Culturing Science – biology as relevant to us earthly beings

Microbe biogeography: the distribution, dispersal and evolution of the littlest organisms

EDIT: This post was selected as a runner up for the PLoS ONE Blog Pick of the Month. Thanks, PLoS! Check out the winner: Greg Laden’s great post on how the victims of Vesuvius died.

ResearchBlogging.orgIn any high school biology class1, we learn that isolation is key to the evolution of species.  For example, take Australia, where an array of marsupials such as koalas and kangaroos reproduce like no other animals on the planet.  Isolation on a continental island allowed ancestral marsupials to evolve gestation via pouch, a trait which was retained as these animals later evolved into multiple (cuddly) species.  In other words: an event that happened in the past resulted in the organisms we see today, or the history of a species influences its current form and life history.

We attribute the distribution of species on this planet, also known as biogeography, to these sorts of historical events.  Organisms evolved, and continue to evolve, the way they do due to historical circumstances out of their control, creating the biodiversity of our world.  The idea of biogeography is generally attributed to Lamarck, and throughout the late-18th and early-19th centuries (pre-Darwin, mind you), scientists suggested many reasons for the non-uniform distribution of organisms, with Lyell summing up these historical factors as a combination of environment and dispersal through migration, passive (e.g. seeds carried in the wind) or active (e.g. elephants walking across the plain).

It's hard to find images for these kinds of posts, ok? Cut me some slack. By the way, image (c) Hannah Waters 2010

However, not all organisms seemed to fit this pattern.  Scientists at this time observed that, while polar bears were limited to the arctic and monkeys to warm climes, organisms such as fungi, sponges, algae and lichens were far more ubiquitous.  The botanist Kurt Sprengel, in summary of a common thought, wrote that organisms of “lower organization” must have greater ability to disperse, allowing them to colonize more broadly and thrive where “circumstances propitious to their production occur.”  (For a full history, see Maureen O’Malley’s commentary in Nature Reviews Microbiology.)

In 1934, the Dutch biologist Lourens Baas-Becking revived this idea, with the thought that the typical explanations of biogeography do not fit with the world of microorganisms.  He saw the same species of microbe living in different places on the globe and in variable environments.  Thus, he posited that historical factors such as isolation and environment could not be the forces determining microbial distribution,  but rather that “everything is everywhere; the environment selects.”  The small size and abundance of many microbe species allowed them to be easily dispersed in water, on wind, on the bodies of animals, spreading them all over the planet.  Many microbes can also lie dormant for a long time until conditions improve, or until the “environment selects” them.  This would, in effect, create what’s been termed a “seed bank” of microbes, where all microbes are in all environments at the same time, lying in wait for environmental conditions to favor their proliferation.

A generic microbial community. Source: Frank Dazzo, Center for Microbial Ecology, Michigan State University

For most of the 20th century, this so-called “Bass-Becking Hypothesis” was widely accepted, but in the past few decades has been hotly debated.  In 2004, Tom Fenchel and Bland Finlay compiled a literature review in Bioscience in favor of the hypothesis, arguing that “habitat properties alone are needed to explain the presence of a given microbe, and historical factors are irrelevant.”  They reviewed studies which showed the ubiquity of microbe species with fewer habitat requirements (generalists, if you will), as well as microbe species that are environmentally specific but are found in their preferred habitats on many continents.  Of note is a 1997  Oikos study that they themselves published, wherein they found 20 living microbe species in a lake sample.  Upon altering conditions (such as food source, temperature, acidity, and oxygen levels), they were able to revive an additional 110 species – evidence supporting the idea of a “seed bank” of microbes.  The authors do note that this theory may only apply to the most common microbe species, since not all are able to dessicate and revive – but perhaps this ability is what made them so widespread in the first place.

One caveat with this study is that the authors advocate for a phenotypic analysis of microbes.  While the ability to study DNA was a huge benefit to the field of microbiology, the authors do not agree that this is useful due to the wide genetic variability even within a single microbial population, and thus rely on morphology to describe species instead of genetic analysis.  A 2006 review, including genetic analyses, found that things aren’t so cut and dry.  The authors cite a number of studies showing reproducible genetic differences within microbe species even along a 10-meter transect in a marsh.  In two hot springs thousands of kilometers apart, despite living in the same environment, two species of bacteria (Synechococcus and Sulfolobus) showed significant genetic differences.  This shows that isolation alone can affect genes, and thus ultimately species, “overwhelming any effect of environmental factors.”

Both reviews note that there is not enough data out there to draw strong conclusions; the 2006 study was relying on 10 articles alone to determine distance and environmental signficance.  To me the differences in these studies come down to how one defines a “species.”  Typically, we differentiate species based on an organism’s ability to produce fertile offspring with another – if they can, they are the same species.  (There are many caveats to the “species problem” beyond my scope right now.  For a really thorough write-up, see this post from the Wild Muse.)  However, most microbes reproduce via cell division, and genes can be transferred horizontally despite “species” boundaries.  So how do we even define a microbial species in the first place?  If we’re looking at evolution alone, it would seem that genetic differences even within microbes that are commonly described as the same species morphologically would be meaningful, as these genetic differences put them on the path to become novel species.

One major question that the idea of “everything is everywhere” brings up is: how do microbes evolve in the first place?  If these organisms are relatively free from the external pressures of isolation and environment, going locally extinct or reviving based on their surrounding conditions, evolution must take an incredibly long time.

I could not find a paper on biogeography and microbial evolution; however, a paper in PLoS published in April 2010 looked at the biogeography and large-scale evolution of phytoplankton in the ocean.   In light of questions I’m asking here, oceanic plankton and microbe communities are very similar.  They are both small organisms  primarily dispersed passively, by ocean currents in the case of plankton.  The ocean hosts a wide variety of environments, and plankton are also generally considered to be everywhere at once.  While it is not ideal, I will use this planktonic model to look at biogeography and evolution in a more specific system.  (Well, as specific as you can get with the ocean…)

A generic planktonic community.

Just as the determinants of microbial biogeography haven’t been concluded, the same is true of plankton.  In this study, the authors sampled planktonic communities in two very different ocean environments: subtropical/tropical oceans, characterized by similar conditions throughout a wide geographical range, highly stratified ocean layers, and nutrient-poor surface waters, and sub-Arctic waters, characterized by high vertical mixing and high nutrient levels across the water column.  They compared 250-ml samples pairwise from each of the oceanic habitats and found that the planktonic communities were “strikingly dissimilar.”  However, when they increased their sample size 100-fold to 25 liters, they found that these contrasting ocean environments shared 76% of their total species pool!  This effect is surely found in many microbial studies: when comparing diversity between smaller plots, you are more likely to find a difference.  But an increase in plot size, even within the same environment, will find more similarities.  (Which is a more meaningful measurement is another question… I’d be happy to hear your comments on that one.)

To look at the evolution of phytoplankton, the authors took core samples from four distinct geographic environments and then identified fossil diatom species within from 240 million years ago to the present, generating “community assemblages” of diatoms through time.  They then compared these communities assemblages with environmental factors: global CO2 concentrations and oceanic upwelling strength.  The authors found that, despite “local determinants such as regional current systems, terrestrial nutrient inputs, atmospheric deposition, physical mixing, etc.,” global climate measures largely predicted the diatom community assemblage, with many species recovering after local extinction.  That’s right: even after the extinction of a species, when preferable environmental conditions returned, so did the diatom.

This study provides a clue regarding the importance of environmental conditions to the global distribution of abundant, passively dispersed organisms.  What is also interesting is that the same diatom species were found again and again over the course of 240 million years.  Their ability for high dispersal and recovery of species enables planktonic communities to evolve “slowly and gradually” over time.

But clearly they have evolved: plankton (and microbes) are incredibly diverse clades.  The question to look at now is how is evolution driven in highly dispersed organisms?

And thus, as usual, they are the tiniest organisms that force us to broaden our view on basic tenets of biology.  Just as horizontal gene transfer did for traditional natural selection, now microbial dispersal does for the evolution of species.

It does give me a great deal of hope regarding life on this planet: the possibility that there is a cache of microbes waiting around for the perfect conditions, even ones not suitable for us.  As my father, Dennis P. Waters (who needs a blog), once put it, “As long as there’s bacteria, there’s hope.”

1That is, in one where evolution is taught at all…

Cermeño, P., de Vargas, C., Abrantes, F., & Falkowski, P. (2010). Phytoplankton Biogeography and Community Stability in the Ocean PLoS ONE, 5 (4) DOI: 10.1371/journal.pone.0010037

Fenchel, T., & Finlay, B. (2004). The Ubiquity of Small Species: Patterns of Local and Global Diversity BioScience, 54 (8) DOI: 10.1641/0006-3568(2004)054[0777:TUOSSP]2.0.CO;2

Martiny, J., Bohannan, B., Brown, J., Colwell, R., Fuhrman, J., Green, J., Horner-Devine, M., Kane, M., Krumins, J., Kuske, C., Morin, P., Naeem, S., Øvreås, L., Reysenbach, A., Smith, V., & Staley, J. (2006). Microbial biogeography: putting microorganisms on the map Nature Reviews Microbiology, 4 (2), 102-112 DOI: 10.1038/nrmicro1341

O’Malley, M. (2007). The nineteenth century roots of ‘everything is everywhere’ Nature Reviews Microbiology, 5 (8), 647-651 DOI: 10.1038/nrmicro1711

Written by Hanner

June 18, 2010 at 10:41 am

29 Responses

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  1. Nice post!

    I was wondering about the 76% of planktonic species that were shared between the different environments.. Did they say anything about abundances for example? I can imagine that certain species thrive much better under arctic conditions than tropic, so that while you may be able to find a tropic species in the arctic, its abundance might be too low to play any ecological role..

    I also assume that the species identification was done on the basis of morpholohy? Because, as you’ve pointed out, the genomes of two morphologically similar diatom species might be wildly different..

    Lucas

    June 18, 2010 at 11:22 am

    • Hey Lucas,

      The main reason the authors widened their sample size the second time around was actually to pick up these rare species that would have been missed the first time. These species may not have a strong ecological role, but the idea behind it was a search for a “seed bank.” Even if they don’t currently play a role, they have the potential to if conditions change in the future. Does that make sense?

      And the species identification was DEFINITELY done by morphology. Think of all those techs in the labs, going through so many liters of sampled seawater to identify plankton to morphospecies!

      I’ve worked or known people who worked in many different ecology labs – and ecologists generally haven’t found a good way to use genetic analyses. I don’t know the exact reason; part fear, I’m sure, since ecologists pride themselves on field work, on the “big picture” instead of molecules. (I know it, I’ve been there.)

      But part of it might be to avoid the “species problem.” Once you start with the genetic analyses, you can get so many subspecies, and how do you draw conclusions off of that? What is the standard difference in genes that separates one species from another? Brings up so many problems….

      Can’t help but ramble, haha.

      Best,
      Hannah

      Hannah

      June 18, 2010 at 2:56 pm

      • To hopefully take away some fears of ecologists: a genetic analysis doesn’t necessarily have to boil down to determining the abundances species/subspecies/quasispecies/whatever-species. I would say one of the strengths is that it is possible to directly measure what the community members are doing (metatranscriptomics) or what they are capable of doing (metagenomics), in a more direct and discrete way than morphological analyses can.

        And I’d be very interested to see how genetic and morphological studies compare in estimating species abundance!

        Lucas

        June 19, 2010 at 3:55 pm

  2. Interesting post. The diatom work is very relavent as picoplankton live in pretty much the same way and carry out similar processes, apart from the fact that their bacteria rather than euks.

    One other thing that is hopeful for soil bacteria is that many of them form spores, which can survive all sorts of negative conditions before sporulating when good conditions return. The ability of bacterial spores to travel long distances (and the huge amount of travel nowadays by people which can transport them) might help to explain why they get everywhere.

    Lab Rat

    June 18, 2010 at 11:38 am

  3. Hey Labrat,

    Any kind of spore-based organism gives me hope – they are so much tougher than we weak humans are! It makes me feel a little warm n fuzzy inside to think that yeast will live on long after us …

    Thanks for the note, LR!

    Hannah

    June 18, 2010 at 2:58 pm

  4. The problem is that we still really don’t know what is a bacterial species… so is very hard to test this hypothesis until we delimit what is an species. Beyond a single gene and a couple of phenotypic traits! good post!

    Luis D.

    June 21, 2010 at 5:49 am

  5. Great post! Microbe biogeography is really a complicated subject.
    I just stumbled onto a recent article that may interest you or your readers (open access):

    Environmental distribution of prokaryotic taxa
    BMC Microbiology 2010, 10:85
    doi:10.1186/1471-2180-10-85

    http://www.biomedcentral.com/1471-2180/10/85

    According to the authors: “This is, as far as we know, the most comprehensive assessment of the distribution and diversity of prokaryotic taxa and their associations with different environments.”

    César Sánchez

    June 22, 2010 at 5:06 am

  6. [...] to the “everything is everywhere” hypothesis about microbial distribution I pondered here), and (2) vent communities are created from larvae supplied by local populations through [...]

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  9. [...] at Culturing Science this month, I wrote about the global distribution of microbial species in the face of the [...]

  10. You wrote: “One major question that the idea of “everything is everywhere” brings up is: how do microbes evolve in the first place? If these organisms are relatively free from the external pressures of isolation and environment, going locally extinct or reviving based on their surrounding conditions, evolution must take an incredibly long time.”

    If the microbes in question are asexual bacteria, I don’t see a problem. Within a “biological species” gene flow can indeed put a limit on divergent local adaptations. But bacteria don’t have to worry about sexual hangups like that.

    Perplexed in Peoria

    July 5, 2010 at 8:18 pm

    • Even though they don’t reproduce sexually, bacteria still have genetic mutations and evolve to suit their environment. Studies have shown that under environmental pressure, the mutation rate in many microbes increases, in a seemingly desperate attempt to change ANYTHING that will help them survive in their new environment.

      And, of course, one of those changes is the ability to go into arrest and hibernate in their new environment, waiting for the environmental changes I mentioned above. But by evolving this ability, they also slow down their mutation rate and thus evolution happens more slowly. These are merely my own inferences – but I think it makes sense.

      Hannah

      July 8, 2010 at 10:58 am

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  25. Hi Hannah,

    I came across your blog through Ed Yong’s blog roll and this post caught my eye. I’m sorry I’m commenting more than 6 months after the fact! The species issue is perplexing and I’ve been reading about it lately with regards to viruses, who appear even more promiscuous with regards to swapping DNA material, and a seemingly (to my untrained eye) messier taxonomic classification. Microbes… so small, yet so incredibly complicated!

    On another note, great blog! :)

    Yee Mey

    January 6, 2011 at 3:13 pm

  26. [...] Microbe biogeography: the distribution, dispersal and evolution of the littlest organisms [...]


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