Big questions in (microbial) ecology
An important element for any philosophy pertaining to microbial ecology is identification of key research questions.
A quick reminder of what I think would constitute progress in resolving questions, and where current research appears to fall short:
Progress in biology can be understood as a deeper understanding of mechanisms. This involves not only identifying the ‘parts’ but also the ‘causings.’
Prosser (2020) concluded that much of the recent work in microbial ecology is ‘descriptive’ – that is, it primarily addressed ‘parts’ but not causings.
Many current studies apply statistical analyses that generate correlations or similarity values – but it is never clear if these are causal
Note that in the post’s title “microbial” is parenthetical – many of the questions I highlight below have been identified in macrobe ecology over the years. For example, perhaps the essential question (still unresolved) posed by some of the giants in ecology has been in regard to the coexistence of species:
G. E. Hutchinson. 1959. Homage to Santa Rosalia or Why Are There So Many Kinds of Animals? The American Naturalist 93: 145-159
MacArthur, R. 1972. Coexistence of species. In: J. A. Behnke, ed. Challenging biological problems: Directions toward their solutions. New York: Oxford University Press, 253–259.
Over the subsequent decades, ecologists have occasionally gathered in symposia or in print to ponder the big questions. To my knowledge, the only instance of microbial ecologists doing so was a 1-day workshop held by the British Ecological Society’s Microbial Ecology Special Interest Group in 2016 (Antwis et al., 2017). Perhaps a session at the ISME meeting or an American Academy for Microbiology Colloquium would be valuable?
Some “hard-core” principles (sensu Lakatos).
Microbial interactions in ecosystems are nonlinear and hence generate very complex systems, even if the underlying rules are simple. Hence, there are no ‘laws’ but there are principles that can be gleaned from one system and applied to others.
The primary role of microbes in the biosphere is as catalysts of biogeochemical cycles. Some microbes may also have strong effects on the ecology of specific micro- or macro-organisms, via their roles as pathogens or symbionts.
Microbial activity is determined by the physical and chemical characteristics of the microenvironment, which is measured on a micrometer scale. However, microbial catalysis can have large effects on physical and chemical characteristics at larger scales.
The types and numbers of different microbes present in a habitat are consequences of deterministic ecological processes (such as the diversity and amounts of nutrient resources available) and stochastic processes (such as immigration and ecological drift).
Microbial ‘infallibility’. Restated here as … if there is a couple between an electron donor (organic or inorganic) and an electron acceptor that yields a Gibbs’ free energy change < 0, there will be a microbe capable of conserving energy and growing on that couple.*
Competitive exclusion principle – “complete competitors cannot coexist”. Of course, the devil is in the details here regarding “complete.” Does the habitat reach a “steady state?” Is the habitat fractured in either time and space? Are organisms competing for some resources but have access to alternatives for which there is no competition?
For resource-based competition some postulates are …
Shortages of a single essential resource are sufficient to limit the microbial biomass that can accumulate (Liebig’s “law of the minimum”)
Growth of microbes on the limiting nutrient (or a set of nutrients) will depress its concentration to a value that limits microbial growth rate.
Competition among microbes for low concentrations of a limiting nutrient and temporal variability in its availability both serve as strong selective forces in natural habitats.
Big questions that need answers
Here are about 15 from my perspective, grouped into various categories of ecological research
Physiological ecology
Are there definable “life-history” strategies among bacteria and what are their physiological bases?
Maybe not? Stone et al. (2023) Life history strategies among soil bacteria—dichotomy for few, continuum for many. ISME Journal 17: 611-619 https://www.nature.com/articles/s41396-022-01354-0
Jones, SE and Lennon, JT (2010) Dormancy contributes to the maintenance of microbial diversity PNAS 107: 5881-5886. https://doi.org/10.1073/pnas.0912765107
How do resource pulses affect resource use and competitive interactions between microbial species?
This gives me the opportunity to cite one of my all-time favorite papers (with the 3 Odum brothers as authors!) — Odum WE, Odum EP and Odum HY (1995) Nature's Pulsing Paradigm. Estuaries 18: 547-555 https://link.springer.com/article/10.2307/1352375
The pulsing in estuaries is of course a no-brainer, but they point out that pulsing occurs at all spatial and temporal scales and can be due to an external force (e.g., tides) or internal oscillations of the system
Population ecology
Is the stability of ecosystem function a consequence of an instability of individual species’ population dynamics?
Are population densities determined primarily by density-dependent factors (e.g., resource supply or predation) or density-independent ones (e.g., water availability or temperature)?
Community ecology
What is the relative importance of different ecological processes – deterministic (selection) vs stochastic (dispersal and ecological drift)? Does this vary systematically across ecosystems? This pits the ‘classical’ view (selection) vs Stephen Hubbell’s neutral theory.
Hubbell, S.P. (2001). The Unified Neutral Theory of Biodiversity and Biogeography. Princeton University Press. ISBN 9780691021287
What is the relative importance of physical/chemical constraints vs biotic interactions in determining the composition and diversity of microbial communities.
How do spatial and temporal environmental heterogeneity influence diversity?
This may also entail a sampling problem (e.g., soils) – are you sampling not “a” community but many communities?
How important are rare species in the functioning of ecological communities?
Which types of biotic interactions have the greatest importance – competition that winnows diversity / results in niche specialization or co-operative behaviors.
When I read articles on the microbiome, there can be a whiff (although rarely explicitly stated) of a Clements-ian view (community / microbiome as super-organism). I suppose the crudest metaphor from economics for this view is that natural selection has operated to create a bunch of socialists, whereas I tend to think of microbes as rapacious capitalists. It is clear that both socialism and capitalism exist in the microbial world, but precious little data on their relative importance.
Which ecosystems and what properties are most sensitive to changes in community composition?
Ecosystem ecology
Is there a “balance of nature”? The concept suggests that there are mechanisms in ecosystems that produce stability such as resilience, variability, persistence, and resistance.
The Balance of Nature?: Ecological Issues in the Conservation of Species and Communities 1st Edition by Stuart L. Pimm (Author)
What is the relationship between microbial diversity (functional type, species, ecotype) and community and ecosystem functioning? Is high stability of ecosystem function associated with instability of individual species’ population dynamics?
What factors determine the resilience of ecosystems to external perturbations? (and what are our criteria for resilience?)
Are there general principles of ecosystem properties and dynamics that are shared between marine, freshwater and terrestrial systems?
How does spatial structure influence ecosystem function – what methods can we apply to integrate between spatial scales?
What do you think are the important questions in microbial ecology? I would love to hear from you!
Coda
Plant and animal ecologists have struggled to answer the very similar questions they grapple with — might it be that microbes, with their small habitat/ecosystem size and relatively short generation times represent much better systems to experimentally resolve these questions under tractable conditions of time, space and replicability?
Note
*See O’Malley MA, Walsh DA (2021). Rethinking microbial infallibility in the metagenomic era. FEMS Microbiology Ecology, 97: fiab092 for the interesting history of this idea.
Reference
Rachael E. Antwis et al. (2017) Fifty important research questions in microbial ecology. FEMS Microbiology Ecology 93 https://doi.org/10.1093/femsec/fix044
Today’s moment of Zen
I’ve been working through some images I took in New York City this past February. This is just outside the Oculus, near the 9/11 Memorial in lower Manhattan
