An unsettled issue that’s relevant to life elsewhere (below the surface of Mars or Jupiter’s moon, Europa) is the extent of Earth’s subsurface biosphere or ‘intraterrestrial life.’ Some scientists suggest that a huge mass of microbes extends a kilometre or two below the seafloor and more than 3 kilometres underneath land. A limit for life at such depths is temperature. As you go downwards, it gets warmer (as miners know) and, at some point, too hot for even the toughest microbes. Earth’s subsurface biosphere biomass is uncertain because deep drilling has not been done for all types of subsurface environments, but estimates range from about 1 per cent to 30 per cent of Earth’s living biomass.
Whatever its precise mass, the biosphere is less than a billionth of the mass of the Earth and yet manages to greatly influence the chemistry of the surface environment. The biosphere can do this because it processes vast amounts of material with rapid turnover. In doing so, individuals live and die almost instantly on geological timescales. Microbes typically reproduce in tens of minutes to days, while large multicellular organisms last only a few thousand years at most before they become dead fodder for microbial degradation. For example, amongst the latter, the oldest non-clonal organism is a Bristlecone Pine in the White Mountains of California, which germinated around 3049 BC, several centuries before the earliest Egyptian pyramids, but a mere blip in geological time.
The main activities in today’s biosphere are oxygenic photosynthesis and its chemical reversal through aerobic respiration and oxidation (Chapter 4). However, microbes possess a huge range of other metabolisms, which we discuss later.
Microbes, of course, are found almost everywhere at the Earth’s surface. A seawater and freshwater bacterium called Pelagibacter ubique is probably the most numerous organism on Earth. Despite that, it was first described only in 2002, which shows how biology is still developing. Overall, there are about 1029 microbes of all varieties in the ocean, far exceeding the 1022 stars in the observable universe. Microbes are also abundant on land. There are typically about 100 million to 10 billion microbes per gramme of topsoil. Indoor air usually has about a million bacteria per cubic metre. An average of one microbe (albeit dead) even floats in every 55 cubic metres of air at 32 kilometres altitude in the stratosphere.
There are four key properties that have allowed the Earth to become so extensively inhabited. The most important is widespread liquid water. All metabolizing organisms contain organic molecules dispersed in aqueous solution. Consequently, we don’t expect life to exist on a completely dry surface, such as Venus. The second essential property is having energy for metabolism. Sunlight is the main source for Earth’s biosphere, but some organisms obtain energy from chemical reactions in darkness, which means that it’s not impossible that microbial-like life might exist below the surface of Mars or Europa. A third life-giving feature is a renewable supply of essential chemical elements. A planet that can’t resupply vital elements through natural cycles (such as the water cycle or tectonics) would be deathly. A fourth attribute, which may be essential for life, is the presence of interfaces between solids, liquids, and gases. It’s advantageous to live at a stable interface, such as on land or the surface of the ocean. This is why it would be difficult for life to exist on a gas giant like Jupiter that has no surface. Life might speculatively be possible at certain altitudes in Jupiter’s atmosphere but deep churning by convection would periodically plunge life into an interior of fatal heat and pressure.
An inside view of terrestrial life: the cell
We have just considered biology on a global scale but under the microscope all organisms are composed of cells of different types that put them into one of three domains, the Eukarya, Archaea, or Bacteria. The last two are microbial and are sometimes lumped together as prokaryotes, although many microbiologists now consider this term antiquated because archaea and bacteria are biochemically dissimilar. DNA floats freely in the middle of the archaeal and bacterial cells, whereas in eukaryotes the DNA is housed inside a membrane-bound nucleus. Archaea and bacteria are single cells, with the exception of some bacterial species that join up in a row to form filaments. Eukaryotes can be single celled, such as an amoeba or a baker’s yeast, but only eukaryotes form large, three-dimensional multicellular organisms, such as mushrooms or humans.
The classification into three domains of life was motivated by genetics and supersedes an older ‘five kingdom’ system of plants, animals, fungi, protists (single-celled eukaryotes), and bacteria. However, these old terms are still used in taxonomy, which classifies an organism below its domain according to Kingdom, Phylum, Class, Order, Family, Genus, and Species. The mnemonic I use to remember these levels (or taxa) is far too rude to mention but another is ‘Keeping Precious Creatures Organized For Grumpy Scientists’. The taxonomic levels of a human, for example, are the animal kingdom, chordate phylum, mammal class, primate order, hominid family, Homo genus, and sapiens species. The Swedish botanist Carolus Linnaeus (1707–78), who gave us the word biology, developed modern taxonomy, including binomial names for organisms, e.g. Homo sapiens. But it took the advent of evolutionary theory and molecular biology to uncover the biochemical unity of life and genetic common ancestry.
While there are some similarities between eukaryotes and the other two domains, there’s also a gulf in complexity. Bacteria and archaea are usually around 0.2–5 microns (millionths of a metre) in size, with rare exceptions, whereas eukaryotic cells are generally bigger, at 10–100 microns size. The larger eukaryotic cells contain organelles to perform specialized functions, analogous to the organs of the human body (Fig. 4). For example, the mitochondria carry out respiration. In plant or algal cells, chloroplasts perform photosynthesis. However, one feature common to all cells is a large number of ribosomes, which are globular structures that make proteins. For example, in prokaryotes or simple eukaryotes such as yeast, the cell might have several thousand ribosomes, while in an animal cell the number might reach several million.
4. a) Schematic of prokaryote (archaea and bacteria) versus eukaryote structure; b) Two bacteria caught in the act of conjugation
Given an astrobiological interest in complex extraterrestrial life, we might ask why only the eukaryotic cell produces large, three-dimensional multicellular life. The answer is not fully known but eukaryotic cells have a more sophisticated internal dynamic cell skeleton or cytoskeleton than archaea or bacteria. This consists of protein microfilaments, tiny protein tubes (‘microtubules’), and molecular motors that control cell structure and help transport signalling molecules to change cell physiology. So the ability to develop into many specialized forms (for example, skin or brain cells) is inherent in the make-up of a eukaryotic cell. Cyanobacteria are able to make filaments of hundreds of cells in a row with some different cell types but that is the limit. Unlike archaea or bacteria, eukaryotes have bigger and more modular genomes, which also allows for more complexity. If there were no eukaryotic cells, the Earth would be much duller. All of the familiar organisms of our world—the animals, plants, and fungi—wouldn’t exist. Thus, when we think about complex life on exoplanets, we should wonder whether evolution would make cells like eukaryotes elsewhere. For this reason, the origin of eukaryotes is of great interest.
Modern genetics implies that the eukaryotic cell is a ‘Frankenstein’s monster’, assembled in evolutionary history from bits and pieces of bacteria and archaea. For example, the mitochondrion in eukaryotic cells was derived from a bacterium originally living symbiotically inside another cell. The larger cell, which may have been an archaeon or some ‘proto-eukaryote’ that no longer exists, swallowed the free-living bacterium and, in the most important gulp in history, the mitochondrial ancestor came into being. Indeed, separate DNA in mitochondria provides evidence of bacterial ancestry. The distinct DNA of chloroplasts in plant and algal cells shows that chloroplasts were derived in a similar way from symbiotic cyanobacteria that ended up living inside larger cells. Effectively, all the cells in the leaves of green plants contain a
ncestors of cyanobacterial slaves that were caged and co-opted long ago. The theory of such an origin for the mitochondria, chloroplasts, and other organelles in eukaryotic cells is called endosymbiosis.
A world without eukaryotes would also be one without sex. Think no flowers or love songs. Archaea and bacteria are not sexed but they do conjugate when two cells are connected by a tube in which genes are transferred in pieces of DNA called plasmids. Bacterial surfaces have protuberances called pili, and during conjugation a special pilus extends to a partner, providing the conduit (Fig. 4). Unlike sexual reproduction in eukaryotes, microbial conjugation doesn’t produce offspring and is quick and easy. It’s as if you brushed up against a person with red hair in a coffee shop and acquired the red-haired gene with an instant change of your hair colour. Archaea and bacteria can also acquire new genes through transformation (uptake of foreign DNA from the environment) and transduction (virus-mediated gene swapping). Indeed, the rapid acquisition of genes allows the quick development of bacterial resistance to antibiotics.
Eukaryotes that are sexed generate gametes, i.e. sperm and egg cells. In complex multicellular eukaryotes, the diversity of life makes it surprisingly hard to define ‘male’ and ‘female’, leaving us with the odd definition that males are those that produce the small gametes, while females produce the big ones. The gametes fuse so that half of the genes come from a father and half from a mother. Usually DNA is a loosely coiled thread but before cell division, DNA curls up into visible chromosomes under a microscope. For example, humans have 46 chromosomes in 23 pairs in each cell, except for the gametes, which have half, i.e. 23 chromosomes.
There are many ideas about why sex is evolutionarily advantageous for eukaryotes. One possibility concerns how it mixes and matches genes from both parents onto each chromosome in a process called recombination. If beneficial mutations occur separately in two individuals, the mixture of both can’t be achieved in asexual organisms, but sexually reproducing organisms can bring them together and reap the benefits. Conversely, sex can also eliminate bad, mutated genes by bringing unmutated genes together in some individuals, whereas self-cloning organisms are stuck with bad genes, and offspring can die because of them.
Outside the three domains, viruses represent a grey area between the living and non-living. Viruses are typically about ten times more abundant than microbes in seawater or soil. They consist of pieces of DNA or RNA surrounded by protein and, in some cases, a further membrane. Viruses are tiny, only about 50–450 nanometres (billionths of a metre) in size, comparable to the wavelength of ultraviolet light. They are generally considered non-living because they are inanimate outside a cell and have to infect and hijack cells for their own reproduction. However, some do this without the host ever noticing, so not all viruses cause disease. One theory of several for the origin of the nucleus of eukaryotes is that it may have evolved from a large DNA virus, but the role of viruses in the evolution of life is still a matter of debate.
The chemistry of life
To discuss many aspects of life, such as genetics and metabolism, requires the vocabulary of biochemistry. The four main classes of biomolecule are nucleic acids, carbohydrates, proteins, and lipids. Like self-assembly furniture, many biomolecules are modular. They are chains or polymers of smaller units called monomers.
Carbohydrates provide energy and structure. They contain C, H, and O atoms in a 1:2:1 ratio, with repeated units of C(H2O), so literally, their chemical composition is ‘carbon hydrated’. Sugars with five carbon atoms are found in DNA and RNA molecules, while six-carbon sugars exist in cell walls, such as cellulose in plants.
Lipids are organic molecules that are insoluble in water but dissolve in a non-polar organic solvent—one without significant electrical charge on any of its atoms, such as olive oil. Thus, if we ground up a dead animal and bathed it in a non-polar solvent, anything that dissolved would be a lipid. Life uses lipids in cell membranes, as fats for energy storage, and as signalling molecules. Major components of membranes are phospholipids, which have a hydrophilic (water-loving) end that contains phosphorus and a hydrophobic (water-repellent) tail that is a hydrocarbon, consisting of carbon and hydrogen atoms. A double layer of phospholipids, called a bilayer, forms a membrane. The hydrophilic ends stick out into an aqueous medium on the interior and exterior of a cell, while hydrophobic tails face each other in the middle of the membrane.
Proteins are polymers made up of amino acid units. Their use includes enzymes and structural molecules, although there is a long list of other functions.
RNA and DNA are nucleic acids, which are polymers of nucleotide monomers. Each nucleotide is made up of a five-carbon sugar, a phosphate, and a part called a base (Fig. 5). In DNA, there are four possible bases. All of them contain one or two rings of six atoms where four of the atoms are carbon and two are nitrogen. Each base has a letter designation of A, C, G, and T, which stand for adenine, cytosine, guanine, and thymine molecules, respectively. Molecules of RNA use the same three bases except that the T of DNA is replaced by a U for uracil.
5. Left: DNA consists of two strands connected together. Each strand is made up of a ‘backbone’ of phosphate (P) and sugar (S) components. The strands connect to each other with base pairs. Right: In three dimensions, each strand is a helix, so that overall we have a ‘double helix’
In 1953, James Watson and Francis Crick famously deduced the structure of DNA: two polynucleotide strands coiled in a screw-like helix (Fig. 5). The bases at the sides of each strand stick together by ‘hydrogen bonds’ in which a slightly positively charged hydrogen atom on one base is attracted to a slightly negatively charged atom on a base from the opposite strand. Structural compatibility only allows a C base to pair with G and an A to pair with T. Each DNA molecule has several million nucleotides, and each chromosome in the cell contains a DNA double helix. In contrast, RNA molecules are mostly single stranded. However, RNA can fold back on itself if complementary bases exist in two separate parts of the strand, noting that adenine pairs with uracil (U) in RNA.
The structure of DNA incorporates two fundamental characteristics of life identified in Chapter 1: an ability to reproduce; and a blueprint for development and maintenance. In replication, the DNA helix splits into two strands with each serving as a template for a new complementary strand. For example, wherever A appears on the template, a T is added to the newly generated strand, or vice versa. The same applies for G–C pairs. In the process, mutations and mistakes allow for evolution.
In fulfilling its other role as the blueprint, the DNA double helix is unzipped by an enzyme to provide instructions to generate proteins. Part of the unzipped DNA undergoes transcription into a strand of messenger RNA (mRNA), which is a complementary copy of the DNA, except that U (instead of T) is inserted wherever A appears in the DNA. Then the mRNA is fed into a ribosome like a ribbon. In the genetic code, groups of three letters (called codons) along the mRNA specify each amino acid in a protein that flows out of the ribosome.
Apart from reproduction, life has to sustain itself through metabolism, which involves breaking down molecules to make energy (catabolism) as well as building up biomolecules (anabolism). The classification of metabolisms depends on the need for energy and carbon. Because each of these requirements can, in turn, be satisfied in two different ways, biologists have 2 × 2 = 4 metabolic terms for organisms: chemoheterotroph, chemoautotroph, photoheterotroph, and photoautotroph (Fig. 6).
6. The classification scheme for metabolisms in terrestrial life
All organisms (probably even extraterrestrial ones) fall into one or more of these categories. The troph suffix means ‘to feed’ and the two ways in which organisms get energy, from chemical sources or sunlight, give rise to the chemo- and photo- prefixes. An additional hetero- or auto- prefix is employed depending upon the method used to acquire carbon. If carbon is obtained by consuming organic carbon compounds (such as sugars), the hetero- prefix applies. If an organism converts inorganic carbon (e.g. carbon dioxi
de) into organic carbon—called ‘fixing carbon’—the auto- prefix is used. In general, heterotrophs must acquire food to make energy, while autotrophs can fix carbon and make their own energy.
We humans are chemoheterotrophs. You and I consume organic chemicals made by other organisms, such as plants. All animals and fungi, many protists, and most known microbes are chemoheterotrophs. In contrast, a chemoautotroph is a microbe that uses inorganic chemicals such as hydrogen, hydrogen sulphide, iron, or ammonia to make energy, some of which it uses to extract carbon from carbon dioxide. For example, chemoautotrophic microbes live in darkness in deep-sea hydrothermal vents by oxidizing hydrogen sulphide and other substances. (Chemoautotrophs are also called chemolithotrophs, from the Greek ‘lithos’ for stone because the inorganic chemicals they use come from geological sources.) Plants, algae, and some cyanobacteria are all photoautotrophs because they use sunlight for energy and acquire carbon from the air. Photosynthetic bacteria from the Chloroflexus genus, which are found in hot springs, are an example of microbes that metabolize as photoheterotrophs using sunlight for energy and acquiring carbon from organic compounds made by other microbes. Chemoautotrophs might inhabit the subsurface of Mars or Europa, while phototrophs might exist in the oceans of habitable exoplanets.
The tree (or web) of life
The history of life on Earth can be deduced from the way that evolution has altered genes. Evolution is the change in inherited characteristics in a population from one generation to the next. Because individuals are genetically variable, in any given environment some will be better adapted and have greater reproductive success than others, which biologists describe as higher fitness. In every generation, individuals of lower fitness are lost. This is natural selection. So, over many generations, lineages accumulate genetic adaptations and new species evolve.
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