Chapter 21: The Living Sea

If anything draws people to the sea—to walk beside its shores, ride along its surface, or plunge into its depths—surely it must be the otherworldly creatures that dwell within it. Part enchanting, part terrifying, the living sea offers an extraterrestrial world on our own planet. Sir Arthur Clarke (1917–2008), creator of numerous fictional extraterrestrial worlds and an avid scuba diver, opined, “No beings from outer space could be more weird than some of the plants and animals that inhabit the oceans of our own world” (Clarke 1960). Indeed, the more we poke, prod, and explore, the weirder the ocean seems: 440-pound jellies with deadly venom, crabs that gather on boiling vents, sea lions that herd oceanic tuna, and octopuses that become friends with humans. 

With much of the ocean unexplored—especially midwater and abyssal regions—it should come as no surprise that we continue to make new discoveries on every expedition. Yet in recent decades oceanographers haven’t had to travel too far to make the most startling of discoveries. By probing the genetic makeup of the “invisible” life-forms in seawater—the microbes—a world beyond our imagination has been discovered. Microbes trade molecules, team up to work, sport enormous metabolic toolboxes, thrive everywhere, and are possibly more diverse than all other marine life-forms combined. What’s more, a good percentage of them are completely new to science, life-forms only recently discovered in the ocean. Our newfound understanding of the importance of viruses in the ocean, our increased recognition of the role of diverse feeding modes, and an emerging perspective of the ocean as a microbial network that responds holistically to changes in the environment—a microbial interactome—have radically changed our view of the ocean in just a few decades.

In the chapters that follow, we explore the living sea, the interconnected, self-replicating, and self-sustaining network of diverse life-forms that inhabit the world ocean. Arguably, the living sea constitutes the most important part of Earth’s biosphere, dominating cycles of carbon, nitrogen, and oxygen. And while it may or may not be as diverse as the terrestrial biosphere—the question remains unsettled—it certainly is the most ancient biological system on our planet. The present-day inhabitants of the ocean and the roles they play in the modern living sea emerge from their evolution over billions of years. We’ll get to that history in a bit. But first we must try to make some sense of the living world, bring some order to the living sea so that we may better appreciate their diversity and function.

21.1 Systems of Classification

The science of systematics aims to discover the diversity of organisms and their relationships with each other (e.g., Raven et al. 2020). As Narendran (2000) expresses it, “Systematics is nothing less than a thorough and complete study of the diversity of living forms.” Not only is systematics useful for understanding the evolution and history of life, it also provides a kind of biological parts list for the Earth system. Knowing who’s who—differentiating one species from another—helps scientists determine who is doing what and where and when they are doing it (Yilmaz et al. 2016). Discovery of abundant cyanobacteria in the 1970s completely changed our ideas about oceanic food webs. Had we not known these organisms existed, our ideas would have been incomplete, if not fundamentally wrong. Systematics has enabled oceanographers to piece together the microbial machinery that underpins how the ocean works as a system. 

Systematics proceeds in part through classification, the organization of life into groups that share certain characteristics. Most of us regularly classify things. For example, when you sort laundry, you separate clothes by color or material. When you put away dishes, you typically place glassware, silverware, and plates in specific locations.

Scientific classification involves the naming of things, a science called taxonomy (e.g., Raven et al. 2020). Traditional rank-based taxonomy, or Linnaean taxonomy, popularized by Swedish naturalist Carl Linnaeus (1707–1778), categorizes life into a series of ever-larger groups from most similar to least similar. The domain category represents the largest grouping of organisms. Wholly related organisms, individuals that share near-identical genetic codes and can produce fertile offspring with each other, are called species. Every species of organism on Earth receives a standardized name—a scientific name—that connects it with its closest relatives—the next highest level of organization, the genus. Scientific names follow binomial nomenclature, a two-part naming system that includes the genus as the first part of the name and the species as the second part. Scientific names also follow strict formatting guidelines: the genus is always capitalized, and both the genus and species are italicized. For example, the properly formatted genus and species for humans appears as Homo sapiens. Additional information may appear as part of a scientific name, but that’s beyond our discussion here.

Higher levels of organization provide additional information on the relatedness of species (see below). Because each of these groupings represents a kind of rank—domains are the highest level of classification—the rank-based system is called a hierarchical system, a system ordered by different levels. The military, with its ranks of personnel, and traditional corporations, with CEOs and managers, use hierarchical systems. However, unlike the military and corporate hierarchies, rank-based taxonomy doesn’t necessarily imply levels of importance in the same way (but see Wilcox 2019). There are no generals in Linnaean taxonomy. In this sense, rank-based taxonomy is a nested hierarchy, like the Russian matryoshka, or nesting dolls—where one rank fits within another.

Rank-based classification helps organize living things into intuitive categories—what biologists refer to as “natural kinds” (e.g., Doolittle 2014). But this system has drawbacks for exploring the evolutionary relationships of organisms, such as who evolved from whom. And it can give a false sense of equivalency between ranks. For example, whereas we find about 89 species of cetaceans (i.e., whales, dolphins, and porpoises) on Earth (Fordyce and Perrin 2023), marine mollusks (i.e., bivalves, shells, octopuses, squids) number in the vicinity of 50–55,000 species (Molluscabase 2023). Mollusks have also lived on Earth about 500 million years longer than cetaceans, having evolved 550 million years ago (e.g., Wanninger and Wollesen 2018) versus 50–53 million years ago for cetaceans (e.g., Bajpai and Gingerich 1998; Thewissen et al. 2007). Though species occupy the same rank, they represent very different evolutionary histories (Understanding Evolution 2023).

With a desire for a more objective and quantitative means of classification, German zoologist Willi Hennig (1913–1976) developed phylogenetic systematics, also known as cladistics (e.g., Lipscomb 1998), a method of classification that uses measurable characteristics to determine degrees of similarity between organisms (Oxford Languages 2023). Cladistics excels at determining who is descended from whom in a more quantitative way than traditional classification. We won’t delve into the details, but a couple terms prove useful for discussing classification based on cladistics. Organisms that share a common ancestor belong to a group called a clade. By definition, a clade includes all members descended from the common ancestor. A group that contains all descendants from a common ancestor is said to be monophyletic. Ideally, all classification would be based on monophyletic clades. But this is easier said than done. 

In many instances, a paraphyletic classification—a clade that doesn’t include all descendants from a common ancestor—is desirable. For example, birds and dinosaurs had been traditionally considered separate groups. As it turns out, however, based on discoveries of feather-adorned dinosaurs in China, scientists now believe that birds and dinosaurs share a common ancestor (e.g., Bhullar et al. 2012; Singer 2015). A long history of distinction between birds and reptiles makes it unlikely that we’ll lump birds in with reptiles anytime soon. And there’s practical reasons to maintain separate classifications: birds do different things than reptiles. Ecologically, the two groups are distinct. Thus, because it doesn’t include all descendants from a common ancestor, the clade “dinosaurs” (or non-avian dinosaurs) is paraphyletic. Similarly, the clade “birds” is paraphyletic (because it doesn’t include dinosaurs). Arizona State University’s Dr. Biology (2017) offers this distinction: if you used phylogenetic classification for storing peanut-derived products in your pantry, you’d put peanut butter, peanut oil, and Cracker Jacks on the same shelf. But if you wanted a more functional system, you’d probably separate these items and group them according to how you use them: peanut butter for sandwiches, peanut oil for cooking, and Cracker Jacks for snacks. 

Both rank-based classifications and cladistics can be used to construct phylogenetic trees, also known as trees of life. These branching diagrams illustrate the hypothetical evolutionary relationships between organisms. They’re like a family tree that shows your ancestors and relatives, except in this case, the relatives and ancestors are different species. Phylogenetic trees depict the evolutionary history of a clade of organisms (or all organisms; see below) based on their inherited characters—the traits of organisms coded in genes passed down by their ancestors. Choosing different characters can yield different trees. Much of the research on the evolution of life on Earth concerns finding the characters that yield the simplest or most statistically likely tree.

Though many types of trees exist, two types are most common: (1) rooted, like a tree with a main trunk and branches; and (2) unrooted, which resembles a starburst pattern. Rooted trees provide a road map of the ancestry of organisms and their evolution from a common ancestor. Unrooted trees illustrate the relationships between organisms without regard to a common ancestor. A three-branch tree—representing the three domains of life—is perhaps the most common (e.g., Woese et al. 1990). Ever smaller and more numerous branches represent groupings based on more specific characteristics and genomes. (See Understanding Evolution for more details on different types of trees and their uses.)

Of course, without time travel or photos provided by extraterrestrials who visited Earth billions of years ago, we can never be absolutely certain who evolved from whom. That’s why phylogenetic trees are considered hypothetical. Nevertheless, they offer enormous insights into the evolution of life and ecosystems on our planet. They are a fundamental tool for modern biology and ecology.

21.2 A Quick Lesson in Classification

For centuries, taxonomists relied on rank-based classification for describing the diversity of organisms. The development of cladistics spurred a new nomenclature and a reshuffling of evolutionary relationships. These reshufflings—some of which are controversial—have resulted in a Game of Thrones–type battle between various groups of taxonomists. (Let’s just hope it ends better than the series did.) Both approaches have merit: traditional classification is easier to remember, but cladistics is more accurate. We briefly review both here. 

The traditional Linnaean rank-based system relies on placement of organisms into different taxa, the different levels in the hierarchical system. The most common taxa—in order from the most specific to the most general—are species, genus, family, order, class, phylum, kingdom, and domain. Modified groupings also exist (e.g., subphyla, superfamily, infraorder), but we’ll stick with the standard eight taxa here. You can recall the order of ranks with this helpful mnemonic: “Didn’t Know Popeyes Chicken Offered Free Gizzard Strips.” There are vegan alternatives, too, if you prefer. (See mnemonic-device.com 2022.) As one example, the largest animal to have ever lived on Earth—yes, bigger than any dinosaur found so far—goes by the common name blue whale—a filter-feeding baleen whale named for the blue hue of its skin when underwater. Its scientific name, Balaenoptera musculus, makes it part of the genus Balaenoptera, a genus with seven other species, including minke, Bryde’s, fin, and sei whales. At the family level, these eight join the lone humpback whale species (Megaptera novaeangliae) in the Balaenopteridae (e.g., Fordyce and Perrin 2023). 

At lower levels it gets trickier. And here’s where classification using cladistics influences rank-based classification. When I learned whale taxonomy, baleen whales (suborder Mysticetes) joined toothed whales (suborder Odontocetes) in the order Cetacea. New fossil finds and molecular evidence joined the baleen and toothed whales with—wait for it—cows, camels, hippopotamuses, and deer, among others (e.g., Poor 2023). The combined group, known as the order Cetartiodactyla or Artiodactyla (depending on the taxonimists), now includes the Cetacea, Mysticeti, and Odontoceti but their ranks remain unclear (e.g., Fordyce and Perrin 2023). Dolphins and porpoises join this group, along with all other even-toed ungulates. These groupings are more accurate, but quite the tongue twisters.

To the layperson, this may seem like pencil straightening. But the discovery that whales and hippos have a common ancestor is truly remarkable and almost makes sense, given how hippos swim. The Royal Ontario Museum calls them “unlikely cousins” (Hirt 2017). Fortunately, at higher levels, blue whale classification is a bit more stable. They are members of the class Mammalia (hey, that’s our class!), the phylum Chordata (our class!), the kingdom Animalia (our kingdom!), and the domain Eukarya (yep, ours). Hopefully, this brief example illustrates the level of detail inherent in the classification of organisms and, more important, the understanding that it brings to the natural world.

Be that as it may, the hierarchical rank-based system proves very useful for making sense of the world before your eyes. A trip to the rocky intertidal zone reveals a cornucopia of life-forms and ecological roles. Green, red, and brown seaweeds—the phyla (the plural of phylum) Chlorophyta, Rhodophyta, and Phaeophyta, respectively—form bands of color arranged by tide height. Tidepools reveal organisms that look like flowers—the sea anemones—the most abundant of which is commonly called the aggregating anemone, or Anthopleura elegantissima. If you snorkel out a ways (or visit a marine aquarium), you might see their gelatinous relatives, the jellies (not jellyfish because they’re not a fish). Sea anemones and corals make up the stinging phylum, the Cnidaria (pronounced nye-DARE-ee-uh). 

A superficially similar gelatinous form—the comb jellies, or phylum Ctenophora—may be the oldest animals on Earth, a position they currently compete for with sponges, the phylum Porifera (see Neilsen 2019; Li et al. 2021; Redmond and McLysaght 2021). If you look closely, you may see a few purple patches with tiny, chimney-like openings spread across the underside of a ledge. These are the purple encrusting sponge, Haliclona—a genus with many representatives around the world. They belong to the demosponges (class Demospongiae), the most diverse class (some 7,000 species) among the more than 9,000 species of sponges (Morrow and Cárdenas 2015; WoRMS Editoral Board 2023). Occasionally, a segmented bristle worm, a polychaete, will crawl across the rockscape. Members of the phylum Annelida—the same phylum as earthworms—polychaetes inhabit nearly every ocean environment, from free-swimming forms in surface waters to benthic forms on abyssal plains, hydrothermal vents, and oceanic trenches. 

You’re also sure to see a mollusk, phylum Mollusca, arguably the most successful phylum in the world ocean.  Mollusks brought us seashells, one of nature’s most beautiful forms. The phylum also includes the octopus, one of the most intelligent invertebrates—animals lacking a backbone. The phylum also includes animals we eat, namely, clams, mussels, and squid. The byssal threads by which mussels attach themselves to rocks, are among the strongest materials on Earth (e.g., Bell and Gosline 1996). 

Of course, the phylum Arthropoda, the jointed appendage animals, which include the insects, are the most successful terrestrial phylum. Nevertheless, they are well represented in the ocean as species of crabs, shrimps, lobsters, barnacles, krill, sea spiders, and the flea-like copepods, possibly the most numerous animals in the ocean. Their movements are hypnotic, like tiny dancers beneath the sea.

And while there are many, many more varieties of incredible marine life-forms that I could talk about for days, I’ll leave you with one of the most iconic forms, the sea star (again, not a fish). Their five arms, spiny skeleton, and legions of water-powered tube feet illustrate the major characteristics of the phylum Echinodermata, to which they belong. Along with the prickly sea urchins (purple and red ones in Southern California), the soft-bodied sea cucumbers (whose internal muscles are a delicacy in some parts of the world), the wavy-armed brittle stars (often found beneath rocks), and the less familiar crinoids (whose arms resemble the headpieces seen in Las Vegas shows), the echinoderms represent the largest ocean-only phylum and the most abundant phylum on the abyssal seafloor. Plastic sea stars make wonderful toppers on a Christmas tree. (Just don’t use the real thing; they belong in the ocean . . . alive.)

21.3 Two or Three Domains?

At the very highest levels of life on Earth, we find three major cell lines, the domains. The domain Archaea includes unique single-celled organisms found throughout the ocean and also in extreme environments (e.g., hot pools, high-salinity ponds). Bacteria, the most diverse domain of life, comprise another unique type of single-celled organism found virtually everywhere on Earth (e.g., Coleman et al. 2021). The third domain, the Eukarya, includes single-celled and multicellular organisms with yet another unique type of cell. This is our domain.

Applications of genetic sequencing in the late 1970s set the stage for establishing the three-domain system in use today. American microbiologist Carl Woese (1928–2012)—hailed as “one of the most significant biologists of the 20th century” (Illinois IGB 2013)—had a hunch that gene sequences could be used to learn something about the evolution and origins of life on Earth (Luehrsen 2014). What he figured out and accomplished—not without controversy—shattered long-held ideas in biology (Nair 2012). In a paper published in 1977, Woese and then-postdoctoral microbiologist George Fox (b. 1945) presented RNA-sequence evidence for a third “domain” of life, the Archaea. Prior to publication of this paper, biologists believed that bacteria and eukaryotes were the only cell lines on Earth. Though met with skepticism, their discovery of the domain Archaea has come to be acknowledged as “one of the most influential in microbiology and arguably, all of biology” (Nair 2012).

Subsequent work over the ensuing decades provided support for three domains. Archaea, Bacteria, and Eukarya each occupied a major branch of a three-branched phylogenetic tree of life. Significantly, the tree of life and its three major branches validated the theory of common descent, the idea that all life on Earth shared a universal ancestor, the last universal common ancestor, or LUCA (e.g., Fox et al. 1980; Doolittle 1999; Weiss et al. 2016; Crapitto et al. 2022). As Darwin put it, “All the organic beings which have ever lived on this earth have descended from some one primordial form” (Darwin 1860). The tree of life depicts this common ancestry and the branching that has occurred since life originated some 3.9 billion years ago.

Until recently, the Archaea, Bacteria, and Eukarya were considered distinct domains on a three-domain tree of life. But an ever-widening body of evidence supports the existence of only two domains—the Archaea and the Bacteria—on a two-domain tree of life (e.g., Rayman et al. 2015; Williams et al. 2020; Doolittle 2020). The Eukarya belong to a branch of the Archaea and either arose within that group (e.g., Williams et al. 2020) or evolved via endosymbiosis (endo meaning “within”; symbiosis meaning “living together”), a “merging” of two organisms (e.g., López-García and Moreira 2020). Some trees depict the Eukarya as an offshoot of the Archaea branch (e.g., Castelle and Banfield 2018), while others depict the Eukarya as a third branch formed between the Archaea and Bacteria branches (e.g., Skejo and Franjevic 2020). 

All of these concepts and definitions serve to bring into focus the evolutionary lineages of life on Earth. But the history of life on Earth is only one part of the story, for life and Earth evolved together, as we shall now see.

21.4 A Brief History of Life on Earth

American evolutionary biologist Stephen J. Gould (1941–2002) believed that the history of life on Earth is the history of microbes on Earth, that they “always have been the dominant forms of life on Earth” (Gould 1996). Using the lens of geologic time, the intervals of time since Earth’s formation, we can sketch some of the major milestones that support Gould’s idea. On the basis of key events in Earth’s geologic history, geologists define four major divisions of geologic time, the eons:

• Hadean eon, 4.56–4 billion years before present (BP)
• Archaean eon, 4–2.5 billion years before present (BP)
• Proterozoic eon, 2.5–0.541 billion before present (BP)
• Phanerozoic eon, 541 million years ago to present

Except for the Hadean (and possibly even then), life has been a part of Earth’s history. So far as we know with certainty, Earth is the only planet in the Universe that harbors life.

Our sketch here is necessarily brief and incomplete. While we focus on a few major events in the coevolution of life and the Earth system, we’re leaving out big chunks of time and omitting major events. Our visit will be more like the three-minute Disneyland Indiana Jones Adventure version versus a 12-hour viewing of all four movies.

21.4.1 The Hadean (4.56–4 billion years BP)

The Hadean eon represents a time of great geological and chemical changes on Earth and includes the origin of the atmosphere, continents, and world ocean, and the startup of plate tectonics (e.g., Brown et al. 2020). Though modern people associate Hades with a “fiery hellscape,” the ancient Greek version of Hades was “the god of a synonymous, mist-shrouded, riverine underworld” (Harrison 2020). Harrison notes the irony of an emerging scientific view of the Hadean as a time seemingly more favorable for early life than previously thought. This view of a benign Hadean supports the possibility of an earlier date for abiogenesis, the formation of living material from non-living material—that is, the formation of life. Previously, scientists thought that intense asteroid and comet impacts, a period called the Late Heavy Bombardment, prevented life from gaining a foothold. But there’s an emerging view that the Late Heavy Bombardment never happened or happened earlier (Mann 2018; Mojzsis et al. 2019; Cartwright et al. 2022). Genomic evidence using calibrated molecular clocks support a possible origin for life as early as 3.9 billion years ago (Betts et al. 2018). From these first organisms—whatever form they may have taken—all life on Earth evolved.

21.4.2 The Archean (4–2.5 billion yrs BP)

By the time of the Archean (from the Greek arkhaios, or “ancient”), hints of our modern Earth began to take shape. An ocean covered nearly the entire planet (e.g., Nutman et al. 1997; Johnson and Wing 2020). Plate tectonics sputtered to a start (e.g., Palin et al. 2020; Roerdink et al. 2022). And life gained a foothold on Earth (e.g., Schopf 2006; Lepot 2020).

Evidence for life by at least 3.5 billion years ago comes in three ways: (1) studies of microfossils, the fossilized remains of microbes, in Archaean rocks; (2) studies of chemical “fingerprints” of life in rocks; and (3) studies of rock formations (i.e., sedimentary structures). We won’t dive into the details here, but a number of studies in recent years support the conclusion that microfossils have biological versus geological or chemical origins (Wacey et al. 2011; Schirrmeister et al. 2015; Delarue et al. 2020). In 2019 geologists working in the Pilbara region of Western Australia found what appeared to be the remains of microbial mats in drill cores of 3.5-billion-year-old stromatolites, layered rock structures created in shallow waters out of fine sediments trapped by filamentous cyanobacteria (Tice et al. 2011; Baumgartner et al. 2019). While modern microbially produced stromatolites can be found in places like Shark Bay in Western Australia, ancient stromatolites can have nonbiological origins as well (e.g., Allwood et al. 2018; McMahon and Jordan 2022). Nevertheless, Baumgartner et al. (2019) report, “our findings provide exceptional evidence for the biogenicity of some of Earth’s oldest stromatolites.” 

Archean life exerted its influence on Earth’s atmosphere as well. Atmospheric oxygen was absent (or present in only trace amounts), but methane originating from the activities of methanogens (discussed in Chapter 10) was likely present at concentrations 100 to 10,000 times present atmospheric levels (e.g., Catling and Zahne 2020). The presence of methane (and possibly carbon dioxide) would have had a warming effect on the Archean Earth, but given that the Sun was about 20 to 25 percent fainter than modern levels, Earth remained quite cool. The presence of liquid water (and likely an ocean) since at least 4.4 billion years ago (Mojzsis et al. 2001; McGunnigle et al. 2022) requires some means to keep Earth above freezing. Greenhouse gases are thought to be one means, but other hypotheses, such as a lowered albedo or Moon-driven tidal heating of Earth’s interior, have also been proposed (Rosing et al. 2010; Charnay et al. 2020; Heller et al. 2021).

These geologic and geochemical data, when combined with genetic data (discussed below), establish in the Archean two domains of life—the Archaea (of course) and the Bacteria. Estimates of their diversity in modern times range from a few million (e.g., Louca et al. 2019) to as many as a trillion different kinds (Lennon and Loucey 2020). 

The presence of archaea and bacteria in the Archean suggests that a multitude of metabolic pathways already existed in ancient times (e.g., Keller et al. 2014; Knoll et al. 2016; Havig et al. 2017). As Knoll et al. (2016) put it, “Halfway through Earth history, the microbial underpinnings of modern marine ecosystems began to take shape.” These metabolic pathways establish the existence of Earth’s biogeochemical cycles—the assembling and disassembling of molecules in a continuous recycling of Earth’s matter—including cycles of carbon, sulfur, nitrogen, iron, and phosphorus (Knoll et al. 2016). For this, bacteria and archaea have come to be known as nature’s little recyclers, turning once-living matter back into a form that can be reused by other organisms.

One other group of organisms merits our attention in this eon. Marine viruses, non-cellular entities with a protein shell that encapsulates genetic information (e.g., Raven et al. 2020), likely existed at this time and may have coevolved with archaea and bacteria (e.g. Harris and Hill 2021). Though some question whether they are alive, there seems to be consensus that viruses have played an important role in the evolution of life (e.g., Forterre 2005; Mughal et al. 2020; Nasir et al. 2020). It’s also likely that they played a role in the establishment of Earth’s biogeochemical cycles, a role they play to this day (e.g., Knoll et al. 2016; Zimmerman et al. 2020; Gazitúa et al. 2020; Zhang et al. 2022).

21.4.3 The Proterozoic (2.5–0.541 billion yrs BP)

When we enter the Proterozoic—the eon of early life (named before we knew about Archaean life)—we find abundant evidence of single-celled bacteria and archaea thriving in an atmosphere and ocean largely devoid of oxygen. Plate tectonics as we know it was in full swing, and some time between 1.9 and 1.5 billion years ago, the first true supercontinent, Columbia, formed. Hundreds of millions of years later—about 1 billion years ago—the pieces of continental crust reassembled into another supercontinent, Rodinia (e.g., Rogers and Santosh 2002; Palin et al. 2020). 

The start of the Proterozoic marked a “decisive time” in Earth’s geochemical history and the history of life (Javaux and Lepot 2018). The ocean and atmosphere gained oxygen—in fits and spurts, but gains, nonetheless. A new form of life arose, one that eventually gave rise to humans. Multicellular organisms evolved, but by the end of the eon, many of them had gone extinct. Nevertheless, the transition from this eon to the next brought a blossoming of new life-forms. And throughout all this, Earth experienced its first glaciations, including some that covered most of Earth’s surface—a phenomenon called Snowball Earth (e.g., Kirschivink 1992; Hoffman et al. 1998; Hoffman et al. 2017; Mitchell et al. 2021).

The Proterozoic begins with a rise in atmospheric oxygen, an event so significant it has been called the Great Oxidation Event. Oxygen may have been present locally in shallow seas or lakes by the late Archaean, perhaps as early as 3.1 billion years ago (Jabłońska and Tawfik 2021). Knoll (2016) calls this “whiffs of oxygen.” Formally, they’re known as Archean Oxidation Events (Ostrander et al. 2021). But a clear shift exists in the chemistry of rocks and sediments during a period from 2.45 to 2 billion years ago that can only be explained by the presence of oxygen. Scientists generally accept that atmospheric oxygen concentrations from 1 to perhaps as much as 40 percent of present atmospheric levels were possible at this time (e.g., Holland 2006; Gumsley et al. 2017; Warke et al. 2020; Ostrander et al. 2022).

Of course, the next big question is what caused the Great Oxidation Event. Because cyanobacteria are the only group of bacteria capable of carrying out oxygenic photosynthesis—photosynthesis that yields free oxygen as a byproduct—scientists believe that cyanobacteria generated the Great Oxidation Event. Genomic and molecular studies have suggested that key components of the metabolic machinery needed for oxygen-producing photosynthesis were present in the Archean (e.g., Sanchez-Baracaldo et al., 2022), if not at the dawn of life (Oliver et al. 2021). And new research points to ancestral origins of cyanobacteria as far back as 3.4 billion years ago (e.g., Fournier et al. 2021). But the Archean environment limited their proliferation. Scientists hypothesize that around 2.4 billion years ago, the tectonic, geochemical, and ecological conditions on Earth began to favor cyanobacteria, permitting their expansion and diversification. As they spread across the planet, the concentrations of atmospheric oxygen rose (e.g., Olejarz et al. 2021; Fournier et al. 2021). 

The rise in atmospheric oxygen forced a reshuffling of strategies for making a living on Earth. Obligate anaerobes, organisms for which oxygen is deadly, were forced to find refuge in anoxic deep ocean basins and muds—places where we find them to this day. Other species were forced to adapt to radically different chemistry of the air, ocean, and rocks brought about by the presence of oxygen. Metabolic pathways for aerobic respiration, the breakdown of organic matter in the presence of oxygen, began to diversify and expand in the bacteria and archaea. Suffice it to say that the Great Oxidation Event altered Earth in ways that we are just beginning to appreciate and understand (e.g., Knoll et al. 2016; Javaux and Lepot 2018; Cole et al. 2020). By expanding the kinds of habitats and chemistries available on Earth, the oxygenated atmosphere set the stage for the evolution, diversification, and proliferation of new forms of life. It’s not correct to say that the Great Oxidation Event caused the evolution of new life-forms; evolution doesn’t work that way. But the Great Oxidation Event did create a very different environment in which the evolution of life appeared to accelerate.

Among the life-forms that evolved during the Proterozoic was a cell lineage that led to humans, the eukaryotes. Based on genetic and fossil evidence, scientists place their evolution at around 1.8 billion years ago (e.g., Betts et al. 2018). Eukaryotic life-forms include the protists—a diverse collection of diverse and numerically abundant single-celled and multicellular species with a eukaryotic cell type—and other multicellular organisms, from seaweeds to sponges to whales. All Eukarya feature cells with a nucleus, the cell structure in which most of a cell’s genetic material is housed. They also host mitochondria, structures that supply energy to eukaryotic cells (e.g., Roger et al. 2017). Biologists refer to the nucleus, mitochondria, and other cell structures as organelles—subcellular, specialized structures present in eukaryotes (and possibly Archaea and Bacteria). Though a defining feature of eukaryotes, we are learning that this distinction may not be so clear-cut.

Traditionally, Archaea and Bacteria represent what biologists call prokaryotes—cells lacking a visible nucleus and other organelles. This designation differentiates them from the eukaryotes. But as biologists probe deeper into the cell structure of archaea and bacteria, it appears that their cells are more organized than previously thought. We now know that archaea and bacteria cells exhibit complex structures analogous to eukaryotic ones (e.g., Jogler 2014; Mahajan et al. 2020; Khanna and Villa 2022)—what some researchers refer to as archaeal organelles or bacterial organelles, respectively (e.g., Greening and Lithgow 2020). There is also increasing agreement among scientists that the Eukarya arose through endosymbiosis, as mentioned above. 

Scientists continue to debate the details of the sequence of events that gave rise to the Eukarya—a process called eukaryogenesis. Recent discoveries point to a lineage of archaea whose genes—the segments of genetic material that code for proteins and serve other cellular functions—share many similarities with eukaryotic genes (e.g., Zaremba-Niedzwiedzka et al. 2017; Liu et al. 2021; Da Cunha et al. 2022). As noted above, this close affinity between archaea and eukaryotes suggests that eukaryotes are a branch of the archaea and not an independent domain. Whether two domains or three, one thing is clear: Archaea, Bacteria, and Eukarya represent different types of cells (e.g., Woese 1994; Koonin 2010; but see also Di Guilo 2018). They employ different strategies for surviving and reproducing in the modern world. And all play a significant role in the modern ocean.

Finally, we arrive at the rise of organisms with more than one cell. Colonial organisms—those with hundreds to thousands of identical cells each of which may produce a whole new organism—may have been present in the form of microbial mats as far back as the Archaean. But true multicellular organisms, organisms with many different specialized cells which carry out specific functions and which cannot independently create a whole organism, likely did not evolve until the mid-Proterozoic. Multicellular red eukaryotic algae have been reported from as far back as 1.6 billion years ago (Bengtson et al. 2017). By at least 1 billion years ago, multicellular eukaryotic green algae can be found (Tang et al. 2020). But their contributions to oceanic food webs were likely limited by mostly inhospitable conditions (e.g., Brocks et al. 2017; Reinhard et al. 2020). 

Nevertheless, multicellular organisms received a boost toward the end of the Proterozoic. Beginning about 800 million years ago, atmospheric oxygen concentrations began to rise again—albeit to only a few percent of modern levels—sufficient to oxygenate at least some deep ocean basins by 570 million years ago (Wood et al. 2019). This event, known as the Neoproterozoic Oxygenation Event (e.g., Knoll and Nowak 2017), set the stage for diversification of multicellular life-forms at the very end of the Proterozoic, from 635 to 541 million years ago—a finer-scale subdivision of geologic time known as the Ediacaran Period (Sperling et al. 2015). Here the first true animals appeared—what biologists called metazoans, multicellular animals with differentiated cells (i.e., cells, tissues, and organs with different functions). While the timeline of the first metazoans remains uncertain, the best estimates place their arrival at around 571 million years ago (Pu et al. 2016; Darroch et al. 2018). Most important, the evolution of all modern animals began with a common metazoan ancestor. You, me, Nemo, and SpongeBob descended from the same ancestor more than 500 million years ago.

Of considerable importance to modern life and its evolution from ancient life was establishment of two major body plans during the Ediacaran. Radial symmetry refers to a shape arranged around a central axis, like a cake or pie. Cnidarians—sea anemones, corals, and jellies—exhibit radial symmetry. Bilateral symmetry refers to a shape that can be divided into two halves. A worm, a crab, a clam, a fish, a whale, and a human illustrate bilateral symmetry. Organisms that exhibit bilateral symmetry belong to the Bilateria, a group with bilateral symmetry that includes all animals except sponges, comb jellies, and cnidarians. Sea stars, sea urchins, and other echinoderms—which appear radially symmetrical as adults—develop from a bilaterally symmetrical larval stage, thus placing them within the Bilateria (Raven et al. 2020). Whereas radial symmetry permits a top and a bottom, bilateral symmetry allows for a head and a tail end, a right and a left half, and an upper and a lower side. Bilateral symmetry provides advantages for motion, development of senses, and evolution of nervous, organ, and reproductive systems (Raven et al. 2020). 

Nevertheless, the Ediacaran was apparently a time of great experimentation. The Ediacara biota—the fossil assemblages that appeared from 571 to 541 million years ago—represent the oldest macroscopic marine communities preserved in rocks. Most were soft-bodied—small and squishy, as some researchers put it—so their fallen bodies left fossilized impressions rather than hard remains (e.g., Tarhan et al. 2016). The Ediacara biota range in size from tiny animals smaller than your fingernails to seaweeds as tall as you are (e.g., Pandey and Sharma 2016; Wendel 2017; Bykova et al. 2020). They also exhibit a range of forms—thread, tube, worm, fan, frond, candelabra, oval with ridges—a veritable Etsy jewelry store of shapes (e.g., Hoffman et al. 2010; Droser et al. 2017). Found in over 40 localities around the world, the highly diverse Ediacara biota provide tantalizing insights into life in the ancient ocean. 

We also know that the Ediacara biota were strictly benthic; that is, they inhabited the seafloor. There they likely grazed upon, plowed across, dug into, burrowed into, and tunneled under carpets of photosynthetic and sediment-dwelling bacteria known as microbial mats (e.g., Buatois et al. 2018; Evans et al. 2019; Bobrovskiy et al. 2022). The plow marks, potholes, trails, scratches, scribbles, spirals, burrows, and tunnels of these activities appear as trace fossils—the fossilized marks of animal activities (e.g., Buatois et al. 2018; Evans et al. 2019; Bobrovskiy et al. 2022). Trace fossils lend support to a wide variety of feeding modes and styles, affectionately referred to as mat encrusters, mat scratchers, mat stickers, and undermat miners (Seilacher 1999; Seilacher et al. 2003; Xiao and Laflamme 2009; Darroch et al. 2023). 

A kind of organic glue secreted by bacteria and algae trapped sediment particles and created one of the most distinctive features of the Ediacaran world: microbially induced sedimentary structures, or matgrounds—surface crusts formed as a result of interactions between microbes and sediments (e.g., Seilacher 1999; Gehling 1999; Buatois et al. 2014). Matgrounds date back to the Archaean eon (e.g., Noffke et al. 2013), but they appear widespread and diverse in the Ediacaran (e.g., Droser et al. 2017). Several common patterns appear in matgrounds, including some that resemble the bumpy texture of an elephant’s skin (Gehling et al. 2009). Matground fossils preserve entire communities of organisms, revealing a complex ecology appreciated only recently (e.g., Gehling et al. 2009; Evans et al. 2019; Darroch et al. 2023). It also reveals a kind of ancient tranquility—what has been called the Garden of Ediacara—a time when algae grew, grazers grazed, and few, if any, predators roamed the neighborhood (McMenamin 1986). That would all quickly change. New evidence suggests that the Ediacaran ended with the first major extinction of life in Earth’s history (e.g., Darroch et al. 2015; Evans et al. 2022). More would follow in the first period of the next eon of geologic time, the Phanerozoic’s Cambrian.

21.4.4 The Phanerozoic (541 million yrs ago to the present)

We now enter more familiar territory. Many of the life-forms of this eon were the ancestors of organisms we find in modern times. Plate tectonics brought us the supercontinent Pangea, which formed and then broke apart over an interval from 320 to 195 million years ago (e.g., de Lamotte et al. 2015). The puzzle-like fit of modern continents offers a lingering reminder of Pangea’s breakup. While the continents were moving about, Earth’s climate swayed between hothouse and icehouse states (e.g., Scotese et al. 2021). The Tethys Ocean—which covered 60 percent of our planet during Pangea—experienced dramatic swings in temperature, too. Though tough to pin down, researchers now believe that seawater temperatures during this eon ranged from 10°C to 30°C (e.g, Veizer and Prokoph 2015; Vérard and Veizer 2019). Some interpretations put paleotemperatures above 40°C (e.g., Sun et al. 2012; Grossman and Joachimski 2022). Perhaps most startling (and alarming for modern times) were the five mass extinctions—rapid and global decreases in the abundance and diversity of organisms—at various times during this eon (e.g., Bond and Grasby 2017). Truly, you can say it was the best of times and the worst of times.

The Phanerozoic—the eon of “visible life”—begins 541 million years ago with the appearance of trace fossils formed by the horizontal burrowing of a worm-like animal named Treptichnus pedum, which, roughly translated from Greek, means “can’t walk straight.” Trep (as we’ll call it) exhibits a complex branching type of burrowing never before seen—the first hints of an infauna, organisms living within a substrate—as opposed to ones on top of it, an epifauna (e.g., Buatois 2017). This small step for burrowing kind places Trep at the beginning of a major expansion in the ecological complexity of life in the ocean (e.g., Xiao and Laflamme 2009; Schiffbauer et al. 2016; Linnemann et al. 2018; Cribb et al. 2019; Mángano and Buatois 2020; Buatois et al. 2020). Because Trep’s fossil burrows can be found worldwide, it also makes a very convenient geologic marker for the start of the first geologic period of the Phanerozoic, the Cambrian (541–485.4 million years ago; e.g., Foster 2014). While interpretations of the ensuing millions of years have changed (e.g., Valentine 2002; Xiao and LaFlamme 2009; Linnemann et al. 2018; Wood et al. 2019; Bowyer et al. 2022), the Cambrian unleashed an astonishing diversity of new life-forms, what has come to be known as the Cambrian radiation, the rapid increase in animal diversity in the Cambrian (e.g., Marshall 2006; Beasecker et al. 2020). A radiation, in this sense, refers to adaptive radiation, “the evolution of ecological diversity within a rapidly multiplying lineage” (e.g., Schluter 2000).

Some scientists and the popular media still refer to this period as the Cambrian explosion, but that name has drawn criticism for failing to include a great deal of evolution that occurred before and after the Cambrian. The term “Cambrian explosion” historically refers to the very rapid appearance of animals in the fossil record starting at about 541 million years ago. The originator of the idea, American Earth scientist Preston Cloud (1912–1991), used the term “eruptive evolution” to describe the evolutionary diversification of animals in the period. He wasn’t too fond of the term “explosive,” noting that the process took millions of years and “probably did not make a loud noise” (Cloud 1948). 

We now know that the diversification of animals—their radiation from a common ancestor—began in the late Ediacaran. While abundant and diverse hard-bodied animals mark the fossil record of the Cambrian, they represent one chapter in the evolutionary history of life (e.g., Lyons et al. 2018). As Schiffbauer et al. (2016) put it, “The earliest stages of animal diversification were neither Cambrian nor explosive . . . removed from their morphological and ecological diversification by a long fuse.” Indeed, while nearly all major groups (i.e., phyla) of modern animals appear in the fossil record of the Cambrian, the next geologic period, the Ordovician (485.4–443.8 million years ago), expanded on that template. 

The Great Ordovician Biodiversity Events, multiple radiations from the Early to Middle Ordovician (497.05–467.33 million years ago), brought its own “explosive” diversification of life-forms, including planktic (i.e., drifting) and nektic (swimming) forms—the drifters and swimmers, respectively. By the middle of this period, the triad of lifestyles that characterize modern ocean ecosystems would be in place (e.g., Servais et al. 2016; Servais and Harper 2018; Servais et al. 2021). Taken together, the diversification of life from the late Ediacaran to the Middle Ordovician encompasses more than 102 million years, a period that witnessed “the construction of Phanerozoic food webs from their Ediacaran precursors” (e.g., Marshall 2006).

One of the most recognizable features of the Phanerozoic is the appearance of organisms with easily preserved skeletons. Though human skeletons are one example, a skeleton is more generally defined as any framework that provides support, shape, or protection to an organism. All organisms—including archaea, bacteria, and single-celled eukaryotes—have skeletons that enable them to hold a shape (e.g., Jones et al. 2001; Ettema et al. 2011; Knoll and Kotrc 2015). The appearance of skeletons in the late Ediacaran to early Cambrian has been called “one of the most momentous events in the history of life” (Vermeij 1989). 

The process by which organisms incorporate minerals into their body structures is called biomineralization. Most skeletons contain a mixture of minerals and organic materials, but some—such as those of insects—are constructed primarily from proteins (Raven et al. 2020). Marine organisms rely primarily on three different minerals for their skeletons: calcium carbonate, silica, and calcium phosphate. Most modern marine organisms have carbonate skeletons (Kouchinsky et al. 2011; Murdock 2020). 

The variety of skeletons mirrors the variety of organisms, though they tend to be similar within a given phylum. A skeleton may appear on the outside of an animal—an exoskeleton—or it may be housed inside an animal—an endoskeleton (Ruppert et al. 2004). Crustaceans like crabs and lobsters possess a rigid, segmented exoskeleton that serves for protection and aids in locomotion and hunting. Of course, bony fishes and marine mammals feature the bony endoskeletons characteristic of most vertebrates. Some skeletons aren’t obvious. The bodies of sponges contain needles of calcium carbonate or silica—known as spicules—embedded in a fibrous network of protein called spongin (Mason et al. 2020). It’s what makes sponges spongy. Cylindrically shaped animals—such as sea anemones, worms, and sea cucumbers—use a hydrostatic skeleton, one whose shape is maintained by water pressure, like a flexible garden hose that expands when filled with water. When arthropods undergo molting—when the animal sheds its exoskeleton to grow a larger one—their newly formed soft skeleton acts as a hydrostatic skeleton until it hardens. That makes hydrostatic skeletons the most widely used skeletal form on Earth (Kier 2012).

Despite more than 185 years of study (e.g., Geyer and Landing 2016), the causes of the Cambrian radiation remain uncertain (e.g., Zhuravlev and Wood 2020). While it’s tempting to point to a single factor as the driving force behind the diversification of life—dissolved oxygen remains the most popular candidate—in fact, any of a number of abiotic and biotic factors may have contributed to the transformation of life-forms from the late Ediacaran to the Ordovician (e.g., Wood et al. 2019). Increases in oxygenation of the ocean—in time- and space-varying episodes, depending on the location—likely expanded organisms’ ability to expend energy in search of food and shelter (e.g., Dahl et al. 2014; Sperling and Stockey 2018; Cole et al. 2022). Changes in seawater chemistry may have altered the biochemistry of organisms’ outer shells and allowed experimentation with new body plans (e.g., Peters and Gaines 2012; Wood et al. 2019). Other factors, such as temperature, salinity, nutrient availability, and ocean acidity/alkalinity, certainly exerted their influence, at least on local scales. These abiotic factors may be viewed as setting the stage for a cast of actors: the scene and its set pieces are in place, but the curtain has yet to be drawn, and the play has yet to be improvised.

The appearance of burrowing organisms—even prior to Trep—had the effect of fragmenting and breaking apart the Ediacaran matground. Paleontologists refer to these kinds of activities as ecosystem engineering, the restructuring of a habitat through the activities of organisms. A study of trace fossils from Namibia, South Africa, revealed extensive ecosystem engineering underway by the late Ediacaran (e.g., Cribb et al. 2019). Using a kind of geological CT scan to get a three-dimensional look, another group of researchers found extensive and complex tunnels in early Cambrian rocks from Siberia (Marusin and Kuper 2020). These studies provide evidence for bioturbation—the disturbance and mixing of sediments by organisms—at the Ediacaran-Cambrian transition. By the middle of the Cambrian, these activities would replace matgrounds with mixgrounds, a deep slurry of “soft” seafloor sediments (Dornbos et al. 2005; Buatois et al. 2014; Buatois et al. 2018). This transformation of the seafloor has been called the agronomic revolution (e.g., Seilacher 1999; Bottjer et al. 2000). It’s the ocean equivalent of plowing on land. Like plowing, the bioturbation of seafloor sediments increased their water content and oxygen concentration, turning a mostly two-dimensional habitat into a three-dimensional one (e.g., Zhang et al. 2017; Mángano and Buatois 2020). The physical transformation of the seafloor also established an exchange of energy, matter, and dissolved nutrients between the benthos and overlying water column, an ecological interaction referred to as benthic–pelagic coupling. In coastal and estuarine environments—where surface waters mix downward and come into contact with the seafloor—benthic-pelagic coupling contributes to some of the highest rates of productivity in the world ocean (e.g., Griffiths et al. 2017). 

The expansion of habitats brought a new stage for improvisation and innovation (e.g., Payne et al. 2020). By strengthening their skeletons, organisms were able to move into and defend new territories, a kind of Cambrian gold rush. For immobile organisms, competition for space meant staking out your territory—erecting barriers or developing antagonistic behaviors—to avoid being pushed out. Competition for food meant exploiting food sources higher in the water column or deeper in the sediments. Competition fueled evolution of bodies and behaviors that made you smarter, stronger, or faster than your competitor. Still, some actors went right for the throat—literally—as making a living by eating your neighbors became a thing. The Ediacaran-Cambrian transition saw the evolution of carnivory—the eating of one animal by another (e.g., Fox 2016). Unprotected soft-bodied organisms were probably helpless against predators. Underdeveloped sensory systems would have made detection of predators difficult. Limited mobility and defenses would have made the Ediacara biota as helpless as the inhabitants of Westeros against the Night King and his White Walkers (Benioff and Weiss 2011–2019). In other words, they didn’t have a chance. On the other hand, if you saw My Octopus Teacher (Ehrlich and Reed 2020), you’ll remember the octopus that covered itself with shells when confronted by a potentially deadly shark. So behaviors to thwart predators kept soft-bodied animals in the game.

These biotic factors may not have triggered the rapid diversification of organisms, but they soon became a major part of it. An evolutionary arms race—the diversification of anatomies, physiologies, and behaviors to better survive—led to many of the biological novelties that appeared in the Cambrian and beyond (e.g., Bengston 2002; Wood and Zhuravlev 2012; Payne et al. 2020; Murdock 2020). Reefs were formed. Tentacles, tube feet, and jet propulsion were invented. Drills, claws, teeth, and toxins came onto the scene. Fish moved into every nook and cranny and hightailed it across the depths. Large reptiles roamed the ocean for a while, then perished. Indeed, no less than five mass extinctions occurred between 440 and 65 million years ago. Climate change, ocean acidification, and changes in sea level, as well as meteorite impacts and massive volcanic eruptions wrote their own chapters in the history of life. Of course, life crept into terrestrial habitats as well. At least one branch of that life returned to the ocean, including the lineage that produced the largest animal to ever inhabit the planet—the blue whale. And lest we get swept up in the Disney parade of visible life-forms, we should not forget for a moment that none of this would have been possible had not invisible microbes created the atmosphere and biogeochemical cycles which sustain this life.

These early events in the history of life provide a better perspective of life in the modern ocean and offer a convenient baseline from which to judge the effects of human activities on the Earth system. 

21.5 Life and Earth as One?

By way of offering a theme to these pages, I’d like to draw inspiration from an uncharacteristic and outspoken scientist, English scientist James Lovelock (1919–2022). In the 1970s, Lovelock wrote a very controversial book called Gaia: A New Look at Life on Earth (Lovelock 1979). The book offered a speculative extension of work he started with NASA in the 1960s, in which he proposed that if a planet’s atmosphere was out of chemical equilibrium, then it probably harbored life. By his analysis, life was not present on Mars because its atmosphere appeared to be in a state of equilibrium (Lovelock 1965). His Gaia book took things a bit further—too far for some scientists at the time. Lovelock presented circumstantial evidence that life didn’t just inhabit Earth, but that Earth itself was a living organism. He called this idea the Gaia Hypothesis. In later years—and admitting that this first work was “poetic”—Lovelock modified the Gaia Hypothesis to state that the evolution of life and Earth’s environment occurred “as a single, tightly coupled process, with the self-regulation of climate and chemistry as an emergent property” (1989). 

This coevolution of life and Earth’s environment forms the basis of a relatively new field of study known as geobiology, the study of life’s interactions with the Earth and their evolution over geologic time. Lovelock calls it geophysiology, but they are essentially the same thing. At the heart of geobiology are the ways in which life has shaped Earth and vice versa. Much of what we have talked about in this chapter falls under the heading of geobiology. In the introduction to their textbook Fundamentals of Geobiology, Knoll and coauthors (2012) credit Lovelock’s Gaia Hypothesis for grabbing “the attention of a broad scientific community.” While the “strong” version of Gaia—that life regulates Earth for its own survival—receives less scientific support, there is now support for and attention given to the significant role of organisms in regulating at least some aspects of the Earth system. Of course, having read this book this far, you already know that.

Lovelock’s Gaia Hypothesis provided a focal point for Earth systems science—the study of the interactions of the spheres introduced in Chapter 1—and brought greater attention to interdisciplinary studies of the Earth system as a whole. Of course, there is no greater need for this approach than today, as we increasingly recognize the negative impacts of human activities on the biosphere. Lovelock was vocal about climate change, too, but that is a story for another chapter.

Hopefully, this sweeping and admittedly imperfect summary of the history of life and our planet has provided a thoughtful perspective for understanding the world ocean and the organisms that inhabit it. We are products of our history—descendants of a drama in progress, if you will—the story of life on Earth. Next time you’re roaming around the neighborhood, camping in the woods, rock-climbing in the desert, or visiting the tidepools, take a moment to consider the life-forms that surround you. You’re here because they’re here. To borrow a quote from a famous American poet, “And that has made all the difference” (Frost 1923; first published 1916).

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