bacteria, archaea, microalgae, and fungi, demonstrating the abundance of diversity in the microbial world. Bacteria and archaea, in particular, have been able to adapt to prevailing energy (light or chemical) and nutritional (organic carbon or CO2) sources, and within this variable energy–nutrition regime they have exploited distinct energy‐producing pathways, for example respiration, using a variety of terminal electron acceptors (such as O2, NO3,SO42, Fe3+). The importance and extent of microbial diversity and metabolism have now captured the attention of the scientific community and as a consequence there is now more interest in assessing biogeochemical ecosystems than at any time in the past.

Until comparatively recently, culture‐based bias had been reflected within reported microbial biodiversity due to the small proportion of microbes from natural environments that are culturable. However, the advent of molecular biology has launched a new era in environmental biogeochemistry, enabling a new evaluation of the diversity and importance of geomicrobiological activities such as global elemental and nutrient cycling (Pace 1985, Woese 1990). Molecular techniques are valuable tools that can improve our understanding of the structure and nature of microbial communities and provide us with the ability to probe for life in all niches of the biosphere. Rapid progress in genomics has resulted in novel innovations in DNA sequencing capabilities, technologies to monitor gene activities, and statistical and mathematical approaches for analyzing genetic data.

Although knowledge of microbial diversity in geologic systems is evolving, and methods to study diversity are improving, there is still little understanding of the complexity of global geomicrobiological processes or the relationship between biodiversity and biogeochemical function. Perhaps the greatest challenge facing geomicrobiology is linking phylogeny with function, as the most widespread molecular methods, which are based on ribosomal gene analysis, provide extensive information about the taxa present in an environment, but little insight into the functional role of each phylogenetic group. This chapter is intended to give an overview of the latest findings in the field of geomicrobiology and to provide a discussion on the influence of microbial populations and activities on geologic habitats.

Section snippets

An Introduction to the Molecular Microbial World

The three‐domain biological classification system (Fig. 4.1) was introduced by Carl Woese in 1990 (Woese et al., 1990). Based on rRNA sequence data, Woese identified 12 major divisions (phyla) in the domain Bacteria, representing almost all major cultured groups of bacteria accumulated during a century of microbiological research. In the years following this breakthrough, culture‐independent surveys have identified at least 40 major well‐resolved bacterial divisions, indicating that there are

Microorganisms in the Environment

Concomitant with advances in understanding genetic diversity, there has been a growth in the appreciation of prokaryotic diversity at the metabolic level. This diversity clearly defines the prokaryotes as a distinct group from the eukaryotes, and illustrates the strong relationship between prokaryotes and the biogeochemistry of the environment in which they live (Table 4.1). There is a remarkable metabolic diversity that characterizes the prokaryotic world; the ability to utilize inorganic

Extreme Environments

Extremophiles are organisms that thrive in environments that lie significantly outside the set of predefined regular conditions (e.g., a temperature significantly above or below 37°C). They are classified further according to the environmental niche required for optimal growth. Extreme environments are often easy to recognize because of the steep geochemical gradients that generally occur at their boundaries. Some examples of extreme environments include low‐temperature ice cores (Price, 2000),

The Origin of Life on Earth, and Beyond

In this chapter we have outlined the existence of microbial life in a wide range of extreme environments, ranging from the deep surface, nuclear reactors, hydrothermal vents and springs, AMDs and rivers (such as the Rio Tinto in Spain), areas of high heavy metal concentrations, and polar ice. Understanding the biology of extremophiles will also permit the development of hypotheses regarding the conditions required for the origination and early diversification of life on Earth, and potential

Conclusions

Microorganisms have played a major role in shaping the biological, climatic, geologic, and geochemical evolution of the Earth. Despite the obvious importance of microorganisms to evolution and function of life on Earth, a great deal still remains unknown about how microorganisms interact with each other and with their environment to generate and maintain their vast diversity of species and function. In the past 20 years, however, the application of genomics tools has revolutionized microbial

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