2 Microbiology

Microbiology is the study of extremely small life forms that cannot be seen without magnification by a magnifying lens or microscope (Heim et al., 2017). This operational definition applies to unicellular organisms that are smaller than about 104 m (0.1 mm or 100 μm) in size (Figure 1). The microscopic world also includes viruses, which are the smallest biological entities in nature (diameter of ~107 m) containing protein and genetic material, either ribonucleic acid (RNA) or deoxyribonucleic acid (DNA). They are infectious agents that depend on host cell metabolic processes to reproduce, so there is some debate as to whether viruses are really alive.

Figure showing the size distributions of macro-eukaryotes, micro-eukaryotes, prokaryotes, and viruses

Figure 1 Size distributions of a) macro-eukaryotes, b) micro-eukaryotes, c) prokaryotes, and d) viruses.

Beyond size, the scope of microbiology is wide ranging. It spans across all three domains of life with different microorganisms classified as Bacteria, Archaea, or Eukarya. All members of the first two domains are prokaryotic microorganisms that lack membranous nuclei. The nickname “bacteria” is often used, as it is in this book, to refer to prokaryotes in general because Bacteria were once classified as Eubacteria, while Archaea were classified as Archaebacteria. The third domain, Eukarya, are eukaryotes that have true membrane-bound nuclei. This defining characteristic is common not only to plants and animals but also a variety of microorganisms including fungi, protozoa, and algae.

The classification of organisms has been revolutionized by extraordinary advances in molecular biology that permit sequencing of entire chromosomes. Among prokaryotes, these methods have exposed an overwhelming amount of genetic diversity that is difficult to reconcile within the traditional hierarchy of taxonomic categories. A major part of the problem is that sexual reproduction as a defining characteristic at the taxonomic level of a species does not apply to prokaryotes, which usually multiply by asexual binary fission. Another intriguing part of this dilemma is that it is now possible to identify microorganisms in nature that cannot be isolated and grown in pure laboratory cultures. Such efforts suggest that unculturable microorganisms account for more than 90 percent of the total diversity of most prokaryotic microbial populations.

In comparison to eukaryotes, prokaryotes are among the most abundant, widespread, and functionally diverse organisms on Earth. There are typically 105 to 106 cells in a milliliter of freshwater and 108 to 109 cells in a gram of soil. Global inventories indicate nearly 1030 cells of bacteria inhabit Earth and include as many as 1012 (i.e., a trillion) different species, according to some ecological models (Mora et al., 2011; Locey and Lennon, 2016; Louca et al., 2019). This is several orders of magnitude greater than the 108 to 109 number of species forecast for eukaryotes. When it comes to total biomass, global estimates are on the order of 500 to 700 GtC (giga metric tons of Carbon), with 1 GtC = 1012 kg of carbon. Overall, prokaryotes are suggested to account for anywhere from 15 to 48 percent (81 to 327 Gt C) of the total carbon mass on Earth, with as much as 90 percent of prokaryotic biomass residing in terrestrial groundwater systems and below the seafloor (Kallmeyer et al., 2012; Bar-On et al., 2018; Magnabosco et al., 2018).


Groundwater Microbiology Copyright © 2021 by F. Grant Ferris, Natalie Szponar, and Brock A. Edwards. All Rights Reserved.