Environmental Microbiology and Microbial Ecology

Larry L. Barton, Robert J. C. McLean

• Publisher: Wiley-Blackwell
• Year: 2019
• ISBN:
  9781118966280
• Edition: 1
• Topic: Biological Sciences
• Subtopic: Microbiology
• Index: Biological Sciences

An authoritative overview of the ecological activities of microbes in the biosphere

Environmental Microbiology and Microbial Ecology presents a broad overview of microbial activity and microbes' interactions with their environments and communities. Adopting an integrative approach, this text covers both conventional ecological issues as well as cross-disciplinary investigations that combine facets of microbiology, ecology, environmental science and engineering, molecular biology, and biochemistry. Focusing primarily on single-cell forms of prokaryotes — and cellular forms of algae, fungi, and protozoans — this book enables readers to gain insight into the fundamental methodologies for the characterization of microorganisms in the biosphere.

The authors draw from decades of experience to examine the environmental processes mediated by microorganisms and explore the interactions between microorganisms and higher life forms. Highly relevant to modern readers, this book examines topics including the ecology of microorganisms in engineered environments, microbial phylogeny and interactions, microbial processes in relation to environmental pollution, and many more.

Now in its second edition, this book features updated references and major revisions to chapters on assessing microbial communities, community relationships, and their global impact. New content such as effective public communication of research findings and advice on scientific article review equips readers with practical real-world skills.

• Explores the activities of microorganisms in specific environments with case studies and actual research data
• Highlights how prominent microbial biologists address significant microbial ecology issues
• Offers guidance on scientific communication, including scientific presentations and grant preparation
• Includes plentiful illustrations and examples of microbial interactions, community structures, and human-bacterial connections
• Provides chapter summaries, review questions, selected reading lists, a complete glossary, and critical thinking exercises

Environmental Microbiology and Microbial Ecology is an ideal textbook for graduate and advanced undergraduate courses in biology, microbiology, ecology, and environmental science, while also serving as a current and informative reference for microbiologists, cell and molecular biologists, ecologists, and environmental professionals.

1
Introduction to Microorganisms and Their Activities

1.1 Central Themes of Environmental Microbiology and Microbial Ecology

The terms “environmental microbiology” and “microbial ecology” are often used interchangeably but there are some subtle distinctions. Environmental microbiology is the study of processes in the environment mediated by microorganisms whereas microbial ecology addresses the interactions between microorganisms as well as between microorganisms and higher life forms. However, many microorganism interactions are dependent on chemicals from the environment or from other biological systems and so microbial ecology overlaps with environmental microbiology where abiotic chemistry occurs. This first chapter provides an overview of the components involved in environmental microbiology and provides a perspective on the breadth of the microbial relationships in the biosphere. The central themes of this chapter include the following:

• Discussion on the continued use of the terms prokaryote and eukaryote and on the Tree of Life
• Horizontal gene transfer and the role of viruses and gene transfer agents
• Perspective of cell size and cell shape
• Bacterial production of dormant cells

1.2 Are the Terms Prokaryotes or Eukaryotes Relevant?

Traditional microbiology classifies microorganisms into two groups: prokaryotes and eukaryotes. Several structural distinctions may be drawn between these groups of microorganisms and the major differences are listed in Table 1.1. This distinction between prokaryotic and eukaryotic life evolved from a publication by Stanier and van Niel (1962), which proved to be the stimulus to include “blue‐green algae” as cyanobacteria. As stated by Stanier and van Niel, bacterial cells were unlike eukaryotic cells in that they lacked true membranes to localize the cell “nucleus” and bacteria used nuclear division by fission and not mitosis. However, after several decades of microbial phylogeny, the term “prokaryote” has become controversial because the designation of a prokaryote is based on the absence of certain characteristics (Sapp 2005; Pace 2009; Whitman 2009). It has been proposed that bacteria and archaea, unlike eukaryotes, display coupled transcription and translation where translation starts before transcription is finished (Martin and Koonin 2006; French et al. 2007). There is a concern that bacteria and archaea themselves are sufficiently distinct and should not be united into the single group prokaryotes. The contrast between the nuclear organization and the presence of a nuclear membrane in prokaryotic and eukaryotic organisms has become blurred. Bacteria have long been considered to lack nuclear organization; however, in the bacterial phylum Planctomycetes, Gemmata obscuriglobus has a nucleoid enveloped in a membrane that forms a structure analogous to the eukaryotic nucleus (Fuerst 2005). The giant bacterium Epulopiscium fishelsoni has DNA highly condensed into chromosome‐like structures that are physically separated from the cytoplasm (Bresler et al. 1998). In contrast, dinoflagellates, eukaryotic algae, lack histones for the condensation of DNA and lack nucleosomes (Rizzo 2003). Histone proteins are found in mesophilic, thermophilic, and hyperthermophilic archaea and the DNA interactions of archaeal histones is like that found in eukaryotes (Reeve et al. 2004).

Table 1.1 Differences between prokaryotes and eukaryotes.

Prokaryotic cells lack a true nucleus with a nuclear membrane. Prokaryotic cells lack histones to provide condensation of DNA into chromosomes. DNA in prokaryotes is circular whereas DNA in eukaryotes is linear. Prokaryotic cells lack organelles in the cytoplasm and cytoplasmic membranes. Prokaryotic cells lack carbohydrates and sterols in the plasma membrane whereas both are found in eukaryotic cells. In prokaryotic cells, ribosomes are 70S; in eukaryotic cells, ribosomes are 80S with 70S found in organelles. Cell division in prokaryotic cells is by binary fission whereas in eukaryotic cells it is by mitosis. Sexual recombination does not occur in prokaryotic cells except for DNA transfer. Sexual recombination in eukaryotic cells involves meiosis. Prokaryotic cells are 0.2–2.0 μm wide whereas eukaryotic cells are 10–100 μm wide.

1.2.1 Intracellular Membranes in Prokaryotes

Models of some of the intracellular membrane structures found in bacteria are presented in Figure 1.1. Bacteria that obtain energy from methane oxidization often use particulate methane monooxygenase (pMMO). which is localized in the membrane. For the greatest efficiency of methane gas oxidation, multiple membrane structures are present in the cytoplasm and, based on internal membrane structure, methanotrophic bacteria may have either stacked (type I) or paired concentric (type II) cytoplasmic membranes (Davies and Whittenbury 1970). A re...