The Evolution of Evolution: Seen through the Eyes of a Slime Mold

Abstract

This article was conceived out of frustration. I have discussed the possibility that microorganisms are affected by natural selection differently from larger ones in two essays (Bonner 2013a, 2013b), and the reception has been largely silent or in one case simply rejected (Futuyma 2013). Here, I want to gather all my arguments in one place and see if I can make my case. This is motivated by my conviction that the evolution of microorganisms is different from that of macroorganisms and is so in very interesting ways, with important consequences.

First, let me describe some observations that led me to this unconventional view. Until very recently (because I no longer have a laboratory), and beginning in 1940, when I started as an undergraduate, I have been experimenting on a group of amoebae know as cellular slime molds—a blissful voyage that lasted 70 years. Therefore, it is quite understandable that I should look at the whole biological world through the eyes of a slime mold. Cellular slime molds are microorganisms, and, as we shall see, many of the things they do are quite different from what trees, birds, mice, or elephants do. Consciously and unconsciously that must have strongly influenced the way I look at things.

Cellular slime molds, or social amoebae, live in the soil, and as separate amoebae, they feed on bacteria. They are small—roughly the size of our white blood cells—and also feed on bacteria that may have invaded our bodies. Cellular slime molds are unique, however, in that when they have licked their plate clean of bacteria, they abruptly become multicellular. The amoebae aggregate by smelling a chemical (chemotaxis) that leads them to central collection points that ultimately turn into delicate, minute fruiting bodies—a small mass of amoebae that have become encapsulated into resistant spores and are held up into the air on a slender stalk made up of dead amoebae that have developed thick cell walls.

What is so unusual in this life cycle compared with that of other forms of life is that they feed first as separate amoebae and then become multicellular. Virtually all other organisms become multicellular as they grow. In the case of animals, the first growth is usually sustained by the yolk that is provided in the beginning, followed by the construction of an alimentary canal, or gut, that allows them access to external energy in the form of food. Things are much simpler for plants that get their energy directly from the sun.

Bacteria are very common in the soil; they are the basic fodder for many soil organisms. Cellular slime molds are one of the prime consumers of those bacteria and are extremely common and abundant all over the globe. When I started working on them in the early 1940s, there were a half dozen species of cellular slime molds known, but today, there are in the neighborhood of a hundred, and no doubt there are more to be discovered. First, Kenneth Raper, followed by his student James Cavender (2013), made major discoveries on the widespread distribution of cellular slime molds. (And there are others who also made important advances.) Similar to the distribution of many other organisms, the closer to the equator, the greater the number of species (Cavender 1973). Furthermore, besides thriving in the tropics, they are found in temperate regions, in the Arctic and Antarctic, and even in moderately arid regions; they apparently thrive pretty much everywhere. Because of their small size and because they cannot be seen in their habitat (the soil), they have been protected from the enquiring eyes of biologists for many years.

In many ways, they differ from standard organisms, but the difference I want to examine is how they appear to be responding to natural selection in a way that differs from the response of larger animals and plants. I am only concerned with eukaryotic microorganisms (whose cells contain a nucleus) and not with bacteria, other prokaryotes, or viruses. They do many things differently and deserve a special essay.

One particularly interesting argument centers on the work of Pauline Schaap and colleagues (2006) and her group at the University of Dundee, in Scotland. She teamed up with Sandie Baldauf, a molecular biologist based then at the University of York, and they and their colleagues constructed an evolutionary tree for 93 species and strains of cellular slime molds, many of them new, discovered and characterized by the taxonomists among the authors of the paper. They were able to separate the species into four groups: group 1 contained the oldest and group 4 the most modern.

This groundbreaking contribution has been extended (e.g., Romeralo et al. 2013), and with further advances in the molecular characterization of the species, the tree will become greatly refined, but even in its present primitive state, it serves my purpose here. In the first place, it is now possible to add some sort of time scale, however crude, and it is thought that cellular slime molds probably existed in the Ordovician some 400 million years ago—and possibly even earlier, some 600 million years ago (Romeralo and Fiz-Palacios 2013).

Schaap and her group (Alvares-Curto et al. 2005) have examined their results in a rewarding way. They have looked into some of the chemicals involved in the development and chemotaxis in one of the modern species. It had been shown by Parent and Devreotes (1996) that there are four proteins that are activated by cyclic adenosine monophosphate (cAMP) in the development of Dictyostelium discoideum, a modern, group-4 species. Cyclic AMP is the substance that attracts the amoebae during aggregation in a number of species; it is part of the process that is responsible for the transition from unicellularity to multicellularity for those species. The last of these proteins to appear during development is the only one involved in the chemotaxis of aggregation. What Schaap and her colleagues (2006) showed was that a member of their group 4, the most modern group, had all the chemical components just outlined. They also examined an older, more primitive species, Dictyostelium minutum, and it had only one of the four proteins, one that was quite removed from any involvement in chemotaxis. D. minutum is a more ancient species (in group 3) that uses folic acid as an attractant for its aggregation stage.

This tells us two things. Even though the morphologies of the two species are roughly similar, except for the fact that the modern species is larger, the internal biochemistry has been altered in major ways: New proteins involved in development have appeared in the modern species, and the chemical nature of the aggregation attractant has changed. Natural selection is active at the molecular level but less so at the morphological level. This difference between morphological variation and genetic variation is known among other microorganisms, as Lahr and colleagues (2014) pointed out; they call it discordance.

The other lesson is the fact that both species, the ancient D. minutum and the more recently evolved D. discoideum, are alive today and are coexisting over great areas on the surface of the earth. D. minutum has not gone the way of the dinosaurs; it has not gone extinct. In fact, it is a living fossil, as Darwin would have called it. And if we look at Schaap and colleagues’ (2006) evolutionary tree with the four groups, all the species are probably living fossils. We do not have any record of any extinctions, although no doubt there were some; in the absence of fossils, we have no way to determine how many.

If we turn to larger organisms, living fossils are rare, whereas there is a large number of known extinctions. The few classic examples of mega living fossils are the horseshoe crab, coelacanth fish, and among plants, ginko and metasequoia trees—mere handful compared with the vast number of known extinctions. And this difference between micro- and macroorganisms is entirely due to their size. How and why did this difference arise?

The explanation will be found in their ecology. Big organisms compete with one another for food on a grand scale. By contrast, slime molds come close to ignoring competition. They live from moment to moment; they eat if the food is there. In this unorganized fashion, they compete with other bacteria-eating organisms. Unlike animals, slime molds do not need to have bigger multicellular structures to be more successful predators. Once the food is gone, they immediately form spores that will stay dormant until conditions in the form of fresh bacteria arrive by chance. There is nothing quite equivalent among larger plants and animals. The closest thing might be dormant seeds in higher plants, but that is mostly dictated by the seasons rather than by the sudden absence of food. Slime molds will also be affected by the seasons, but in addition, they are also able to survive unexpected minor fluctuations in the presence (or absence) of their bacteria food. This means that they are subject to the random changes of local weather; if the conditions, such as the temperature and the humidity, are right for the bacteria to grow, then the amoebae can eat and thrive. If suddenly there is a drought or a freeze, then all activity will stop, but their future is locked in their dormant spores. As soon as it rains or warms up after a cold spell, the spores will burst open, and the emerging amoebae will immediately start engulfing bacteria. New fruiting bodies with a new collection of dormant spores will appear as little as 4 days later. Their life cycle is adapted to cope not only with random, short-term fluctuating environmental conditions but with long-term ones as well. The resistant spore can remain viable for long periods; in cooler climates, the spores can survive a winter and hatch an amoeba in the spring. (In the laboratory, spores kept in the refrigerator will remain viable for a number of years.) And only one spore is needed to start a next generation because this is an asexual life cycle.

Let us add to this picture the role of spore dispersal. These slime molds are built to facilitate the spreading of their spores. Here is a brief list of how they do this: The most obvious way is they stick up in the air on their slender stalk. The spore masses are sticky and will glom on to anything they touch. The soil surface is crawling with all sorts of invertebrates, and they will transport the spores into new territories short distances away. They accomplish greater distances by being picked up by animals; cellular slime molds are found in the dung of many animals. A study in India from the Mudumlai forest reserve has shown cellular slime molds in the dung of spotted deer, tiger, elephant, wild dog, sambar, porcupine, gaur (Bison), panther, hyena, and barking deer (also, Yak dung from the northwestern Himalayas at 5300 meters was a rich source, too; Sathe et al. 2010).

The champion distances for dispersal were revealed by Suthers (1985) in my lab. She is an ardent bird bander and decided to see whether migrating, ground-feeding birds carried slime mold spores, and indeed, they did, carrying them thousands of miles.

Now, if we add the arbitrariness of the weather, we will see unpredictable, seemingly random changes from ideal bacteria-foraging conditions to the total paralysis of feeding conditions by freezing or drought. Cellular slime molds are ideally equipped to cope with such environmental fickleness. This is also true for other small beasts that live in the soil. For instance, the many species of small fungi, or mold, with their fruiting bodies that are similar to those of slime molds, follow the same survival tactics. All the organisms that exhibit these properties are small.

If we use cellular slime molds as a representative microorganism, we find fundamental differences in larger eukaryotic forms. One is that there appears to be a lack of competition in the smaller forms. If food is there, then it is gobbled up; if it is gone then immediate suspended animation takes over until new food arrives. By contrast, larger organisms are perpetually in competition to get their share of the food; it is always a struggle for their existence. They lack the ability to turn into a spore; the closest they come to it is quite different, such as hibernation in animals and dormancy in the seeds of plants.

Large organisms have persisted across evolutionary time by adopting another approach to environmental change. It is a strategy that is fundamentally different: Rather than specializing in extreme flexibility, they specialize in the maintenance of stability and an internal resistance to environmental change. With increased size, organisms become more self-sufficient and independent. Their size increase is initially due to multicellularity, and these multicellular groups of cells become progressively sealed off from the environment. Instead of bowing to unpredictable changes in the environment, which, as we have seen, is the way of small cellular slime molds, they isolate themselves so that they become impervious to environmental fluctuations; they gain in independence while they lose in flexibility and are no longer at the mercy of the minor ups and downs of their surroundings. Their bodies, be it that of a tree or our own bodies—all larger animals and plants—allow life to carry on stolidly in the most unsettled environments. In our own case, we even improve this isolation by behavior; when it turns cold, we put on extra clothing, and when it rains, out come our umbrellas and raincoats. With increased size, there has been a progressive trend toward an increase of independence from the vagaries of the environment; every mega-organism has become a self-contained and impregnable castle.

Now, I would like to briefly summarize some of my arguments that I have presented in previous essays. The most all-encompassing essay is in a small book (Randomness in Evolution). Some of the points made earlier in this article have been briefly mentioned before. What has not been mentioned here and is discussed at some length in the book is that there is an inordinately large number of species of microorganisms that have mineral shells; this is true for Radiolaria (approximately 50,000 species), Foraminfera (approximately 279,000 species), and Diatoms (approximately 100,000 species). The easiest explanation for this surfeit of forms is that for each group, they are not competing with one another; each species can manage just as well as the others, and they are selectively neutral. And this neutrality shows itself in another way, too: Because they all have mineral shells (silica or carbonate), they have been preserved as fossils in rock, and many of their shapes have remained unchanged for eons. This falls in step with the idea that they are relatively immune to the effects of natural selection. It is a point that puzzled Darwin (1861): “Why have not the more highly developed forms everywhere supplanted and exterminated the lower? …. If it were of no advantage, these forms would be left by natural selection unimproved or but little improved; and might remain for indefinite ages in their present little advanced condition. And geology tells us that some of the lowest forms, as the infusoria and rhizopods, they have remained for an enormous period in nearly their present state” (p. 135)

It is important to emphasize—and it must be firmly admitted—that the very existence of these microorganisms is the product of natural selection, which reigns supreme over all evolution. This is true even though all the forms they create might not be within reach of selection and therefore are neutral as far as selection is concerned.

Perhaps the most important difference between small and large organisms has to do with their development. A singe-cell diatom or radiolarian has a very abbreviated development, with very few steps compared with any larger organism. Both the adult and its offspring are very small, and the time to get from one generation is minimal, whereas it may take ages for a larger plant or animal. And during this extended time, there are innumerable steps that lead to their great increase in size. Each one of those steps is controlled by genes that supervise the building of the large adult. In order to do that, they must be perfectly attuned to be consistent generation after generation; any deviations are likely to be lethal. This has been called internal selection by Whyte (1965).

This process—this size increase, this increase in complexity—builds an organism with increasing powers to isolate itself from the environment. This brings us back to our previous point that one of the main differences between large and small organisms is how they are affected by natural selection. Large organisms are subject to internal selection and are fine-tuned by natural selection; small organisms are virtually unaffected by internal selection, so one might imagine that they are entirely at the mercy of external natural selection. But the evidence says otherwise: Rather, they are relatively immune to it and instead show an increase in selection neutrality. Their differences are of such a nature that selection cannot distinguish between them.

If we look at evolution from a great distance, we see a progression. Initially, when single cells were the only eukaryotic organisms living on the surface of the earth, they relied on a dormant stage—a spore or a cyst—to carry them over periods of a hostile environment. And this was also true of some of the primitive attempts of multicellularity, such as cellular slime molds. With a persistent selection for size increase, two of those early experiments of multicellularity managed to have the necessary materials to get even bigger; they were the ancestors of animals and plants. In this transition, natural selection favored organisms that isolated themselves from the vagaries of their environment, so size increase went hand in hand with increasing self-sufficiency. It is not natural selection that had changed with the increase in size over geological time, but it is its effects—its results—that have changed: Small organisms are more likely to be ignored by selection and commonly have neutral phenotypes; larger ones can no longer escape the tentacles of natural selection, and they have become progressively entangled. Larger organisms become self-contained, isolated bastions that are more independent of all that is about them. They have entered the world of Darwin.

With the various early versions of this essay, I needed help. I needed to know what were likely to be sticking points from the point of view of evolutionary biologists, and I wanted to be sure that my slime mold facts were correct. I want to give heartfelt thanks to the following, who were of invaluable help in guiding me: Peter Grant, Rosemary Grant, Laura Katz, Vidyanand Nanjundiah, Pauline Schaap, and Mary Jane West-Eberhard.

References cited