Figure 2.1 Small subunit rRNA phylogenetic tree of Life, with division into the three domains of bacteria, archaea, and eukarya. The highlighted taxa contain photosynthetic organisms. The color coding represents the type of reaction center complex found in the organism, with purple indicating Type II reaction centers and green indicating Type I reaction centers. The red arrow indicates the endosymbiotic origin of chloroplasts from cyanobacteria.

      Source: Blankenship (2010) (p. 435)/The American Society of Plant Biologists.

It is clear from analysis of complete genome sequences for many organisms that there has been significant horizontal transfer of genetic information among various bacteria and even between bacteria and eukaryotes (Soucy et al., 2015). Therefore, the image of a single, branching evolutionary tree that applies to all organisms is increasingly being replaced by a more complex netlike arrangement, in which some parts of an organism bear different evolutionary relationships to other organisms (Doolittle, 1999). However, the process of horizontal gene transfer has apparently not been so extensive as to blur the essential distinctions among the different groups of organisms, as the groupings according to more traditional classification methods are reasonably consistent with those predicted by the RNA analysis, at least in broad outline.

      The evolutionary history of any gene or gene family reflects the development of that gene, regardless of what organism has been its host during the course of evolution. An evolutionary tree of a particular gene is therefore called a gene tree and may be very different from the species tree of organisms. The origin and early evolution of life with special emphasis on photosynthesis are discussed in more detail in Chapter 12.

       2.2.1 Nomenclature

      Living organisms are classified according to the binomial nomenclature method, introduced by Linnaeus in the 1700s. The first name (always capitalized) is the genus name (plural, genera), while the second name (never capitalized) is the species name. Both names are italicized. The grouping of organisms into species, genera, and higher order taxa is based on a number of characteristics and represents a useful, but ultimately arbitrary, decision as to where to place the divisions along the continuous variations among related organisms. A genus is a group of organisms that share many but not all characteristics. Higher‐order classifications that are intermediate between the genus and phylum, such as family and order, serve to classify groups of organisms into broader categories.

2.3 Prokaryotes and eukaryotes

      An older, but still very useful, concept to distinguish among living things is the division into prokaryote and eukaryote. Prokaryotes are the structurally simplest life forms, including bacteria and Archaea. No Archaea that carry out chlorophyll‐based photosynthesis have yet been found, so our discussion of them will be limited. Both these groups of organisms are nearly always single‐celled and have a relatively simple cellular organization without a nucleus or other subcellular organelles. A bilayer lipid cytoplasmic membrane surrounds the cell and serves as the main permeability barrier. In Gram‐negative bacteria, including most types of phototrophic bacteria, a second, more permeable, outer membrane is present, as well as a tough cell wall that provides mechanical stability (Madigan et al., 2017). The space between the outer surface of the cytoplasmic membrane and the inner surface of the cell wall is called the periplasm. This region contains a number of soluble proteins, including some cytochromes and chemosensory binding proteins. These proteins are actually topologically outside the cell, but are prevented from being lost by the cell wall. The cell wall has several layers and a complex chemical structure consisting of lipids, proteins, and polysaccharides. Nutrients pass into the periplasm from outside the cell through pores, which are made of proteins called porins. A porin is an integral membrane protein that forms a small hole in the outer membrane. Ions and small molecules, such as sugars and amino acids, can easily pass through the pore, but larger molecules cannot. Bacteria are almost always submicroscopic cells, with typical dimensions on the order of one to a few micrometers. They usually divide by binary fission, producing two daughter cells.

Eukaryotes, which are identical to the eukarya domain discussed earlier, are more sophisticated cells than prokaryotes. They are usually much larger than bacteria, up to hundreds of microns in size. In many cases, eukaryotic cells make up multicellular organisms, in which different cells are highly specialized or differentiated. Eukaryotic cells also contain a number of internal structures called organelles. These organelles are surrounded by membranes and include the nucleus, the mitochondrion, the endoplasmic reticulum, and, most importantly for photosynthesis, the chloroplast. At least two of these organelles, the mitochondrion and the chloroplast, have complex evolutionary histories, having been acquired by an early eukaryotic cell by a process called endosymbiosis (Margulis, 1993).

2.4 Metabolic patterns among living things

      Organisms can also be classified according to their metabolic capabilities. While this method does not strictly follow evolutionary relationships, it is still very useful for understanding patterns of energy and metabolite flow, which is especially important in phototrophic organisms. A number of these patterns can be present simultaneously in a single organism, leading to names that are often intimidating. However, they are simply combinations of the individual metabolic patterns.