Cooperation and Competition Were Primary Driving Forces for Biological Evolution Open Access

Charles Darwin (1809–1882), sometimes considered to be the greatest, most influential biologist who ever lived [1], established the generally accepted principle that “Evolution of Species Depends on Survival of the Fittest” [2]. In fact, the phrase “survival of the fittest” was made famous in the fifth edition (published in 1869) of On the Origin of Species. It suggested that organisms that were best adjusted to their environments, and able to effectively compete with their neighboring organisms by competing for nutrients and favorable conditions, are the most successful in surviving and reproducing. However, Darwin borrowed the phrase “survival of the fittest” from English sociologist and philosopher Herbert Spencer, who first used it in his 1864 book, Principles of Biology. The word symbiosis was first used in 1876, 6 years before Darwin’s death, and it is unlikely that Charles was aware of this term. Nevertheless, he certainly knew that two or more species, even of greatly different types of organisms, could live in a cooperative systemic group where each of these organisms contributed to their successful co-existence. In fact, Darwin was aware of Ramalina menziesii, the world’s largest lichen, although he was not in a position to explain its intricacies [3]. In many such cases, symbioses allow survival and growth when, without them, the unavailability of one or more essential nutrient(s) under specific conditions prevents survival [4, 5].

A prime example of a symbiosis, often cited as an example of this occurrence, is the three-way symbiosis of a lichen growing on a bare rock, in which a fungus breaks down rock to provide minerals for the colony, an alga provides organic carbon through photosynthesis, and a cyanobacterium provides ammonium via nitrogen fixation [6, 7]. While this example has been known for many years, and other examples were similarly recognized before Darwin’s time, most biologists had no idea of how important symbioses might have been to the early development of life on earth [8‒10].

The realization of this last suggestion provides one of the bases for the present postulate regarding the early development of life on earth. Survival of the fittest may have relied as much on cooperation as on competition (or even more so), especially during early life on earth, before the development of autonomous large-genome organisms. However, we now know that these symbioses are still prevalent today, especially in the prokaryotic world as discussed here [11‒13]. This discovery also has implications regarding how large fractions of the living world coexist today, and how these cooperative relationships contributed to the evolution of simple organisms into the more complex [11, 14]. Also, of interest is the probability that pathogenesis is closely related to and may have arisen from symbioses as noted previously [13]. They also provide clues as to why we humans preferentially live in peaceful cooperative groups of societies rather than at war [15] (see concluding section).

In 1905, Konstantin Merejkowsky (also spelled Constantin Mereschkowsky), a little-known Russian botanist, published a paper concerning his view on the nature and origin of chromatophores (chloroplasts/plastids) in plants and algae [16]. The general concept expressed is largely accepted today by the biological scientific community and is often called the “endosymbiotic theory of eukaryotic organelle evolution,” or simply “the endosymbiotic theory.” It accounts for the appearance of mitochondria from alpha-proteobacteria and plastids from cyanobacteria. Merejkowsky postulated that plastids in plants arose from cyanobacteria via a pathway involving first endosymbiosis of this photosynthetic bacterium within the cytoplasm of the future plant cell, followed by selective functional loss (from the cyanobacterium) with retention of the photosystem that mediates photosynthesis. This suggestion was based on a body of information, much of which proved to be erroneous or irrelevant, but which nevertheless led to the right final conclusion [16]. It is wonderful when one can arrive at the right conclusion for the wrong reasons; as such, scientists are usually forgiven for their experimental or conceptual errors! Interestingly, Merejkovski based his revolutionary suggestion in part on the much earlier work (in 1883) of the German botanist, Andreas Franz Wilhelm Schimper, who had used primitive microscopes to observe chloroplasts in plants growing and dividing independently of the host plant cell in which these plastids were found (see [17]).

Following World Wars I and II, the endosymbiotic theory fell into disrepute and remained so for nearly half a century. This was in part due to the fall of German science resulting from the disastrous impact of these two wars which left Germany in shambles, physically, economically and mentally. These wars effectively prevented the continuance of fruitful science in this country and much of Europe (see, for example, [18‒20]). In fact, many of the early scientific advances made around the turn of the 19th to the 20th century, for example, by T. Engelmann and W. Pfeffer, were largely forgotten, leaving advancements in biology at a near stand-still.

Merejkowsky’s endosymbiotic hypothesis [21] was rejected and replaced with another theory, suggesting that chloroplasts derived from the cytoplasmic constituents of the developing plant cell. The great advantage of the originally postulated endosymbiotic theory was and still is that two or more organisms can combine their dissimilar metabolic capabilities within a single cooperative and complementary entity that allows both organisms to have greater evolutionary potential than does either one alone. This evolutionary potential may include (1) increased growth rates, (2) greater reproductive frequencies, (3) greater sustainability, (4) a broader range of nutrients, and (5) decreased sensitivities to toxic compounds and conditions.

Recently, the earlier suggestion that chloroplasts arose via endosymbiosis from cyanobacteria has been extensively confirmed and revised, particularly using comparative plastid and cyanobacterium genomics, although other standard physiological and biochemical approaches have also been used [22]. Now there is essentially no doubt in the scientific community that plastids in plants and mitochondria in most major Eukaryotic subdivisions arose via initial endosymbiotic events from cyanobacteria and proteobacteria, respectively (Portier, 1918, cited in [23]). This view was hotly supported by Dr. Lynn Margulis who had been exposed to the early ideas put forth by Merejkowsky and others [16, 23‒25]. This now well-established concept represents only one aspect of the general idea presented here that cooperation (i.e., symbiosis) played a dominant role in the evolution of life on earth, particularly during the early periods when living organisms were gaining the ability to survive independently of other organisms.

Among the earliest well-characterized associations of prokaryotic organisms are the pathogenic relationships of small bacteria of the genus Bdellovibrio with other Gram-negative bacterial species, many of which (E. coli, Salmonella, Klebsiella, etc.) can be parasitized by Bdellovibrio species, δ-proteobacteria [26]. Two types of parasitic modes are recognized for these nasty creatures: B. bacteriovorus (Bba) and B. exovorus (Bex) are normally obligate predators of other Gram-negative bacteria, but while Bba grows in the periplasm of the prey cell after penetrating the outer membrane, Bex grows externally, often attached to the outer surface of the outer membrane of the host bacterium [27]. Surprisingly, these two species exhibit very different complements of transport systems: Bba has 103 more transporters than Bex, 50% more secondary carriers, and 3 times as many major facilitator superfamily-type carriers. Moreover, Bba has far more metabolite transporters than Bex; it has 2 times more carbohydrate uptake and drug efflux systems as well as 3 times more lipid transporters [27]. Bba also has polyamine and carboxylate transporters apparently lacking in Bex [28]. The genomes of both contain unexpectedly large numbers of pseudogenes and incomplete metabolic systems, suggesting that they are undergoing genome size reduction with a rapid loss of function. This observation suggests that their virulent lifestyles were a relatively recent evolutionary development [27].

The life cycle of Bba consists of four phases: (1) an attack phase, (2) an outer membrane penetration phase, (3) a periplasmic growth phase, and (4) a final synchronous cell division stage accompanied by host lysis [29, 30]. Figure 1 shows this cycle in some detail. During the attack phase, Bba swims rapidly, collides with its prey with a “bang,” and attaches. During the penetration phase, Bba becomes irreversibly anchored on the prey cell surface before penetrating into its periplasmic space using a complement of cell wall/outer membrane hydrolases for cell envelop digestion. Once it has crossed the outer membrane barrier, the outer membrane of the host apparently reseals, and the parasite grows without cell division, forming an elongated, “snake-like,” multinuclear cell. After forming this osmotically stable “bdelloplast,” the Bba snake-like structure synchronously undergoes septation, generating multiple uni-nuclear progeny cells, which lyse the host envelope and escape to infect other host cells [31].

Bex infects Gram-negative bacteria using a very different approach. Bex grows completely outside the prey cell instead of in the periplasm, but it utilizes the prey cell contents as nutrients for growth. This epibiotic (cell surface) predator shares 93% of its 16S ribosomal RNA (rRNA) gene sequence with Bba, showing that they belong to the same genus. Molecular data and their different life cycles revealed their commonalities and differences [26]. How it remains attached to the prey cell surface is not known, as membrane fusion does not occur. During epibiotic growth, instead of the long aseptate filament as observed for Bba, division occurs by binary fission [33]. While these two obligatory pathogens use different modes of pathogenesis, they can mutate under specific conditions, allowing them to grow axenically, in the absence of a host cell [34]. It is worth noting that in the single circular chromosome of Bba, there are about 30% more protein-encoding genes than in Bex. Since pathogenic and symbiotic bacterial lifestyles probably have common origins, the latter could have given rise to the former [35].

In 2002, a novel small type of archaeon was discovered in an apparent symbiotic relationship with a different, larger-sized, archaeal species. This tiny archaeon was called Nanoarchaeum equitans, and it was much smaller than most previously studied prokaryotes [36‒38]. This organism could not grow by itself, could grow only very slowly in the presence of its primary co-symbiotic archaeal partner, and required the presence of other prokaryotes, including bacteria, to grow at more substantial rates. The symbiotic pair is portrayed in Figure 2, showing the established and presumed metabolic pathways in both organisms. N. equitans has minimal metabolic capacity comparted with its symbiotic partner.

The “Nanoarchaeota” comprise a novel archaeal phylum, forming a unique, deep branch in the 16S ribosomal (r)RNA-based phylogenetic tree of life. N. equitans was the first cultivated representative in this new phylum and proved to be a hyperthermophilic, anaerobic, nano-sized coccus. The genome of N. equitans was sequenced, yielding many details of this unusual organism [40]. It is an obligate symbiont, growing in co-culture with the crenarchaeon, Ignicoccus hospitalis [41]. Ribosomal protein and rRNA-based phylogenies placed its branching point early in the archaeal lineage. The N. equitans genome encodes the machinery for information processing and repair but lacks genes for lipid, cofactor, amino acid, and nucleotide biosyntheses. When it was discovered, it was the smallest microbial genome sequenced, and it was also one of the most compact, with 95% of its DNA predicted to encode proteins and stable RNAs [38]. Its limited biosynthetic and catabolic capacities indicated that N. equitans’ symbiotic relationship with Ignicoccus could be parasitic, and if so, it would be the only known archaeal parasite. Unlike the small genomes of bacterial parasites/symbionts that had undergone reductive evolution [42], N. equitans was found to have few pseudogenes or extensive regions of noncoding DNA. It may therefore have been a basal archaeal lineage with a highly reduced genome that might not have resulted from gene loss during its association with its host; instead, it may have had a small genome size as a characteristic of its presumed fellow phylum members [43].

Lipid analyses of N. equitans and its host revealed that both archaea contained simple and qualitatively similar glycerol ether lipids, showing only differences in the amounts of certain components; total lipid extracts revealed that archaeol and caldarchaeol were the main core lipids, sometimes glycosylated [44]. In fact, the predominant polar headgroups consisted of one or more sugar residues attached either directly to the core lipid or to it via a phosphate group [44]. Moreover, horizontal gene transfer (HGT) between N. equitans and archaeal species of other phyla has been demonstrated [45]. Unexpectedly, N. equitans was found to create functional tRNAs from separate genes encoding their 5′- and 3′-halves [46, 47], and this property has been considered to be ancestral [48]. In fact, split and intron-containing tRNA genes as well as some protein-encoding split genes have been identified [49]. Thus, N. equitans may be a “living archaeal fossil” [50], and RNA processing in N. equitans may exhibit unique properties not found in most prokaryotes [51].

The highly specialized association of N. equitans and I. hospitalis could not be assigned to classical symbiosis, commensalism, or parasitism; it appeared to be unique [52]. Ultra-structural analyses revealed that the two membranes of I. hospitalis are frequently in direct contact with that of N. equitans, possibly as a prerequisite for transporting metabolites from the cytoplasm of one cell to that of the other [53]. This interaction probably involves major envelope proteins of the two archaea [54]. N. equitans apparently diverts some of its host’s metabolism and cell cycle control to compensate for its own metabolic shortcomings [55]. It has been suggested that this mechanism might have contributed to the endosymbiotic origin of eukaryotes [56]. Regardless of this possibility, more recently, other symbiotic nanoarchaeota species have been isolated [57, 58]. Cellular compartmentalization in I. hospitalis has prompted speculation that much of the eukaryotic endo-membrane system could have originated from Archaea [59].

In 2015, a revolutionary paper appeared describing a group of roughly 35 novel phyla of bacteria, none of which had been recognized previously [60]. This number of phyla has more recently increased to over forty [61]. These candidate phyla radiation (CPR) genomes proved to be small, and most lacked genes encoding numerous biosynthetic pathways. Owing to divergent 16S rRNA gene sequences, 50–100% of organisms sampled from specific phyla would evade detection in typical cultivation-independent surveys. Thus, these organisms had sequences that were not recognizable by the traditional techniques and assumptions available at that time. Additionally, CPR organisms often had self-splicing introns encoding proteins within their rRNA genes, features rarely reported in previously studied bacteria. Furthermore, these organisms had unusual ribosome compositions. Most were missing a ribosomal protein often absent in symbionts, and specific lineages were missing ribosomal proteins and biogenesis factors previously considered universal in bacteria [60, 62].

Studies by Heimerl et al. [59] led to the realization that our previous idea of the prokaryotic domain had been sorely deficient [63], and that previous methods used to identify organisms were inadequate [64]. Further work revealed that these organisms exhibit phenomena that are atypical of bacteria. For example, unusual respiratory and nitrogen metabolic pathways were discovered [65, 66], and novel tRNAs, not previously identified in other bacteria, were also found [67]. Retro-element-guided protein diversification proved to abound in vast lineages of these bacteria as well as in archaea [68]. It was proposed, with good reason, that a large percentage of these organisms were obligatory symbionts that could not survive on their own [69]. The diversity of the many novel phyla of CPR bacteria (presented on the upper left side of the tree, shown in Fig. 3) approaches that of all previously known bacteria (shown on the upper right side of the tree). All archaea and eukaryotes cluster together at the bottom of this radial tree.

The recent recovery of genome sequences for organisms from phyla with no previously isolated representatives (candidate phyla) via cultivation-independent genomics (meta-genomics) enabled the delineation of major new microbial lineages, namely, those that belonged to the bacterial CPR groups of organisms, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaeota, Woesearchaeota, Pacearchaeota, and potentially Altiarchaea) archaea (a superphylum of archaea with many members showing novel signs of HGT from other domains of life; they were called nanoarchaea due to their small sizes [nanometric] compared to other archaea) [72‒74], and Asgard archaea (see below) [69]. CPR, DPANN, and Asgard organisms are inferred to be mostly symbionts [75]. These organisms as well as many others have multiple origins, leading to the appearance of tangled phylogenetic trees [76‒78].

Asgard genomes (see the next section) encode proteins previously thought to be eukaryotic-specific, and their inclusion in phylogenetic analyses results in the placement of eukaryotes as a branch within the Archaea (see below). Castelle et al. [69] further illustrated how these new genomes have changed the structure of the tree of life and altered our understanding of biology, evolution, and metabolic roles in biogeochemical processes.

It was also discovered that newly identified CPR bacteria had unusual lipid compositions with higher concentrations of lyso-lipids [79]. Most importantly, for the arguments to be made in this article, the widespread occurrence of nano-prokaryotes in Nature today suggests that they have existed on earth, perhaps from the earliest times when life first appeared. If so, the existence of cross-organismal cooperation in the form of symbioses may have provided the primary guiding force for early organismal community organization. This may not have involved simple pairs of interconnected organisms, but whole communities of microbes, each member of which contributed one or more element(s) to the entire community, allowing the Community as a Whole to grow, although not one of these organisms, when alone, could survive. In support of this suggestion, many CPR bacteria have rich repertoires of quorum-sensing protein-encoding genes in their genomes, and these are presumably responsible for intra- and inter-species as well as inter-phylum communication [80].

These discoveries became possible due to the development of meta-genomics, whereby the DNA of entire communities of organisms was sequenced without separation of the different species from each other [75]. The characterization of CPR bacteria has led to findings regarding symbioses involving distantly related organisms. For example, the discovery of niche partitioning in the shrimp, Rimicaris exoculata holobiont, revealed the first case of a symbiotic Zeta-proteobacterium [81]. Symbiotic chemosynthetic microbial communities established primary production and higher trophic levels in deep-sea hydrothermal vents. R. exoculata, which dominates animal communities along the Mid-Atlantic Ridge, houses a complex bacterial community in its enlarged cephalothorax. The dominant bacteria present are from the taxonomic groups: Campylobacteria, Desulfobulbia, alpha-proteobacteria, Gamma-proteobacteria, and some recently discovered iron oxyhydroxide-coated Zeta-proteobacteria. This epibiotic consortium uses iron, sulfide, methane, and hydrogen as energy sources, and functional diversity in a consortium enables multiple symbiotic strains to coexist in animals [81].

Another example involves the stable binary cultures of symbiotic Saccharibacteria within the oral cavity [82]. A unique predatory mode in the CPR bacterium, Vampirococcus lugosii, has also been reported [83]. As still another example, genome-centric metagenomics has revealed the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system [84]. Finally, these symbiotic relationships can cross domain boundaries, as in the cases of bacterial-archaeal associations such as the soil CPR bacteria, which encode components of aerobic metabolism and co-occur with nano-archaea in the rare biosphere of rhizosphere grassland communities [85, 86].

The archaea include a substantial fraction of the microbial diversity on earth, being members of marine and soil microbial environments. With the emergence of metagenomics, the diversity of the Archaea rapidly increased. The diverse domains of Archaea have been divided into the superphyla of (1) Euryarchaeota, (2) TACK (Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota), (3) DPANN, and the most recently described (4) Asgards (named after the home of the Norse gods). The Asgard archaea originally consisted of four phyla, named after four of the Norse gods: Lokiarchaeota, Thorarchaeota, Odinarchaeota, and Heimdallarchaeota. However, a recent report claims to have expanded the superfamily with 6 additional phyla [87], and further expansion is likely to result from further sequencing studies. Metabolic pathways identified or presumed in the four originally characterized Asgard phyla are summarized in Figure 4.

Members of the Asgard archaeal superphylum have been described from a diverse range of habitats, including hydrothermal sediments [89], microbial mats [90], and a range of freshwater [91] and marine [92] environments. In all such environments, most organisms are small with small genomes, insufficient to code for the biosynthetic and catabolic enzymes and transporters that are required for substrate metabolism, energy production, and the synthesis of essential cellular macromolecules. Consequently, it seems that these small cells must depend on cooperative relationships among large numbers of dissimilar species, each one contributing one or more essential metabolites; these organisms can survive only via the exchange of all essential life-endowing compounds derived from different members of the microbial community.

For many years, the origin of eukaryotes represented an unresolved puzzle in evolutionary biology [93]. Current research is providing compelling evidence that eukaryotes evolved from a merger between a host of archaeal descent and an alpha-proteobacterial endosymbiont that de-evolved into mitochondria and then into still other eukaryotic organelles. Asgard archaea so far appear to be the closest archaeal relatives of eukaryotes yet discovered [93]. This suggestion has helped to elucidate the identity of the putative archaeal predecessor of eukaryotes. Whereas Lokiarchaeota are assumed to employ a hydrogen-dependent metabolism [93], little is known about the metabolic potential of other members of the Asgard superphylum.

It is possible, and seems likely, that the central metabolic pathways of Asgard archaea provided the essential framework to help explain the origin of multi-organellar eukaryotes. Several analyses indicated that Thorarchaeota and Lokiarchaeota encode proteins necessary for carbon fixation via the Wood-Ljungdahl pathway and for obtaining reducing equivalents from organic substrates [93, 94]. By contrast, Heimdallarchaeum genomes encode enzymes potentially enabling the oxidation of organic substrates using nitrate or oxygen as electron acceptors [93]. The gene repertoires of Heimdallarchaeum and Odinarchaeum indicate that these organisms can ferment organic substrates and conserve energy by coupling ferredoxin reoxidation to respiratory proton reduction [93]. Altogether, the genome analyses clearly suggest that Asgard representatives are primarily organoheterotrophs with variable capacities for hydrogen consumption and production.

On this basis, a “reverse flow model,” an updated symbio-genetic model for the origin of eukaryotes that involves electron or hydrogen flow from an organoheterotrophic archaeal host to a bacterial symbiont, has been proposed [93]. In summary, the presence of eukaryotic signature proteins and the affiliation of Asgard archaea in phylogenetic analyses appears to suggest a two-domain topology for the tree of life (Fig. 3), with eukaryotes emerging from within the domain of archaea, as opposed to the eukaryotes being a separate domain of life [95, 96]. If a three-branch phylogenetic tree is preferred, two of the branches may be bacterial while the third will comprise all archaea and eukaryotes [97]. The greater apparent diversity of the bacterial domain, relative to the archaeal/eukaryotic domain, as indicated by the configuration of the tree, representing its diversity, tentatively suggests (but does not prove) that bacteria were the first inhabitants on earth, and that all else derived from them. In confirmation, an analysis has similarly led to the suggestion that the last universal common ancestor of all cells on earth (LUCA) had an autotrophic origin involving the Wood-Ljungdahl pathway in a hydrothermal setting. LUCA may have been a bacterial/archaeal hybrid or a bacterium with some archaeal properties [98].

Candidatus Atelocyanobacterium thalassa, or UCYN-A, is a metabolically streamlined N₂-fixing cyanobacterium previously reported to be an endosymbiont of a marine unicellular alga. Coale et al. [99] showed that UCYN-A has been tightly integrated into algal cell architecture and organellar division and that it imports proteins encoded by the algal genome. These are characteristics of organelles that show that UCYN-A has evolved beyond endosymbiosis and functions as an early evolutionary stage N₂-fixing organelle, or “nitroplast.” It seems to be the most recently identified eukaryotic organelle.

Cooperation rather than competition may have been the defining feature that allowed the early evolution of life on earth. The extensive consideration of symbiosis with respect to the importance of organismal cooperation rather than competition discussed here must have been particularly apparent during the early phases of life on earth [100]. No primordial life form could have had a full complement of metabolic and biosynthetic catalytic proteins that would allow it to reproduce in the presence of only abiotic sources. Instead, it seems much more likely that throughout early biological evolution on earth, most or all organisms were “partial” organisms, none of which had enough DNA to encode all life-endowing proteins/properties [101]. It thus seems likely that a consortium of “incomplete” organisms cooperated in allowing the entire community to grow, albeit slowly, by the exchange between divergent cells of essential small molecular compounds upon which life depends.

From these metabolites, macromolecules must have been constructed, but even these were probably synthesized in processes that involved exchange of the intermediates across cell boundaries [102]. The fact that symbiotic behavior, as we know it today, due to metagenomic developments, is far more prevalent and has always been so than was ever recognized in the past. Evolution “tends from simplicity to complexity,” not the other way around, although exceptions clearly exist, and the symbiotic hypothesis as enunciated here could have provided that pathway, leading from simple organisms to more complex organisms that could provide an increasing number of life’s essential molecules and processes from within [103]. Genetic recombination and interspecies gene transfer, mediated by transposons and plasmid-like elements as well as by phage and apparatuses of conjugation, would certainly have facilitated the events that brought these genetic elements together in a single cell [104].

Ecologists have suggested that the illusion of cooperation in biological communities, which are admittedly ubiquitous, may be a consequence of loss of function mutations arising in fully competent organisms [105, 106]. Symbioses are thus thought of as secondary consequences of genetic loss, and not as an ancient characteristic of primordial organisms [107]. Instead, apparent cooperativity among organisms may have resulted from fitness benefits gained from genomic streaming [108], that is, initially from mutational loss of function. Indeed, mutations in a microbe or any other organism can be induced by the investigator and then studied in the laboratory, as has been a favored approach taken by many microbial ecologists, primarily because it provides an easy means of creating an apparent cooperative relationship for study [105]. It has thus been suggested that the numerous examples of cooperativity cited in this article could have been a consequence of Black Queen dynamics. Indeed, mutational events have certainly accounted for the inabilities of many organisms to synthesize small molecules such as essential amino acids, nucleobases, and vitamins [109, 110] as the precursor organisms presumably had these capabilities, although they had been lost via mutations through evolutionary time due to the widespread availability of these metabolites and co-factors in the environment.

The Black Queen hypothesis cannot explain how life began; if life began here on this planet (or elsewhere in the universe, if we accept panspermia [111]), small genetically deficient primitive cellular organisms must have predominated during the early stages of life on earth [112‒114]. Complex large genome organisms encoding much greater metabolic capacities must have come along much later. It seems likely that the present-day relatively simple, small-genome organisms, such as nano-bacteria and nano-archaea, are relevant to early life [115]. In other words, the small, present-day, coccoidal prokaryotes (e.g., CPR bacteria and Asgard archaea [69, 116]) that live in microbial communities as a means of survival may be similar in state to the first life-forms that developed on earth [117].

In accordance with the arguments presented above, and in agreement with the suggestions of Chatterjee [117], we consider that current communities of small-genome organisms, referred to above, may reflect how life began. Virtually all such cases, revealed using metagenomic techniques, indicate that there are numerous deficiencies in these small organisms that do not fit the arguments put forth by the researchers who proposed the Black Queen hypothesis [69, 116]. It is much more likely that early organisms had minimal genomes, encoding very few metabolic pathways rather than large genomes encoding several or even many pathways, and they shared their metabolic potentials via inter-organismal metabolite and DNA exchange [118]. We need to think of a microbial community as an evolutionary unit that has been so throughout its long and ever-changing existence. While some cells have acquired the genetic capacity to encode all proteins necessary to generate a robust anabolic and catabolic metabolic network, allowing the minimization of symbioses via cell fusion and/or HGT, others have remained simple and “primitive” [119]. This is the argument presented here, namely, that mutualisms were important in the early biotic earth, and they still are in numerous microbiological communities today. Indeed, these nano-prokaryotes do not show signs of genetic loss such as partial gene fragments, pseudogenes, and retention of incomplete metabolic pathways.

It is worth noting that cooperation and competition are not necessarily in evolutionary opposition; one such process can enhance or promote the other [120]. In fact, it is not only true that cooperation obviates the need for complexity but also that complexity can obviate the need for cooperation [121, 122]. In this regard, it is interesting that, even today, we find millions of entire microbial communities everywhere in nature that rely on symbioses for their existence and propagation [116]. Thus, these two phenomena can even be cooperative; for example, some models of cooperativity depend on competition, and in these cases, cooperation involving multiple species, forming a competitive team, allow effective competition with another organism or team of organisms [123]. Thus, effective competition may create a need for cooperation. However, such cases can only be considered as examples, as millions of symbioses, such as that of a lichen, do not appear to depend on competition as far as is currently known [124].

Figure 5 presents illustrations of cooperation at different levels of cellular and organismal development as discussed in the previous sections of this article. Figure 5a shows cooperation at the cellular level for bacteria, some of which can differentiate with the formation of spores and fruiting bodies from vegetative cells (top), and cooperation between archaea and bacteria with the formation of organelles in an evolving eukaryotic cell (bottom). Figure 5b provides a more detailed illustration of the latter process by which endosymbiotic bacteria within an evolving archaeon become organelles of a eukaryote with permanent interdependences of the cell and the organelle (i.e., mitochondria that initially evolved from a proteobacterium and subsequently evolved into other organelles such as hydrogenosomes in some organisms) while chloroplasts, derived from cyanobacteria, arose in a similar endosymbiotic process. Figure 5c shows hundreds of cell types, developing into and giving rise to the formation of a multicellular animal from an egg and sperm to a fertilized egg, to an embryo, to a fetus, and then into a young animal. Finally, Figure 5d shows cooperation among members of a single species in the example selected, Homo sapiens.

This article focuses on the fascinating hypothesis that early life consisted of a community of “incomplete” (small genome) organisms rather than on distinct autonomous microbes such as E. coli. Thus, the concept of LUCA, according to the hypothesis put forth in this article, may not have been a single distinct microorganism, but a consortium of metabolically incomplete organisms from which the bacterial and archaeal lineages may have “crystallized” out. This concept provides a simple explanation for the fact that phylogenetic trees are quite different, depending upon which genes/molecules are used for their construction. If HGT was common in the early stages of life as we propose, this easily explains this composite situation. An additional early evolutionary scenario to consider may have involved the appearance of viruses. They may have co-evolved with the organisms from early times, that is, during the time of LUCA (or even before), and they easily could have contributed to the large scale HGT events that we propose led to the complexity that allowed microbes to develop autonomy.

How do these evolutionary considerations affect how we humans think about our own existences? When listening to the international news, one is led to believe that conflict and war are the dominant activities of the human species. It is worth mentioning, however, that war depends on cooperation among the members of both sides of a conflict. When we realize how many people are in conflict, versus how many live in peaceful cooperatives, or when we think about how many of the more than 200 countries that make up our international human community are at war, versus those that live in peace, we realize that also, in human societies, there are far more cooperative “symbioses” compared to those that perform conflicting activities, both at the individual level and at the level of countries or groups of related religious (or non-religious) beliefs or values [15, 125]. Moreover, each multicellular organism, whether animal, plant, fungal, archaeal or bacterial, is a cooperative organism in which all cell types that form the tissues, which in turn form the organs in plants and animals, function together as an incredibly complex synthesis in which each of the hundreds of cell types performs a function that supports the needs of the organism as a whole [126]. When any one of these functions is defective, disease or even death can result. Thus, it appears that “survival of the fittest” depends, and may have always depended, far more on cooperative behaviors than aggressively conflicting behaviors at many levels of biology, even in cases of complex multicellular organisms.

Recognizing these facts should provide an incentive for all human societies to live together in peaceful co-existence rather than in conflict [15]. This, however, can only happen if the citizenries of all or most societies have the resources needed to survive, and the availability of these resources depends on the ratio of our available resources to our human numbers. The human population is currently greatly in excess of what our planet can sustain, that is, sustain indefinitely [127]. If we do not peacefully solve this problem of human overpopulation, no matter how much we have, no matter how much we know, no matter how much we try, we shall never achieve a peaceful, considerate, cooperative coexistence of our planetary human societies with each other and the biosphere [128]. We need a new way of thinking, with respect to all components of the many life forms that comprise our complex interconnected web of life.

I thank Peter Kopkowski, Arturo Medrano-Soto, and Steve Baird for discussions and assistance with the preparation of this manuscript.

The author has no conflicts of interest to declare. Prof. Milton H. Saier, Jr., was a member of the journal’s Editorial Board at the time of submission.

This work was, in part, funded by the National Institutes of Health (Grant GM077402) and in part by private funds, both awarded to MHS. The funder had no role in the design, data collection, data analysis, and reporting of this study.

M.H.S. designed and performed all research required for this article. Published research efforts from his laboratory are cited.