Tag Archives: diversity

Bacterial Niche Finally Defined

The following scholarly contribution comes from my wife Madeleine Lenski after conversing with her “sister” (my former postdoc) Valeria Souza.

For those with an itch for criteria,

Scratch this: What’s a niche for bacteria?

Don’t take me to task

If I answer “a flask” –

It’s a bitch from warm broth to Siberia.

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January 19, 2016 · 9:08 pm

Thirty Years

No, the LTEE did not suddenly jump forward by almost 3 years. That milestone will be reached on February 24, 2018.

Next Friday is the end of the semester at MSU and, for me, it will mark 30 years that I’ve been on the faculty: six at UC-Irvine, and 24 here at MSU. (I also taught for one semester at Dartmouth as a sabbatical replacement, while I was doing a postdoc at UMass.)

Holy cow: 30 years. Where did all that time go?

Well, a lot of it was spent advising, supervising, and mentoring graduate students. And those have been some of the most interesting, enjoyable, and rewarding professional experiences that I can imagine.

In fact, this afternoon Caroline Turner defended her dissertation – congratulations Dr. Turner! Her dissertation is titled “Experimental evolution and ecological consequences: new niches and changing stoichiometry.” It contains four fascinating and meaty chapters, two on the interplay between evolutionary and ecological processes in the LTEE population that evolved the ability to grow on citrate, and two on evolved changes in the elemental stoichiometry of bacterial cells over experimental time scales.

Caroline is the 20th student to complete her Ph.D. with me serving as the advisor or co-advisor. Here they all are, with links to their professional pages or related sites.

  1. Felisa Smith, Ph.D. in 1991 from UC-Irvine.
  2. John Mittler, Ph.D. in 1992 from UC-Irvine.
  3. Mike Travisano, Ph.D. in 1993 from MSU.
  4. Paul Turner, Ph.D. in 1995 from MSU.
  5. Greg Velicer, Ph.D. in 1997 from MSU.
  6. Brendan Bohannan, Ph.D. in 1997 from MSU.
  7. Phil Gerrish, Ph.D. in 1998 from MSU.
  8. Farida Vasi, Ph.D. in 2000 from MSU.
  9. Vaughn Cooper, Ph.D. in 2000 from MSU.
  10. Danny Rozen, Ph.D. in 2000 from MSU.
  11. Kristina Hillesland, Ph.D. in 2004 from MSU.
  12. Elizabeth Ostrowski, Ph.D. in 2005 from MSU.
  13. Bob Woods, Ph.D. in 2005 from MSU.
  14. Dule Misevic, Ph.D. in 2006 from MSU.
  15. Gabe Yedid, Ph.D. in 2007 from MSU.
  16. Sean Sleight, Ph.D. in 2007 from MSU.
  17. Zack Blount, Ph.D. in 2011 from MSU.
  18. Justin Meyer, Ph.D. in 2012 from MSU.
  19. Luis Zaman, Ph.D. in 2014 from MSU. (Charles Ofria was the primary advisor.)
  20. Caroline Turner, Ph.D. in 2015 from MSU.

There are also 8 doctoral students at various stages currently in my group at MSU including Brian Wade (Ph.D. candidate), Mike Wiser (Ph.D. candidate), Rohan Maddamsetti (Ph.D. candidate), Alita Burmeister (Ph.D. candidate), Elizabeth Baird, Jay Bundy, Nkrumah Grant, and Kyle Card.

My own advisor – the late, great Nelson Hairston, Sr. – said that he expected his graduate students to shed sweat and maybe even occasional tears, but not blood. I would imagine the same has been true for my students.

Thirty years, holy cow. Time flies when you’re working hard and having fun!

Added November 4, 2015:  And now #21 in my 31st year, as  Mike Wiser successfully defended his dissertation today!

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An Absence of Posts, an Abundance of Talks, and More

Dear Reader:  No, I have not given up on this blog.  But I’ve been busy, busy, busy!

In the last four weeks alone, I have traveled to the University of Arizona, Harvard University, Duquesne University, and Princeton University.  Besides giving talks at each place (two public lectures and two academic seminars, with cumulative audiences of well over a thousand people), I have met with dozens and dozens of amazing scientists, from graduate students and postdocs to faculty both young and old.  It’s been a blast:  an exhausting blast, but a blast all the same!

And next week?  I’m hosting four terrific colleagues from two continents who will work with me to begin making sense of hundreds of newly sequenced genomes from the LTEE.

Oh, and we have some more job searches starting next week.

And did I mention?  We just had a fascinating (if I may so myself) and complex paper come out today in Science (on-line express for now) on the most deeply divergent (i.e., oldest sustained polymorphism) of the 12 LTEE populations.  And no, it’s not about the citrate eaters from population Ara–3.

Plucain, J., T. Hindré, M. Le Gac, O. Tenaillon, S. Cruveiller, C. Médigue, N. Leiby, W. R. Harcombe, C. J. Marx, R. E. Lenski, D. Schneider.  2014.  Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli.  Science.

It’s population Ara–2 instead, where two lineages—dubbed the Larges (L) and Smalls (S)—have coexisted for several tens of thousands of generations.  In superb research led by Dr. Jessica Plucain that she did in the lab of my long-time collaborator (and dear friend!) Prof. Dom Schneider (Grenoble, France), Jessica led the work to identify—out of hundreds of mutations—three that are sufficient to allow a “constructed” S ecotype (i.e., the ancestor plus three derived alleles) to invade and stably coexist with the evolved L ecotype.  Ecological context and specific genetic interactions are key to establishing this “half” of the polymorphism … and the other “half” of the story— what makes the L ecotype special—might well turn out to be just as complex, or perhaps even more so.

The S and L types are especially challenging (even painful!) to work with because this population became a mutator very early on—before the two lineages diverged—and so there are many, many mutations to contend with; moreover, they make colonies on agar plates that are quite challenging to score and count.  So congratulations to Jessica, Dom, and other members of Dom’s lab for their perseverance in studying this extremely interesting population.

Also on the list of authors are Prof. Chris Marx and two members of his lab.  They performed metabolic analyses showing how the carbon fluxes through the central metabolism of the S ecotype have diverged from both the ancestor and the L ecotype.  Chris was a postdoc in my lab almost a decade ago, but most of his work (then and since) has been on experimental evolution using Methylobacterium, and so this is the first paper we’ve co-authored.

There was a production error, though, in the on-line version of our paper; the final sentence of the abstract was dropped (except for one word).  The abstract, in total, should read as follows:

“Ecological opportunities promote population divergence into coexisting lineages. However, the genetic mechanisms that enable new lineages to exploit these opportunities are poorly understood except in cases of single mutations. We examined how two Escherichia coli lineages diverged from their common ancestor at the outset of a long-term coexistence. By sequencing genomes and reconstructing the genetic history of one lineage, we showed that three mutations together were sufficient to produce the frequency-dependent fitness effects that allowed this lineage to invade and stably coexist with the other. These mutations all affected regulatory genes and collectively caused substantial metabolic changes. Moreover, the particular derived alleles were critical for the initial divergence and invasion, indicating that the establishment of this polymorphism depended on specific epistatic interactions.”

[Edited on 07-Mar-2014:  The on-line PDF at Science Express now has the complete abstract.]

~~~

The picture below shows Dom Schneider and Richard Lenski in Paris in 2013.  They are holding a petri dish that Jessica Plucain made to celebrate the 25th birthday of the LTEE.

Dom and Rich, Paris, 2013

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Blogging’s Long Reach, Updated

At WordPress, I can see statistics showing where the visitors to my blog have come from.  I first posted on this topic back in September, and the total then was 72 countries.  Now, it’s a nice round: 100.  Wow!

The US has the lead by a large margin – no surprise there – followed by the UK, Canada, Germany, Australia, Switzerland, Sweden, The Netherlands, France, and India making up the top 10.  New Zealand has dropped out of the top 10, being replaced by India.

The US has had over 10,000 visitors.  Three others have each had over 1,000 visitors to my blog.  Twenty-two countries – including India, Brazil, Romania, South Africa, and Taiwan – have produced more than 100 visitors, while 46 countries have generated more than 10 visitors each.

Fifteen countries (or territories) have had one visitor to this blog so far including: Belarus, Cuba, Cyprus, Ethiopia, Fiji, Guam, Jordan, Kuwait, Lebanon, Nicaragua, Qatar, Rwanda, Saudi Arabia, Serbia, and Uganda.

Not a single visitor, though, has come from China …

Whoever you are, and wherever you come from, welcome to this blog!

Countries Dec 2013

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What We’ve Learned about Evolution from the LTEE: Number 4

This is the fourth in a series of posts where I summarize what I see as the most important findings and discoveries from the LTEE.  The previous entries are listed here:

Number 1.  The LTEE offers a simple, compelling demonstration of adaptation by natural selection.

Number 2.  Although the rate of improvement decelerates, it appears that fitness can increase indefinitely even in a constant environment.

Number 3.  The LTEE has produced many striking examples of both parallel and divergent evolution across the replicate populations.

Number 4.  The LTEE provides fascinating cases of the origin and subsequent evolution of both a novel function (citrate utilization) and complex ecologies (cross-feeding interactions).

These examples are particularly interesting—and surprising—because I chose the environment of the LTEE to be as simple as possible, thereby limiting the opportunity for novel functions and complex ecologies to emerge.  However, the evolving bacteria have proven me wrong by discovering new ways of making a living in the simple flask worlds where they live.

Novel function

Complex ecology

This photo shows the increased turbidity (cell density) of the population that evolved the ability to use citrate in the middle, along with two others from the LTEE.  Brian Baer and Neerja Hajela took this picture in my lab in 2008.

LTEE lines centered on citrate #11

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Remembering Barbara McClintock’s Laugh

A twitter conversation about women scientists who should be honored with Bobbleheads reminded me of the time I met Barbara McClintock.  My postdoctoral advisor, Bruce Levin, had brought me along to a small discussion meeting on the possible ecological and evolutionary effects of genetically modified organisms being released into the environment.

The meeting was held at the Cold Spring Harbor Laboratory in 1984.  There were two Nobel Prize winners there, at least part of the time, along with seven ecologists and evolutionary biologists.  The Nobelists were James Watson, who was then director of the Laboratory, and Barbara McClintock.  The ecologists and evolutionary biologists were Jim Brown, Rob Colwell, Monte Lloyd, Phil Regal, Dan Simberloff, Bruce Levin, and myself. I think there were also a few participants from the EPA and other agencies with an interest in the issues.  As I recall, Barbara McClintock was the only woman at the meeting.

The meeting was held in an old house.  There were two small restrooms, one for men and one for women; each had just a single toilet and a sink.

Because there were many men at the meeting, there was a line for the men’s room at the coffee breaks.  Bruce Levin, being the smart guy that he is, decided during one break that it would be faster and more efficient to use the women’s room.  The door was open, and so he went in.  Meanwhile, Barbara McClintock also had to use the facilities.  Seeing that the door was closed, she waited her turn.

As Bruce came out, he was already a bit embarrassed to see Barbara waiting.  And then she said, in a serious, almost scolding, tone, “Did you put the seat down?”  Bruce – who usually has a quick comeback – was befuddled and didn’t know what to say.  After a comic pause, Barbara just laughed heartily and went on in.

So there was a warm and funny person, as well as a visionary scientist, behind that Nobel Prize!

McClintock

[This picture is from the Wikipedia entry for Barbara McClintock; it has no known copyright restrictions listed there.  It comes from the Smithsonian Institution.]

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Teaching Competition and Predation from a Microbiological Perspective

Life has been busy, very busy.  And life has been good!  But the busy-ness has made it hard for me to keep up with this blog.  In the next few weeks, I hope to share some of the things that have kept me so occupied this past month.

For starters, I’d like to discuss some recent teaching where I tried to emphasize the interplay between theory and experiments in ecology.

I recently taught part of our graduate-level course called “Integrative Microbial Biology.”  Some years ago this course replaced several other graduate courses (microbial ecology, microbial physiology, microbial diversity, etc.) that each had a low enrollment.  The idea is that we now offer a single, annual, intensive, team-taught course that covers all these topics, albeit more superficially but with the hope that it encourages students and faculty alike to develop a more integrated perspective of microorganisms as organisms.  More specialized courses, with a focus on reading and discussion, are offered as occasional seminar-style courses.

I teach two parts of the course – one on aspects of microbial ecology, the other on microbial evolution.   Many of the students have not had an undergraduate course in general ecology or evolutionary biology, and so I try to bring them up to speed, albeit with examples that focus on microorganisms.

So, for the ecology portion I begin with population growth and competition.  I’m a fan of resource-based competition theory, as opposed to the more familiar logistic growth and Lotka-Volterra competition models.  The key strength of resource-based competition theory is that one can predict the outcome of competition based on parameters that can be measured separately for each species or strain, without requiring that one compete them in order to understand their competition.  Of course, there are many reasons the predictions might fail, but the resource-based model (and extensions to it) provide a mechanistic framework for understanding competition.

I then present predator-prey interactions, surveying the extraordinary diversity of microbe-on-microbe predation and parasitism, and then providing again a dynamical framework for understanding those interactions.  Here, Lotka-Volterra predator-prey models do provide a reasonable starting point because one can measure key parameters that have mechanistic interpretations (e.g., attack rates, conversion efficiencies) and use them to make new predictions about the dynamics of the system as a whole.

Besides presenting the general theory, I also present empirical studies from the primary literature.  In some cases, I summarize the papers in my lectures, while in other cases the students read the papers and we then discuss them.  Here are four of the papers with summaries; I hope to blog someday in greater depth on at least the Hansen & Hubbell and Rainey & Travisano papers, which I view as “must-read” papers in the field of ecology.

Hansen, S. R., and S. P. Hubbell.  1980.  Single-nutrient microbial competition: qualitative agreement between experimental and theoretically forecast outcomes.  Science 207:1491-1493.

This paper presented an early, concise, and compelling demonstration of the utility of resource-based competition theory.  By choosing three pairs of competitors that differed in various parameters, and then competing them in chemostats, the authors showed that the outcome depended on the two competitors’ relative “break-even” (equilibrium) concentrations of the growth-limiting resource.  For any student who wants more information on this approach – and every year at least some students ask for more – I recommend they read David Tilman’s outstanding book, Resource Competition and Community Structure (1982, Princeton University Press).

Rainey, P. B., and M. Travisano.  1998.  Adaptive radiation in a heterogeneous environment.  Nature 394:69-72.

This paper is a beauty.  The authors showed that the evolutionary emergence of diversity can sometimes depend on something as simple as whether a flask is shaken or not.  In the absence of shaking, an initially monotypic population of Pseudomonas fluorescens evolved into a community of three distinct ecotypes that differentially exploit the environmental gradients that arise without constant mixing; that diversity is stably maintained, as was shown by analyzing pairwise interactions.  By contrast, simply shaking the flask, with all else being equal, homogenizes the environment and the ecotypic diversity does not evolve; and if the diversity had already evolved, then it was eliminated as a single type came to dominate the well-mixed system.

Lenski, R. E., and B. R. Levin.  1985.  Constraints on the coevolution of bacteria and virulent phage: a model, some experiments, and predictions for natural communities.  American Naturalist 125:585-602.

Virulent phage infect bacteria, and they have life-cycles like those of insect parasitoids; that is, a successful infection is lethal to the host, and many phage are produced from a single infection.  In this paper, we examined the ecological and evolutionary dynamics of the interactions between E. coli and four different virulent phages.  First, the Lotka-Volterra predator-prey model – modified to include resource-based growth for the prey (bacteria) and a time-lag associated with predator reproduction (phage replicating inside bacteria) – predicted reasonably well the short-term dynamics of the interaction between E. coli and one of the phages, called T4.  Second, the model was extended to include the evolution of bacteria that are resistant to phage attack.  Resistance mutations changed the equilibrium density of the bacteria by several orders of magnitude, as the bacterial population went from top-down predator limitation to bottom-up resource limitation.  Yet despite complete resistance, the phage population persisted because there was a “cost of resistance” – in the absence of phage, the sensitive bacteria out-competed the resistant mutants.  In essence, the system becomes one of predator-mediated coexistence of sensitive and resistant prey populations.  Third, the interactions between E. coli and three other phages were examined.  Each interaction had somewhat different dynamics depending on whether resistance was costly or not, whether resistance was partial or complete, and whether the phage population produced host-range mutants that could infect the mutant bacteria that had become resistant to the progenitor phage.  [This paper built on related work that Lin Chao had done a few years earlier with Bruce Levin, and which inspired me to contact Bruce about joining his lab.]

Bohannan, B. J. M., and R. E. Lenski.  2000.  Linking genetic change to community evolution: insights from studies of bacteria and bacteriophage.  Ecology Letters 3:362-377.

This paper reviews the research that Brendan Bohannan did for his dissertation in my lab.  His work examined the same four bacteria-phage interactions studied in the Lenski and Levin paper above, but the work was extended to include some elegant new manipulations and analyses.  In particular, by changing the levels of resource available to the bacteria, the classic “paradox of enrichment” predicted by Lotka-Volterra predator-prey models was confirmed, with respect to the effects of enrichment on both equilibrium densities and the temporal fluctuations in population densities.  These experiments also provided compelling evidence for predator-prey cycles and the effects of bacterial resistance on the dynamics of the interaction between the remaining sensitive bacteria and phage populations.

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