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Linking evolution and dynamics of microbial ecosystems through theory and model organisms
OR
Exploring the evolution and metabolic balance of marine ecosystems across multiple scales of
space, time and biological organization
OR
The Need for conjoint studies in microbial ecology and evolution: the unity of biological
organization across multiple scales of space, time, and phylogeny
Using model systems and theory to explore the evolution and metabolic balance of marine
ecosystems across multiple scales of space, time and biological organization
CO-PI’s: , Nigel Goldenfeld, and Carl Woese
This project to understand the structure, dynamics and energy flow in Prochlorococcus and its
phages in the oligotrophic oceans will address the way in which collective interactions determine
population structure, metabolic balance and response to exogeneous perturbations in marine
microbial ecosystems.
Synopsis
The last decade of research on Prochlorococcus has significantly advanced our understanding of the
forces that shape the diversity and dynamics of marine microbial populations, and revealed the power of
model systems for advancing microbial oceanography. The next decade calls for the development of
tightly integrated experiments, observations, and theory. Here we propose an alliance that will
contemporaneously blend these branches of scientific inquiry through a single focus on the
Prochlorococcus model system. TOO PUSHY; more subtlety needed
Background
A major challenge in microbial oceanography is understanding how the interactions between microbes
and their biotic and abiotic environment manifests itself in emergent biogeochemical processes. A
powerful way to address this challenge is through theory-driven study of model organisms. As the
simplest, and most abundant, well-defined1, and well-studied, microbe in the oceans, Prochlorococcus is
a model worthy of continued development.
Research on Prochlorococcus to date has revealed, for example, that:
• Closely related cells (< 3% different in rRNA sequence) can display vastly different physiological
properties: Environmental conditions that are lethal to one, can be optimal for another.
• 3% seems about like E. coli vs Salmona sp. In any case some standard of comparison is needed
1
It can be “seen” in real time in the field using flow cytometry, and all Prochlorococcus cells differ by
< 3% in rRNA sequence.
• These ‘ecotypes’ display different relative abundances along gradients imposed by spatial and
temporal environmental variability.
• The degree to which ribotype can predict abundance along environmental gradients of light,
temperature, and nutrients in the field is a function of both the degree of sequence identity used to
define a taxon and the environmental variable.
• The global gene pool of the roughly 1027 Prochlorococcus cells in the ocean is enormous: The cells
share a core of 1200 genes, and on average carry 800 additional genes, 200 of which are unique to that
cell.
• A significant fraction of the non-core gene pool is located in hypervariable genomic islands which
carry signatures of horizontal gene transfer, hold clues as to important selective agents in different
environments, and to mechanisms of adaptation and evolution on environmentally relevant time
scales.
• Phage carry an arsenal of host-like genes that they employ to redirect host metabolism serving as an
exchangeable expanded gene pool that is subject to different selective pressures than the host
homolog.
• [Something about how finding nitrate reductase genes in DNA fragments of wild Prohlorococcus
instantly changed our image of the global nitrogen cycle: Suddenly a very significant fraction of the
global chlorophyll – ie. Prochlorococcus -- could utilize nitrate. Our culture collection, which
contained only strains that lacked this gene, had given us an entirely wrong impression of what
Prochlorococcus was capable of. What else are we missing?]
These and other observations have helped solidify a paradigm shift in our thinking about the very nature
of microbial systems and their evolution. Letting go of ‘Darwinian thinking’ in which communities are
shaped by the relative fitness of individual cells through ‘bottom up’ (growth limitation) and ‘top down’
processes (cell death), we view Prochlorococcus-and-its-phage (and by extension the entire microbial
system) as a single entity shaped and sustained by complex information exchange mechanisms.
Understanding the design of this system and how it responds to exogenous forces is essential for
developing predictive models of ocean biogeochemical processes. Moreover this “emerging picture of
microbes as gene-swapping collectives demands a revision of such concepts as organism, species, and
evolution itself” [your words… I love them!].
In concert with this paradigm shift has been the proliferation of theory designed to unveil the
mechanisms that underlay the structure and dynamics of microbial systems and their phage. What is
rare, however, is contemporary partnerships between theorists and experimentalists in which the theory
guides experiments and field observations and vice versa. That is the one of the goals of this work.
Driving Questions:
(1) What controls Prochlorococcus genomic diversity and ecotype abundance along gradients, and
in fluctuating environments with strong (e.g near Bermuda), and weak (eg. near Hawaii) external
forcing?
With a 6 year historical data set for Prochlorococcus ecotypes (along with all of the ancillary data) at
these sites, and archived DNA samples, we are in a good position to address this question. Classical
ecological theory is unable to account in detail for the observed phenotypic diversity, being based upon
the assumed role of periodic selective sweeps. Further, our previous work using the Prochlorococcus-
cyanophage model system has established that it is too simplistic to view their microbe-phage
interactions as purely antagonistic: the populations co-evolve and appear to establish a collective state
whose detailed features are still unexplored. We can test these ideas explicitly in Procholorococcus, as
well as construct detailed individual-based models emanating from the observational data that are
spatially-extended, and properly treat demographic fluctuations to model predation. Related questions
concern the distribution of ecotypes along a temperature/photon gradient, which appear to track growthoptima curves. Is this an expected outcome of (antagonistic) phage-predation, (cooperative) communal
dynamics, or something else? What is the sensitivity of communities to noisy environments – can
external variability in time and spatial heterogeneity drive diversity and quantitatively account for the
observed abundance distributions?
(2) What accounts for the population stability of Prochlorococcus-cyanophage communities? Thus
far there is no evidence for lysogeny in this system, but we have reason to suspect that it must be there,
and envision a number of approaches to reveal it – particularly though single cell sequencing. We also
propose experimental evolution studies designed to understand the rates of co-evolution of host-and
phage, greatly facilitated by next-gen sequencing. Are mutation rates, for example, elevated in cells
that are exposed steadily to viral attack? ISN’T LYSOGENY JUST AN EASILY RECOGNIZED
FORM OF STRESS RESPONSE
(3) How do we link population dynamics with energy flow in the Procholorococcus system? A
major challenge in ecology is linking population dynamics and biogeochemistry. The function of life is
to saturate every thermodynamic gradient in a biogeochemical system, and it can be argued that we do
not need to understand the details of “who” is doing it. But we suspect that the key to dynamics and
adaptability is in these details, and insights can be gained through studying Prochlorococcus which – in
a sense – defines the boundaries of the light harvesting zone of the oceans. Can thermodynamic ideas
be used together with the determined microbe-phage interactions to understand the abundance tails?
RANDOM SCRAPS BELOW HERE
Gaps in our Knowledge/Proposed Work (just listing random thoughts- not well formed at all!)
• Need a genetic system for Prochlorococcus to directly test hypotheses, and get at function of
hypothetical genes (the most highly expressed gene in the wild is a hypothetical!)
• Need to develop ways to understand the co-evolution of host and phage... and which phage can infect
which host in the wild
• Need to find the lysogens. They have to be there. (Relevant: Your paper modeling sysem with and
without lysogeny (I certainly cannot not understand that paper!)?)
• Experimental Evolution Experiments in the lab and the field: Sequence - Perturb- Select - Sequence
• Directed/selected isolation of Genomic variants
• Single cell genomics and population genetics in fluctuating environments.
• Programmed cell death equivalent
• Cell Cell communication
Why this would not be funded through conventional mechanisms
ONE GOOD REASON IS THAT IT CALLS INTO SERIOUS QUESTION, SOME “WELL
ESTABLILSHED” EVOLUTIONARY DOGMA, AND UNLESS THE WORK IS TREATED AS A
SYNTHETIC WHOLE, IT WILL INVITE REJECTION BY CONVENTIONAL WISDOM
[Other things the rfi asks us to address, but I don’t think it is necessary as it is obvious]
• What is well-characterized about the system (physics, chemistry, community)
[this could be what is well characterized about Prochlorococcus/Phage system]
• Results must be generalizable <<<<==== Nigel, I took you as saying “but not beyond photosynthetic
metabolism and Prochlorococcus”. But I think that this statement gives us the go- ahead to go beyond
that, to make some telling suggestions as to the overall evolutionary dynamic itself;.
• Please both of you express yourselves on this; because that consensus is what I will follow.
• ecosystem must have a tractable level of complexity
• ecosystem must be experimentally manipulable