Thinking Small: Part I

It isn’t easy to study life forms we can’t see. It’s not easy to talk about them, either. This is the first installment in a series about why and how we (try to) do it anyways.

rsz_11535797_10205060585775774_6958456103789566742_nContributed by Alice Vislova

You can imagine that microbes make tricky research subjects, being invisible to the naked eye, and all. I’m a microbial oceanographer, and, speaking of eyes, I can make people’s eyes glaze over at a party by the mere mention of my research topic by name: microbial metatranscriptomics. No don’t walk away – it only sounds boring because it’s so cutting-edge (wink). We can’t observe the behavior of microbes in the ocean by snorkeling around, but we can get a clue by sequencing RNA in seawater to learn which genes are being expressed. More on that later. For now, I want to discuss why we go to such technological lengths to microbes despite their small size.

The Illumina DNA sequencer is super cool, I promise.

The Illumina DNA sequencer is super cool, I promise.

People are surprised that as an ocean biologist, I study microbes and not something more…visible, like dolphins. It’s true – dolphins are pretty great. But their impact on the planet is nowhere near that of, say, Prochlorococcus – a genus of marine photosynthetic bacteria (cyanobacteria) responsible for at least a quarter of global oxygen production. Microbes can make a big impact despite their individual size because there are so many of them.

But first…what is a microbe, anyway?

Before I got into microbial oceanography as a grad student, I associated microbes mostly with disease. I didn’t know they were such a big deal. In fact, I didn’t even know what they were exactly. So, just to get everybody on the same page: microbes are simply organisms invisible to the naked eye. The vast majority of microbes are single-celled. This diverse group spans all three domains, making up the majority of life on Earth. 

A Bottlenose Dolphin surfs the wake of a research boat. These majestic creatures just can't compete with microbes when it comes to global biogeochemical impact Photo credit: NASA

A Bottlenose Dolphin surfs the wake of a research boat. These majestic creatures just can’t compete with microbes when it comes to global biogeochemical impact
Photo credit: NASA

Microbes – they’re kind of a big deal

Microbes are everywhere. Take a look in the mirror. You’re looking at an aggregate of human and microbial cells – 10 microbial cells to every human cell! We eat, breathe and poop microbes. That dolphin to the left is an aggregate of dolphin and microbial cells! There are a million microbes in a teaspoon of seawater and a billon in that amount of soil. With the water cycle, they rise from oceans and lakes and rain down again. And they’re not just along for the ride. In their vast numbers, microbes seriously impact the environment and organisms they live on, in and around. My aim here is to explain why microbes might matter to us.

s each individual strives to obtain the energy and 

Microbial metabolism affects the chemical composition of the earth.

A great example of both unusual microbial metabolism and symbiosis: 6-foot-tall giant tube worms living on hydrothermal vent fields are mostly bacteria-filled gonads on the inside, processing no mouths or stomachs because they depend exclusively on sulfate-reducing bacteria for energy. Photo credit: NOAA Okeanos Explorer Program, Galapagos Rift Expedition 2011

Great example of both unusual microbial metabolism and symbiosis: 6-foot-tall giant tube worms living on hydrothermal vent fields are mostly bacteria-filled gonads on the inside. Possessing no mouths or stomachs, they depend exclusively on sulfate-reducing bacteria for energy.
Photo credit: NOAA Okeanos Explorer Program, Galapagos Rift Expedition 2011

Like all living things, ourselves included, microbes are chemical factories. Certain molecules go in, enzymes mediate reactions, different molecules come out; this affects the chemistry of the environment. As with the example of photosynthesis by cyanobacteria, although the amount of a certain chemical (oxygen in this case) produced by an individual microbe over time may be small, microbes’ collective impact can have major consequences. In fact, a couple billion years ago in what has been called the Great Oxidation Event, photosynthesis by microbes raised the oxygen concentration in the atmosphere to the point that allowed for something called oxygenic respiration (a.k.a. breathing), while simultaneously wiping out the majority of anaerobic life that had populated the planet at that time.

Furthermore, microbes possess a much more diverse metabolic repertoire than multi-celled organisms. One such example of exotic metabolism is nitrogen fixation. Where animals like ourselves can only obtain nitrogen by eating other living things, diazotrophs possess the ability to incorporate inorganic nitrogen from water or air. Another example: unlike plants and cyanobacteria which obtain energy from sunlight, or the many organisms that get energy from eating those lower on the food chain, some microbes get energy by reducing sulfate emitted from hydrothermal vents. The bottom line – microbial metabolism is diverse and has considerable impacts on our planet.

Microbes are part of a network of interactions between all living things.

The samples I collect in the field just look like water with nothing in it. But in reality, each drop contains a rich hidden world that looks something like this illustration published in Science magazine, an image that has really stuck with me:

From cover of Science, 5 February 2010, used with permission from R. Stocker, J. R. Seymour, G. Gorick

Image from cover of Science, 5 February 2010, used with permission from R. Stocker.

As each individual strives to obtain the energy and particular nutrients it requires, a complex web of ecological relationships is formed. Competition is rampant, especially in the nutrient-poor open ocean around Hawaii, where my research takes place. But collaboration can be found too. For example, take our old friends the diazotrophs. In environments where nitrogen is particularly low, we find nitrogen-fixing bacteria living on or inside diatoms’ silicate shells. This is an example of mutualism, or perhaps commensalism. The bacteria provide a source of organic nitrogen to diatoms, and the diatoms provide protection, or perhaps something else.

Photomicrographs of bacterial symbionts (denoted by arrows) with rectangular host diatoms. Scale bars: 50 μm. Credit: Hilton, J. A., Foster, R. A., Tripp, J., Carter, B. J., Zehr, J. P., and Villareal, T. A. Genomic deletions disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont. Nature Communications. 4, April 2013.

Photomicrographs of bacterial symbionts (denoted by arrows) with rectangular host diatoms. Scale bars: 50 μm.
Source: (Hilton et al., 2013)

In fact, it seems that many species of environmental microbes depend on their neighbors for survival. Perhaps this is the reason for the ‘Great Plate Anomaly’ in microbiology – the longstanding mystery of why, despite effort by many researchers, only a fraction of microbes from the environment have been successfully isolated in culture.

Favia pallida (hard coral) with signs of bleaching. Source: Nick Hobgood

Favia pallida (hard coral) with signs of bleaching. Source: Nick Hobgood

The lives of microbes are interdependent not just with one another but also with multi-celled organisms. For example, coral bleaching, the process caused by rising water temperatures and acidification that is decimating reefs around the world, is the loss of single-celled photosynthetic algae that live in and feed the coral. Just last month, NOAA declared a third major global coral bleaching event underway.

So…if you weren’t an avid microbe fan already, hopefully I’ve convinced you that microbes matter. In further installments of the Thinking Small series, we’ll explore some tools we use to study microbes, and what they’ve allowed us to discover.

Stay curious


Alice Vislova is a graduate student at UH Manoa’s Center for Microbial Oceanography Research and Education. She is interested in feedbacks between ecology and evolution. Her current focus is using molecular tools (mostly DNA and RNA sequencing) to study circadian patterns in microbial behavior and life cycles. She’s also the editor of this blog. She welcomes questions and comments at avislova@hawaii.edu.                                                                                                                                   


Works Cited:

Hilton, J. A., Foster, R. A., Tripp, J., Carter, B. J., Zehr, J. P., and Villareal, T. A. Genomic deletions      disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont. Nature         Communications, 4 (2013), p. 1767.

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