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Powerful new tools, especially in molecular biology, remote sending and deep-sea exploration, have led to astonishing discoveries of the abundance and diversity of marine microbial life and its role in global ecology. New tools and an increased interest in ecological factors have caused an upsurge of interest in this field of study. Initial studies were based on the protein-sequencing methods that were then available and progress was slow. However, in the s Carl Woese and colleagues pioneered the use of ribosomal RNA rRNA sequencing in order to develop a better view of prokaryotic 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. Ribosomes are composed of two subunits that can be separated by high-speed centrifugation.
Based on the sedimentation rates, a prokaryotic ribosome is termed 70S and is composed of 50S and 30S subunits. The eukaryotic ribosome is 80S overall, with 60S and 40S subunits see Figure 2. For various reasons discussed in Section 2.
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 SSU 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 Section 2. The domains Bacteria and Archaea have a prokaryotic cell structure, whilst the domain Eukarya has the more complex eukaryotic cell structure.
From this hypothetical ancestor, it appears that life developed in two main directions. One division evolved into the Bacteria, whilst the other division split again, with one subdivision forming the Archaea and the other forming the Eukarya. The three- domain system of classification is now almost universally adopted by micro biologists.
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Apart from our preference for a phylogenetic system, it allows microbiologists to say that we study two entire domains of life, and a significant proportion of the third! The most important consequence of the three-domain tree of life is that we now realize that the Archaea are not a peculiar, specialized group of bacteria as originally thought for many years they were called the archaebacteria , but are in fact closer phylogenetically to the Eukarya than they are to the Bacteria.
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The Bacteria and Archaea are completely different groups, each with their own evolutionary history. The root of the tree is the hypothetical universal ancestor that evolved from precellular life progenotes. This simplified representation does not take account of extensive lateral gene transfer between the domains.
Table 1. Following the discovery of the phylogenetic relationships of the three domains, Wolfram Zillig has suggested that the original eukaryotic cell evolved through a fusion event between a cell of a pre-Bacteria type and a pre-Archaea type. As shown in Table 1. According to the Margulis hypothesis, subsequent symbiotic events led to the evolution of the chloroplast perhaps from a cyanobacterial ancestor and mitochondria perhaps from a protobacterial ancestor.
In modern marine systems, there is much evidence to support this hypothesis. The processes of endosymbiosis, retention of organelles by phagotrophs and mixotrophy are very common in marine protists Section An important factor, which confounds our understanding of evolution, is the increasing recognition of horizontal lateral gene transfer. As our knowledge of genomes increases, we find increasing evidence of extensive gene transfer within, and between, domains.
Bacteria and Archaea contain genes with very similar sequences, and Eukarya contain genes from both prokaryotic domains. Some bacteria have even been shown to contain eukaryotic genes. We will probably be forced to abandon the simple tree of life with its single trunk and three main branches depicted in Figure 1. Prokaryotes were the first life forms to evolve over 3.
The metabolic processes that they carry out in the transformation of elements, degradation of organic matter and recycling of nutrients play a central role in innumerable activities that affect the support and maintenance of all other forms of life.
Marine Microbiology: Ecology & Applications (Advanced Texts)
Microbial life and the Earth have evolved together and the activities of microbes have affected the physical and geochemical properties of the planet. Indeed, as we shall see in later parts of the book, they are actually the driving forces responsible for major planetary processes like changes in the composition of the atmosphere, oceans, soil and rocks. This is especially relevant to our consideration of the marine environment, in view of the huge proportion of the biosphere that this constitutes.
Despite the preponderance of microbes and the importance of their activities, they are unseen in everyday human experience Box 1. Microbes live and grow almost everywhere, using a huge range of resources, whereas plants and animals occupy only a small subset of possible environments and have a comparatively narrow range of lifestyles. Their very small size is the main reason why appreciation of their abundance eluded us until quite recently.
As described in Chapter 2, this realization depended on the development of fine-pore filters, direct counting methods using epifluorescence microscopy and flow cytometry. Small cell size has great significance in terms of the physical processes that affect life. At the microscale, the rate of molecular diffusion becomes the most important mechanism for transport of substances into and out of the cell.
Small cells feeding by absorption osmotrophy can take up nutrients more efficiently than larger cells. Estimated numbers of prokaryotes in various habitats adapted from Whitman et al.
Marine microbiology: ecology and applications Colin Munn (with foreword by Farooq Azam)
Water, upper m 3. Water, below m 6. Sediment, top 10cm 1. Marine habitats, which are mostly very low in nutrients, contain about half as many prokaryotes as terrestrial soils. Since the introduction of direct counting by epifluorescence microscopy see Section 2. In their calculations, Whitman et al. Calculating the number of other marine microbes is much more difficult. Estimates for the number of marine protists vary from about to per ml in surface waters, but much less is known about their distribution in deep water and sediments.
By contrast, Archaea are a small proportion of the total count in the upper layer, but increase sharply at m, so that below m they are as common as Bacteria.
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Karner et al. The total estimated number of marine prokaryotes is thus within the same order of magnitude as that obtained by Whitman et al. The number 4. To make the point, it is quite instructive to write it in the form 44 thousand, million, million, million, million. The vast majority are smaller than about 0. Since the first description of such small cells, termed ultramicrobacteria, their size has provoked considerable controversy. Such extremely small cells could result from a genetically fixed phenotype maintained throughout the cell cycle or because of physiological changes associated with starvation.
The latter explanation is supported by the fact that some cultured bacteria become much smaller when starved. Because most naturally occurring bacteria have been impossible to grow in culture, it has been difficult to determine whether small size is a genotypically determined condition for marine bacteria. However, studies with some recently cultured marine bacteria from low-nutrient oligotrophic ocean environments show that addition of nutrients does not cause an increase in cell size. If nutrients are severely limiting, as they are in most of the oceans, selection will favor small cells.
It is quite possible that both explanations could be true for different members of the population and these points are considered further in Section 4.
Small cell size also has important implications for mechanisms of active motility and chemotaxis, due to the microscale effects of Brownian movement bombardment by water molecules and shear forces. As discussed in Box 3. In fact, spherical cells are the least efficient shape for nutrient uptake and many marine bacteria are long, thin filaments e. Many organisms have extensive invaginations of the cytoplasmic membrane, which results in increased SA.
Although the majority of marine bacteria are very small, there are some notable exceptions. The bacteria Epulopiscium fishelsoni Table 1.
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