48 pages • 1 hour read
Ed YongI Contain Multitudes
Nonfiction | Book | Adult | Published in 2016A modern alternative to SparkNotes and CliffsNotes, SuperSummary offers high-quality Study Guides with detailed chapter summaries and analysis of major themes, characters, and more.
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BetaChapters 6-8 Chapter Summaries & Analyses
Chapter 6 Summary: “The Long Waltz”
The impact of microbes on evolution and the passing on of important microbes to our offspring have been recurring themes in I Contain Multitudes. The examples that have been cited in previous chapters have been more focused on relationships between animals and bacteria that have been working in tandem for a long period of time. As with every long-term relationship, what Yong calls “the long waltz” between the parties began with an initial contact.
The chapter opens with the story of man whose hand was pierced by a piece of a tree branch as he was cutting it down (143). His hand eventually became infected, and a cyst formed. After the cyst was removed, scientists sequenced the DNA and found unusual bacterial DNA among the sequences. The sequences matched a bacterium called Sodalis, which up until this point was known to live only in the bodies of insects (143). This story is one of coincidences: A branch happens to cut someone, and a bacterium happens to begin to grow within the person.
Most symbioses most likely started with similarly random event that just so happened to turn into a long-term relationship (145). Microbes can be passed along during sex or by eating food containing a new bacterium that then takes hold in the gut. It takes many successful events for a microbe to become a permanent resident, though; the environment, the nutrients, the toxins, and the immune response all must align perfectly to create a hospitable environment for a new gut microbe (146).
Many species have found ways to pass these connections horizontally to their offspring. When beewolves lay their eggs, they secrete a paste out of their antenna over the burrow. When the offspring hatch, they use the paste as a signal to dig in that direction. That paste is swarming with bacteria called Streptomyces, which are known for killing other bacteria. The thought is that the microbes in the paste protect the offspring from infection, and parts of the paste become protective fibers in their cocoons. Without the paste, the beewolf grubs die of fungal infections. When the offspring emerge from their cocoons, they pick up the same strain of bacteria, and they subsequently inoculate a new batch of offspring.
The transfer of bacteria from parent to offspring is important for continuing the thread of generational symbiosis (148), and both parties evolve better ways to keep their partnerships going.
The koala would not be able to digest eucalyptus unless they ate the pap secreted from their mothers’ backs and took up the microbes within it. Termites will suck fluids out of their relatives’ backsides to get their own set of microbes to digest the cellulose of wood (150). Every time termites molt, they lose their microbes, so they continually lick other termites’ behinds to get their important microbes back.
In the case of humans, all it takes is contact to pass along skin microbes. When groups are in constant contact with each other, their skin microbes start to look more similar. Some theories even suggest animals came to live in larger groups because they are better able to pick up bacteria from each other this way (151). Our microbes are important, as is finding new, beneficial species to become part of our microbes.
The two main types of transfer from parent to offspring are vertical transfer and horizontal transfer. Vertical transfer is the direct passage down the lineage and is a much stricter process. An example of this is the colonizing event of vaginal birth. Horizontal transfer is much less strict and comes from our peers and surrounding environments (152). Regardless of the transfer method, a selection process determines what bacteria will stay in partnership. Animals have ways of selecting for sets of bacteria that will be beneficial to them. In fact, one can transfer the microbe of a zebrafish to a mouse (or vice versa) and see that, although cross-colonization can occur, those animals still shape their bacterial communities to be closer to what they would have natively (155).
The composition of our microbiome is controlled not only by our genes but by environmental factors as well. According to Yong, Richard Dawkins suggests that “an animal’s genes (its genotype) do more than sculpt its body (its phenotype). They also indirectly shape the animal’s environment” (155). A beaver’s genes not only build the body of the beaver but also allow them to make dams (155-56). Just as our genes make our hands, eyes, and brains, they also allow us to create art and music. Dawkins calls this concept “extended phenotypes.”
The products of our genes can be an extension of our own body, and those extensions can be shaped by bacteria as well (156). However, this idea goes a step further with bacteria. as Yong explains:
[M]icrobes—unlike the dam or this book—are themselves alive. They have their own genes, some of which are important or essential to their hosts. They aren’t just extensions of a host’s genome, any more than the host is an extension of the microbe’s genomes! (156).
In a way, we and our bacteria become a sole entity.
Demonstrating this idea of becoming a single being with our bacteria is the concept of endosymbiosis. This is the theory that our mitochondria were bacteria that eventually became a permanent part of our cellular structure. This theory was dismissed by much of the scientific community for a long time but eventually became the leading theory in the field. Lynn Margulis, the brain behind endosymbiosis, has coined another term that looks specifically on the connection between living things and the unity they form: holobiont. This term refers to a group of organisms that spend the majority of their life together (157). For example, to understand how corals operate (and die) we must consider both the coral and the bacteria. Some scientists even argue we can’t consider an animal’s genome alone, as we also need to consider the genome of the bacteria colonizing it; together, these are called the hologenome (158).
Just as our genes are selected for through evolution, bacteria are as well. Evolution by natural selection operates under three conditions: 1) individuals must have variation, 2) those variations must be heritable, 3) those variations must impact the animal’s ability to survive, thrive, and reproduce (158). These same conditions apply to our microbes, and there are evolutionary pressures at work to pass on the best set of microbes to one’s offspring so they can survive better.
There is contention between camps in the scientific community in regard to the importance of the hologenome and whether symbiosis can be a driving force in deriving new species in the same way that evolution can. There is evidence that removing specific bacteria can cure reproductive isolation between species of wasps, enabling them to reproduce into new hybrids that were previously dying (162-63). It’s possible that having the wrong microbes created an incompatibility with their genome, or “death by distorted hologenome” (163). Critics argue that the hybrids’ immune system was not working correctly, and any bacteria would cause them to die. No matter the correct answer, it’s clear that the microbes are the culprit in the reproductive isolation of these wasps.
The idea of creating new species by symbiosis is still new, and much remains to be studied to identify the correct theories. However, it is clear that our bonds with microbes are critical and span generations.
Chapter 7 Summary: “Mutually Assured Success”
There are plenty examples of symbionts being critical factors in the survival of their hosts, to the point that the survival of entire species hinges on the fact that their own bacteria allow them to thrive. Chapter 7 focuses on how critical this relationship can be in the case of survival of the fittest.
The chapter opens with the example of the Hemiptera, a group of insects that includes bed bugs, assassin bugs, scale insects, and leaf hoppers (166). The common thread among them is their mouthparts, which stab and suck. Most of these bugs drink sap as their main source of nutrients, but without their microbes, these species would die. Buchnera is one of those bacteria, specifically found in aphids, and they play a role in ensuring aphids are getting all the amino acids that they are unable to produce (168). Sap is deficient in 10 essential amino acids. Neither the bacteria nor the aphids can build all the equipment to make all the needed amino acids, so they combine the abilities of both of their genomes to get the full set of amino acids and survive on sap.
The only way to survive without Buchnera is to find another way to get all needed amino acids, which some Hemiptera have done by eating plant cells whole; the cells contain all essential nutrients (169). These Hemiptera do not have the symbionts their amino-deficient friends do. The bacteria have allowed an entire group of insects to overcome deficiencies to exploit a food source for their gain.
Another species that survives and gains needed nutrients thanks to bacteria is the giant underwater worm Riftia pachyptila. These weird creatures live near the bottom of the ocean in high-temperature and high-pressure conditions. They consist of hard tubes with red shoots of worms sticking out of them, like a tube of lipstick (171). Those worms have no mouth, no gut, and no anus, and they have a large organ filled with crystals of sulfur. This sulfur is key to the creature’s survival: The same sulfur-filled organ is filled with bacteria that break down the sulfur and fix carbon. This method of making food using chemical energy is called chemosynthesis (173). These worms would not survive without their chemosynthetic bacteria, and they are not the only species to rely on this type of bacterial counterpart. Some use two bacteria to accomplish this task: One bacterium converts sulphates to sulphides, while the other bacteria convert the sulphides into power through chemosynthesis (175).
Mammals have formed an important bond with bacteria to digest plant material. Plant tissue is much more difficult to break down in comparison to meat, so we turn to bacteria that can break down the tough plants to get their nutrients (176). With the right microbes and the right amount of space in mammal guts, we have been able to co-opt microbes for our benefit. In the case of mammals who use fermentation and regurgitation to help the bacteria break things down, there is even diversity between the bacteria in the front of the gut and those in the back of the gut. Microbes have played a role in the evolution of mammals, but we have given them space to evolve as well (178).
The gut of a vertebrate has some of the most diverse arrays of bacteria, even more diverse than bodies of water or areas in our environment (178), and the gut of a plant-eating vertebrate is more diverse than that. Plant-based diets create pools of extremely diverse microbes. Termites are another group of creatures that utilize microbes to digest their plant food: the cellulose in wood (179). The ability for termites to digest cellulose allows them to build massive nests and become critical sculptors of the ecosystem by moving nutrients and water. Without microbes, the termites would die, and the ecosystem would collapse. The ripple of the impact of just one symbiosis is a large one.
There are many more examples throughout the chapter of how bacteria have allowed different species to survive under difficult conditions and specific niches. The desert woodrat hosts a microbe that allows it to break down toxins on the leaves of the creosote bush (183). Any other rodent would die from the amount of creosote that the wood rat consumes, but microbes give it the upper hand. Lichens are filled with poison as well, but with the help of their gut microbes, they can gobble up lichen whenever they please (185). Through the combination of gut microbes and their own abilities, plant-eaters can occupy niches and consume more broadly available food. For the most part, plants are unharmed and still able to flourish. Sometimes, however, the microbes are too good at their job.
Western North America is home to an abundance of pine trees. They are meant to be able to stay green their entire lives, but some turn shades of red. The culprit is the mountain pine beetle. The beetles carve out tunnels under the bark and lay their eggs, and the hatchlings feed on the phloem sap of the tree. Not only do the beetles bore around the tree, but they bring with them two fungi that move deeper into the tree and pump nutrients back out to the newly hatched pine beetles (186). Thousands of these beetles seeding thousands of fungal spores drain the nutrients in the tree and eventually kill it.
In retaliation, the pines produce a chemical, called terpenes, that kill the beetles and the fungus (187). The tree keeps these toxic defenses at high levels, and the bacteria thwart that defense using another bacterium that ends up on their exoskeleton. These bacteria have large sets of genes that allow them to break down terpenes, thus allowing the beetles to live without danger of that defense (187). These terpene-eating bacteria seem to be a part of the tree’s natural microbe population, so it’s a possibility that this is another case of normal microbes going haywire when terpene levels rise. In any case, microbes are key to the destruction of the pine trees and the success of the pine beetles.
Chapter 8 Summary: “Allegro in E Major”
Microbes can be critical to the survival of a species because of the genes that they carry, but there is another way that an animal can co-opt the useful genes from bacteria: by acquiring the bacterial genes for its own genome.
We typically understand the inheritance of our DNA through sexual reproduction: something that is passed to our offspring vertically. There is another option for passing genes on, though: from one individual to another (191). This is horizontal gene transfer (HGT), and it is a critical tool for bacteria to pass on beneficial genes to their peers. A single bacterium is full of genes it has acquired from the bacteria around it. This transferring ability allows bacteria to evolve at a high speed when faced with a challenge rather than waiting for the right mutations (192). Although it may seem that HGT goes against what Darwin wrote about in On the Origin of Species, it is still in line with the basic tenants he proposed. HGT gives another route for variation in a population, and natural selection still acts upon those same genes (193).
One example of humans taking up genes from bacteria relates to the consumption of seaweed. In Japan, nori has been a staple of the diet for the past 1,300 years (193). Humans are not equipped with the proper enzymes to digest seaweed carbohydrates. There are bacteria that can do so, however, one example being Zobellia galactanivorans, which was discovered around a decade ago (194). A Japanese family consuming nori with their dinner would also be consuming the Zobellia on the surface of the seaweed. The bacteria join the bacteria in our gut and share their genes with them, as bacteria are known to do in large groups.
Scientists have found Zobellia genes in a few different gut bacteria, but the bacteria itself is not able to survive in the gut. Japanese people’s gut microbiomes are full of these genes from marine bacteria, due to the long-term consumption of seaweed. Even the children of Japanese mothers have these genes in their microbes without ever having eaten nori (195). The consumption of seaweed has grown such that North Americans now have these seaweed digesting genes as well. Rather than evolving to gain a gene that can break down the marine carbohydrates in seaweed, we utilized the bacterial method of HGT and let our own bacteria do the evolutionary work.
Chapters 6-8 Analysis
Chapters 6-8 focus on how microbes impact the evolutionary path of the animals that they hold symbioses with. These chapters cover how we have come to be entangled with bacteria for the long haul, and how bacteria have shaped how we survive and thrive in the face of environmental stress.
Chapter 6 focuses on the ways we have become entangled with bacteria and the debate among scientists on how much we should be considering bacterial genomes as part of our own when looking at evolution. Our ability to survive and thrive is certainly impacted by the bacteria that we interact with, but scientists are still debating whether we should be looking at the entirely of our hologenome when thinking about evolution and our genomes.
Holobionts and hologenomes are examples of controversial thoughts in science, and they exemplify the potential to overstate the importance of something we are still learning about. Many camps are still torn on whether we should consider our bacteria a part of ourselves or a separate entity, even though there is evidence that they play a direct role in our evolution. It’s possible that, by focusing on the microbiome and host as a full unit, we are missing the point that symbiosis is not inherently positive, as discussed in earlier chapters. Some scientists feel that the hologenome leaves those conflicts out of the discussion. The hologenome represents a controversial scientific theory and must be viewed critically, like all new concepts in a growing scientific field. Whether the hologenome is simply a concept of togetherness or one that leaves out important details of the symbiosis between organisms, we must understand all sides of the argument and await new evidence to determine whether this hypothesis will be accepted.
Chapters 7 and 8 focus on the ways that bacteria have allowed us to survive and thrive over the course of time and have sped up the way natural selection acts upon us. The addition of specific microbes, along with horizontal gene transfer, have changed the way we think about evolution. Evolution is typically viewed as change over thousands of years. An individual of a species gains a random mutation that is advantageous, and it survives and passes that gene on to its offspring. Over the course of generations, that mutation spreads. Sometimes bacteria may act as that mutation, but rather than a DNA-based mutation, they show up as an addition to our microbiome.
The transfer of microbes over time may be a slow process, but the ability for bacteria to transfer their genes to the rest of the population in the gut is much faster. Realizing how important bacteria have become to natural selection has not only changed the way that we see evolution moving, but also has challenged the way we think of Darwin’s concepts of evolution. We now understand that bacteria allow us another route toward variation in the population, which natural selection can then act upon. Whether that additional variation is important enough to consider our symbionts and ourselves as one entity is still up for debate, but microbes are changing the way we think about evolution.
