Marine Microbiology

Ecology & Applications

Colin Munn, Colin B. Munn

• Publisher: CRC Press
• Year: 2019
• ISBN:
  9780429590429
• Edition: 3
• Topic: Scienze biologiche
• Subtopic: Biologia cellulare

The third edition of this bestselling text has been rigorously updated to reflect major new discoveries and concepts since 2011, especially progress due to extensive application of high-throughput sequencing, single cell genomics and analysis of large datasets. Significant advances in understanding the diversity and evolution of bacteria, archaea, fungi, protists, and viruses are discussed and their importance in marine processes is explored in detail.

Now in full colour throughout, all chapters have been significantly expanded, with many new diagrams, illustrations and boxes to aid students' interest and understanding. Novel pedagogy is designed to encourage students to explore current high-profile research topics. Examples include the impacts of rising CO2 levels on microbial community structure and ocean processes, interactions of microbes with plastic pollution, symbiotic interactions, and emerging diseases of marine life.

This is the only textbook addressing such a broad range of topics in the specific area of marine microbiology, now a core topic within broader Marine Science degrees. A Companion Website provides additional online resources for instructors and students, including a summary of key concepts and terminology for each chapter, links to further resources, and flashcards to aid self-assessment.

Chapter 1

Microbes in the Marine Environment

Viewed from space, it is clear why our planet would be better named “Ocean” than “Earth.” More than 70% of the planet’s surface is covered by interconnected bodies of water. Life originated in the oceans about 3.5 billion years ago and microbes were the only form of life for two-thirds of the planet’s existence. The development and maintenance of all other forms of life depend absolutely on the past and present activities of marine microbes. Yet the vast majority of humans—including many marine scientists—live their lives completely unaware of the diversity and importance of marine microbes. Such understanding is vital, as we now live in a period of rapid global change. This chapter introduces the scope of marine microbiology, the different types of marine microbe (viruses, bacteria, archaea, fungi, and protists), and their place in the living world. The activities of microbes in the many diverse habitats found in the marine environment are introduced to provide the background for more detailed consideration in later chapters.

Key Concepts

• Modern methods have led to new ideas about the diversity and evolution of microbial life.
• Marine microbes are highly diverse and exist in huge numbers, forming a major component of biomass on Earth.
• The most abundant marine microbes are exceptionally small.
• The oceans provide diverse specialized habitats, in which physical and chemical conditions determine microbial activities.
• Planktonic microbes are responsible for primary productivity and recycling of organic compounds in a continuum of dissolved and particulate matter.
• Microbes are important in the formation and fate of sediments and there is abundant life below the seafloor.
• Microbes colonize the surfaces of inanimate objects and other living organisms by the formation of biofilms and microbial mats.

ORIGINS AND SCOPE OF MARINE MICROBIOLOGY

Marine microbiology has developed into one of the most important areas of modern science

Ever since a detailed study of the microbial world began in the late nineteenth century, scientists have asked questions about the diversity of microbial life in the sea, its role in ocean processes, its interactions with other marine life, and its importance to humans. However, despite excellent work by pioneering scientists, progress in understanding accumulated gradually and some aspects were poorly understood until recently. However, toward the end of the twentieth century, several factors conspired to propel marine microbiology to the forefront of “mainstream” science. The involvement of more investigators and the subsequent application of new technology mean that it is now one of the most exciting and fast-moving areas of investigation. Today, our subject is characterized by multidisciplinary investigations and widespread application of powerful new tools in molecular biology, information technology, remote sensing, and deep-sea exploration, leading to astonishing discoveries of the abundance, diversity, and interactions of marine microbial life and its role in global ecology. These continuing new discoveries necessitate radical rethinking of our understanding of ocean processes. We now realize the vital role that marine microbes play in the maintenance of our planet, a fact that will have great bearing on our ability to respond to problems such as the increase in human population, overexploitation of fisheries, climate change, ocean acidification, and marine pollution. Studies of the interactions of marine microbes with other organisms are providing intriguing insights into the phenomena of food webs, symbiosis, pathogenicity, and the important role microbiomes play in metazoan biology. Since some marine microbes produce disease or damage, we need to study these processes and develop ways to control them. Finally, marine microbes have beneficial properties such as the manufacture of new drugs and materials, and the development of new processes in the growing field of marine biotechnology. This chapter sets the scene for the discussion of all these topics in this book.

Microbes include microscopic cellular organisms and non-cellular viruses

Defining the terms “microbiology” and “microorganism” is surprisingly difficult! Microbiology is the study of very small organisms that are too small to be seen clearly with the naked eye (i.e. less than about 1 mm diameter), but most microbiologists are concerned with the activities or molecular properties of microbial communities rather than viewing individual cells with a microscope. The term “microorganism” simply refers to a form of life that falls within the microscopic size range, but there is a huge spectrum of diversity concealed by this all-encompassing term. Indeed, some “microorganisms” are large enough to see without using a microscope, so this is not entirely satisfactory either. Some scientists would argue that the distinguishing features of microorganisms are small size, unicellular organization, and osmotrophy (feeding by absorption of nutrients). The osmotrophic characteristic is important because diffusion processes are a major limitation to cell size, as discussed in the next section. However, this characteristic would exclude many microscopic unicellular eukaryotes, many of which feed by phagotrophy (engulfment of particles). For many years, these microorganisms were studied by specialists who had a traditional background in botany or zoology and classified into “plant-like” (algae) or “animal-like” (protozoa) groups. However, many of these organisms are mixotrophic and can switch from photosynthesis to phagotrophic feeding, so the “plant” or “animal” similarity is meaningless. This loose grouping of organisms is therefore called “protists,” a diverse category encompassing most of the diversity within the domain Eukarya. Depending on their size (see below), they may also be referred to as microeukaryotes or picoeukaryotes. The study of marine protists and recognition that they are microbes with a major role in ocean processes has lagged behind the study of bacteria until recently. Where do viruses fit? Viruses are obviously microscopic, so I consider them to be microbes. However, they are not cellular, so cannot be described as microorganisms and many would argue that they are not living (this question is explored in depth in Chapter 7). In summary, in this book I use the term “microbe” as a generic descriptor for microscopic cellular organisms including bacteria, archaea, fungi, and protists, together with the non-cellular viruses.

TINY MICROBES…HUGE NUMBERS

Whitman et al. (1998) estimated the total number of bacterial and archaeal cells in the oceans to be about 10²⁹. This figure was confirmed by Bar-On et al. (2018) in a recent recalculation based on analysis of many new datasets; they also estimated the biomass of marine bacteria and archaea at 1.3 and 0.3 gigatons (Gt) of carbon, respectively. Suttle (2005) calculated the number of viruses to be about 10³⁰—again, this was confirmed by Bar-On et al. (2018). This is an unimaginably huge number—1 million, million, million, million, million. If all the marine virus particles were placed end to end, they would span about 10 million light years (100 times the distance across our own galaxy).

Marine microorganisms are found in all three domains of cellular life

Biologists usually rely on the study of morphology and physiological properties to classify living organisms, but these characteristics have always proved frustratingly unhelpful when dealing with microbes. Modern methods of classification group organisms by attempting to determine the evolutionary relationships. Such phylogenetic systems of classification depend on comparisons of the genetic information contained in their macromolecules, especially nucleic acids and proteins. If two organisms are very closely related, we expect the sequence of the individual units (nucleotides or amino acids) in a macromolecule to be more similar than they would be in two unrelated organisms. In the 1970s, Carl Woese and colleagues pioneered the use of ribosomal RNA (rRNA) sequencing in order to develop a better view of microbial diversity. Our view of the living world has since been revolutionized by advances in this approach, made possible because of the parallel advances in molecular biological techniques and computer processing of the large amounts of information generated. Because the secondary structure of rRNA is so important in the ribosome and the vital cell function of protein synthesis, base sequence changes in the rRNA molecule occur quite slowly in evolution. In fact, some parts of rRNA are highly conserved and sequence comparisons can be used to ascertain the similarity of organisms on a broad basis. The methods and applications of this major technique are described in Chapter 2.

In 1990, Woese identified three distinct lineages of cellular life, referred to as the domains Archaea, Bacteria, and Eukarya. A phylogenetic “tree of life” based on rRNA sequences envisaged divergence of these three domains from an original “universal ancestor” (Figure 1.1A). A phylogenetic approach to classification is now widely accepted, although some biologists prefer other systems. Microbiologists like it because we can say that we study two entire domains of life and a significant proportion of the third! Traditionally, members of the domains Bacteria and Archaea have been grouped together as “the prokaryotes,” because they share a simple internal cellular structure without a nucleus. However, the most important consequence of the three-domain tree of life is that we now realize that the Bacteria and Archaea are completely different phylogenetic groups. Archaea are not a peculiar, specialized group of bacteria as originally thought (for many years they were called the archaebacteria) but are in fact a completely separate group that actually has closer phylogenetic relationships to the Eukarya than to the Bacteria. This concept has proved to be very influential in shaping our thinking about the evolution of organisms. As new methods and knowledge about genomes has developed, the simple three-domain tree has changed, as illustrated in Figures 1.1B and 1.1C. These developments are discussed in detail in Chapters 4 and 5.

Figure 1.1 Representations of the three domains of life. A. Simple tree based on early interpretation of ribosomal RNA sequencing. In this model, the root of the tree is envisaged as a hypothetical universal ancestor from which all life evolved. B. A three-domain tree based on evidence of extensive lateral gene transfer, revealed by studies of other genes. (Drawn before discovery of other archaeal branches; see Box 5.1). C. An artistic representation of major divisions of the tree of life by Hug et al. (2016). The numerous known groups of the Bacteria are shown on the left, with the large group of currently uncultivable Bacteria termed the Candidate Phyla Radiation at upper right. The Archaea are shown at the left of the lower branch, with the Eukarya at the lower right. (See Figure 4.1 for an updated detailed version of the tree). Credits: B. Gary J. Olsen, University of Illinois, based on concept of W. Ford Doolittle. C. Zosia Rostomian, Berkeley Lab.

The members of the Eukarya domain are the protists, fungi, plants, and animals. Their cells are distinguished by a membrane-bound nucleus and organelles with specific functions. Mitochondria occur in all eukaryotic cells, with the exception of a few anaero...