Comment on “Ecological constraints to mirror life”

Deepa Agashe1, Damon J. Binder2, Vaughn S. Cooper3, Kevin M. Esvelt4, Richard E. Lenski5,6, David A. Relman7,8,9

Authors are listed in alphabetical order. Affiliations: 1 National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India; 2 Coefficient Giving, San Francisco, California, USA; 3 Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; 4 Media Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; 5 Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA; 6 Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, Michigan, USA; 7 Department of Medicine, Stanford University School of Medicine, Stanford, California, USA; 8 Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA; 9 Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA

We welcome mathematical modeling of mirror bacterial invasion dynamics, and are glad to see some of our earlier comments taken into account in Version 2 of this preprint. Nonetheless, we continue to have significant concerns about certain points in this preprint. In particular, many of the models presented show that evasion of chirality-dependent sources of mortality could facilitate the invasion of mirror bacteria in diverse environments, consistent with prior work on the subject. Such sources of mortality are ubiquitous in densely populated marine and terrestrial ecosystems, as well as within multicellular hosts. Despite their own models demonstrating invasion is possible once such mortality is included, the text of the preprint repeatedly concludes that ecological dynamics “strongly limit” the ability of mirror bacteria to invade the global environment.

For a mirror bacterium to invade an ecosystem, it must be able to reproduce faster than it dies. As outlined in the 2024 Science commentary “Confronting risks of mirror life”, mirror bacteria would be largely or wholly resistant to predation and chirality-dependent microbial antagonism, which are major sources of bacterial mortality in many environments. They are similarly expected to evade most immune recognition in multicellular hosts, and thus the downstream responses that are a primary cause of pathogen mortality. The key question is whether the advantage from reduced mortality outweighs the disadvantage from reduced nutrient access. The answer is likely to depend on the specific environment and mirror bacterium. Chapter 8 of the Technical Report on Mirror Bacteria (https://doi.org/10.25740/cv716pj4036), which we co-authored and which accompanies the Science commentary, considers this question in detail, and finds that invasion appears plausible in many settings with bacterial predators, including most biodiverse and human-relevant ecosystems.

Many of the models highlighted in the main text of the preprint do not address this key issue. They represent mortality as chirality-independent (e.g., δ in the closed system, D in the chemostat), and in these cases the models indicate that mirror bacteria cannot invade. This result follows standard resource-based competition theory (Tilman 1982), in which, in the absence of predation, an invader unable to access a sufficient amount of limiting resource is excluded at equilibrium. But in the real world, the mortality rates of bacteria are not chirality-independent, and so these models do not capture the conditions underpinning the substantial concerns about mirror life.

When the preprint’s models do include chirality-dependent mortality, for example via a predator targeting the native population (Figure 4), mirror bacterial invasion is shown to be possible, even likely. This result, again, follows standard ecological theory: predation on a dominant competitor can allow invasion by a less competitive but predation-resistant species (Levin, Stewart & Chao 1977; Tilman 1982; Thingstad 2000). The preprint downplays this critical result, however, as “... context-dependent: it applies primarily when the natural ecosystem is already degraded, or when the predator exerts unusually strong top-down control over the natural population despite the availability of resources that could otherwise support growth.” But in resource-rich environments like surface waters, biologically active soils, biofilms, and host tissues, microbial mortality is often dominated by phage lysis, protist grazing, microbial antagonism, immune clearance, and other chirality-dependent processes. (Carlson et al. 2022 is one relevant reference for the surface ocean; many more are provided in Chapter 8 of our Technical Report). Top-down control in these ecosystems is not an aberration, and the evasion of chirality-dependent mortality could allow mirror bacteria to invade a wide range of environments.

The text of the preprint repeatedly neglects this essential point. For example, the abstract concludes that nutrient limitations and competitive exclusion “constrain [mirror bacterial] growth and persistence across a broad range of ecological conditions”, and the discussion states that “intrinsic nonlinearities associated with resource incompatibility and ecological competition function as an effective form of distributed containment”. Additionally, the Table I caption states that invasion “is highly unlikely under realistic conditions” and that “all models consistently indicate that mirror life faces strong ecological constraints”. Neither the abstract, introduction, results, nor discussion make it clear that this containment is a general result only when mortality is chirality-independent, even though many human-relevant or species-rich real-world environments are dominated by chirality-dependent mortality.

In fact, the preprint’s updated Supplementary Material (SM) presents additional models showing that invasion is plausible in realistic cases. Part I of the SM models a mirror autotroph (e.g., a mirror Prochlorococcus or Synechococcus), and concludes that invasion is possible “provided [the mirror autotroph’s] reduction in mortality from escaping predators and phages outweighs any catalytic handicap” – which it likely would, as explained in Chapter 8 of our Technical Report. Part II of the SM extends the closed-ecosystem model to explicitly incorporate chirality-dependent mortality from microbial warfare or antibiotics, and it again shows that invasion is predicted for a wide range of parameters (SM Figure 1). Unfortunately, the main text of the preprint neglects to discuss these important results, providing only a one-sentence note that the SM contains two other relevant case studies.

There are other important considerations that further weaken the nutrient-limitation hypothesis as a potential ecological containment for mirror bacteria, which are also not discussed in the preprint. For example, mirror heterotrophs could be engineered to catabolize natural-chirality sugars (e.g., via incorporation of the Paracoccus laeviglucosivorans pathway; Shimizu et al. 2012), whether for benign reasons like facilitating laboratory studies or possibly for nefarious ends. In any case, such engineering would substantially improve the growth rate and competitiveness of mirror bacteria, pushing the authors' model results deeper into the invasion regime (Figure 4). Mixotrophic and autotrophic mirror bacteria would enjoy still greater advantages. Further, even environments that cannot be stably colonized by mirror bacteria could still harbor significant populations through repeated re-introduction, for example from animal hosts. Both of these scenarios are discussed in Chapter 8 of the Technical Report, and they would expand the conditions under which invasion succeeds in this preprint’s own framework.

The paper also draws on two other arguments that we think are less than compelling. First, the absence of a "shadow biosphere" is cited as evidence that alternative biochemical systems like mirror life could not persist within the extant biosphere. This is a weak inference, as the absence is more plausibly explained by there being no evolutionary pathway to mirror life from the present biosphere on relevant timescales. Second, the preprint cites evidence that biodiversity can act as a “firewall” to invaders. While we agree that biodiversity can affect the likelihood that an ecosystem is invaded, it is important to note that biological invasion still occurs frequently in the real world, including in biodiversity-rich ecosystems like those in the tropics (Chong et al. 2021). Biodiversity may well raise the bar for invasion in some cases, but its effects can demonstrably be outweighed by the advantages discussed earlier.

Mathematical models can be useful in clarifying the conditions under which mirror bacterial invasion is possible, and the models presented in the preprint are a valuable contribution. However, it is important to interpret and present the results of these models as comprehensively and accurately as possible. We hope that the authors will consider further revising their article to clarify and emphasize how invasion risk depends crucially on the different types of microbial mortality (chirality-dependent and chirality-independent); to highlight that chirality-dependent mortality occurs across real-world environments; and to more accurately reflect what their models predict.

References:

Adamala, K. P., Agashe, D., Belkaid, Y., Bittencourt, D. M. D. C., Cai, Y., Chang, M. W., et al. (2024). Confronting risks of mirror life. Science, 386(6728), 1351-1353.

Adamala, K. P., Agashe, D., Binder, D. J., Cai, Y., Cooper, V., Duncombe, R., Esvelt, K., et al. (2024). Technical report on mirror bacteria: Feasibility and risks. https://doi.org/10.25740/cv716pj4036

Carlson, M. C., Ribalet, F., Maidanik, I., Durham, B. P., Hulata, Y., Ferrón, S., ... & Lindell, D. (2022). Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean. Nature microbiology, 7(4), 570-580.

Chong, K. Y., Corlett, R. T., Nuñez, M. A., Chiu, J. H., Courchamp, F., Dawson, W., et al. (2021). Are terrestrial biological invasions different in the tropics? Annual Review of Ecology, Evolution, and Systematics, 52(1), 291-314.

Levin, B. R., Stewart, F. M., & Chao, L. (1977). Resource-limited growth, competition, and predation: A model and experimental studies with bacteria and bacteriophage. The American Naturalist, 111(977), 3–24.

Shimizu, T., Takaya, N., & Nakamura, A. (2012). An L-glucose catabolic pathway in Paracoccus species 43P. Journal of Biological Chemistry, 287(48), 40448-40456.

Thingstad, T. F. (2000). Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnology and Oceanography, 45(6), 1320–1328.

Tilman, D. (1982). Resource competition and community structure. Monographs in Population Biology, 17. Princeton University Press.