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Science  29 May 2009:
Vol. 324, Issue 5931, pp. 1150-1151
DOI: 10.1126/science.1173088

Microbes use a broad palette of chemical transformations to harvest energy and nutrients, but they do not always accomplish these conversions on their own. Particularly in anaerobic environments, various metabolisms are stimulated by, or depend upon, partnerships (1). In this form of interaction—termed syntrophy—one organism typically converts the primary resource to an intermediate that can be used by a partner (which perhaps passes it along to the next, and so on). In other cases, one partner may use a resource and provide a different type of service in return, such as a trace vitamin or motility. Recent studies are beginning to shed light on the mechanisms by which such partners communicate and interact and on how such interactions emerge in the first place.

Recently, a novel interspecies signaling mechanism was found (2) between two syntrophic partners present in high-temperature anaerobic sewage digesters: the bacterium Pelotomaculum thermopropionicum strain SI and the methanogenic archaeon Methanothermobacter thermautotrophicus strain ΔH. P. thermopropionicum can ferment propionate to acetate, bicarbonate, and three H2 molecules, but this conversion is highly endergonic (ΔG° = 76.1 kJ mol−1). Propionate oxidation can proceed if the partial pressure of H2 is kept low by M. thermautotrophicus, which consumes four H2 molecules for every CH4 produced (combined ΔG° = −25.6 kJ mol−1). This interaction provides an energy source to M. thermautotrophicus while enabling propionate oxidation by P. thermopropionicum.

When grown together, these two strains form aggregates that are held together by the flagellum of P. thermopropionicum (3). The average distance between cells of each species needed to achieve the observed growth rate is just 2 µm (see the figure, panel A). Shimoyama et al. (2) have uncovered an additional role for flagellum adherence: an interspecies signal that stimulates methanogenesis in M. thermautotrophicus (see the figure, panel B). The flagellar tip protein (FliD) from P. thermopropionicum induced widespread changes in gene expression in M. thermautotrophicus, including transcripts encoding hydrogenases and many of the enzymes of methanogenesis. In M. thermautotrophicus monocultures, stimulation by FliD led to a sharp increase in the rate of H2 use, and hence CH4 formation. Given that FliD adherence was only found with two methanogens across 21 genera screened, this appears to be a fairly specific, but not unique, characteristic of this pair.

This flagellum-dependent communication system differs from other known interspecies signaling systems (4) in that it is not mediated by a small molecule or peptidoglycan, but rather by a protein constituent of a cellular appendage. In this regard, the system resembles within-species recognition, for example, in slime mold (5), yeast (6), and the bacterium Proteus mirabilis (7). In these systems, recognition via shared surface loci is relevant for partner recognition and mediates multicellular behaviors such as forming a fruiting body, flocculation, and the formation of swarm boundaries, respectively. It may be that non-diffusible signals such as appendages are preferable for associations in which the partners must be arranged within a few micrometers to function optimally.

Perhaps the most intricate, highly developed microbial consortium thus far identified is the pairing known as “Chlorochromatium aggregatum” (8). This assemblage contains a single, motile β-proteobacterium (central bacterium) encrusted with a layer of nonmotile photosynthetic green sulfur bacteria (epibionts) (see the figure, panel C). Rather than overcoming thermodynamic constraints, the driving force for this consortium appears to be behavioral: The nonmotile photosynthesizers hitch a ride on their partner to move to their optimal depth in stratified lakes (no O2, plenty of H2S, and light of a wavelength matching the absorption maximum of their pigments). The photosynthesizers appear to pay their fare through supplying the central heterotroph with fixed organic carbon. Wanner et al. (8) have reported evidence for specialized attachment structures at the point of contact of each photosynthesizer with the central cell; furthermore, periplasmic tubules extending from the central bacterium appear to generate a continuous periplasmic space between all partners (see the figure, panel D). Well-developed signaling mechanisms—perhaps mediated by surface structures—probably also underlie this partnership.

From an evolutionary perspective, these sophisticated symbioses illustrate two very different classes of interactions. In C. aggregatum, there appears to be reciprocation of two costly acts: motility in exchange for fixed carbon. Where investing in a partner comes at an expense, natural selection will only favor making this investment if the investing individual disproportionately benefits from its partner relative to genotypes that invest less (9). For microbes, there are two ways to disproportionately collect benefits: live in a structured population or recognize your partner (or kin) to bias interactions in your population. The sophisticated coupling of photosynthesizers to a central motile bacterium achieves the structure needed for positive feedback between the reciprocal altruistic acts.

Physical associations in microbial consortia.

In a first example of microbial symbiosis, P. thermopropionicum flagella adhere to M. thermautotrophicus (A) to facilitate between-organism H2 exchange (3). Furthermore, the FliD protein at the tip of the P. thermopropionicum flagellum stimulates methanogenesis by M. thermautotrophicus (B). In a second example, nonmotile epibionts completely surround a motile central bacterium in C. aggregatum (C). Specialized morphologies such as periplasmic tubules connect partners in this system (D). Laboratory studies of synthetic consortia have shown how P. putida (green) evolves to cover over the Acinetobacter sp. strain C6 (red) microcolonies from which they receive metabolites (E).

CREDITS: (PANEL A) FROM (3). (PANEL B) ADAPTED BY P. HUEY/SCIENCE. (PANELS C AND D) FROM (3). (PANEL E) FROM (12)

In contrast, the between-organism H2 exchange between P. thermopropionicum and M. thermautotrophicus is a type of mutualism in which there are, seemingly, no costs to the parties involved. Each party exerts a positive effect on the growth of the other, but doing so appears to be in both organisms' immediate self-interest. Although neither party incurs a cost, this pair uses the same classes of mechanisms outlined above (structure and recognition) to take advantage of the positive feedbacks that emerge from interactions that are both local and selective.

How do microbial associations such as these emerge in the first place? One powerful approach to address this issue has been to take advantage of synthetic consortia in the laboratory. In these experimental populations, new partnerships can emerge through the action of selectively advantageous, naturally arising mutations. With the emergence of low-cost pyrosequencing, the mutations underlying cooperation can now be unraveled fairly easily (10).

Thus far, the closest laboratory incarnation to the physically structured metabolic exchanges described above has been the development of a coculture of Acinetobacter sp. strain C6 and Pseudomonas putida (11). In this system, benzyl alcohol is consumed by the first organism, but a portion is excreted as benzoate, which can be used by the second. Although this is a syntrophy, benzoate consumption is not necessary for substrate use, and in fact, growth by P. putida suppresses that of Acinetobacter, likely due to limiting O2 supply. Hansen et al. (12) found that P. putida quickly evolves altered lipopolysaccharides that allow it to overgrow its partner in biofilms, leading to greater exploitation of the supplied resource and further suppression of its partner's growth. This observation is in contrast to the prediction that growth in biofilms promotes altruism within a species because yield from substrate—and not just growth rate—contributes to fitness such that efficient use of substrate can be considered cooperative (13). Thus far, no laboratory experimental systems have shown the evolution of increased cooperation that came at a cost to the investing individual.

The study of the physiology, ecology, and evolution of synthetic consortia opens the door to many fascinating problems: Do outcomes predicted for mutualist pairs hold when combined into multiway interactions involving layers of cooperation and conflict? What factors influence the emergence of reciprocal specificity for partners? Can metabolic models provide testable predictions of conditions that will permit mutualisms? Will synthetic consortia evolve to stick together and enhance nutrient exchange (while also perhaps helping cheaters stick)?

Beyond these fundamental questions, there are myriad practical applications of engineered communities, such as the recent demonstration that a synthetic consortium based upon formate exchange can be used for H2 production (14). Through a synthesis of knowledge from studies of sophisticated natural interactions, as well as the evolutionary processes that transpire in novel partnerships, microbial consortia can serve as an exciting tool for a synthetic biology in which the assembled parts are not just genes, but organisms and communities.

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