At the end of my summer, (just a few weeks ago) I had the privilege to visit Montreal, Canada. I have wanted (for almost 6 years) to attend the national conference for the science I like to do, microbial ecology! Studying microorganisms can be tedious or overly technical to describe, but the research is awesome and improving our daily lives and resource management at many scales. While at the conference, I decided to use twitter as a way to convey what was happening at the conference as well as increase my focus for a concise ‘take-away’ from each of the presentations I attended. My summary of the conference follows with the subject of my tweets (~20 #ISME16 @MicroNYC tweets) in bold text. As you read (or just scroll down), there are photos of the bits of time spent outside of the conference center.
The ISME conference is the meeting for The International Society for Microbial Ecology, where ~2000 attended from 52 countries!
The week started with a great performance from a local, traditional dance group. So, for us, the audience, some with many years of experience, I had a funny thought about traditional elements of the performance and microbial ecology: Mouth harps & mouth pipetting. The traditional music and dancing of Montreal featured a mouth harp. Mouth pipetting is an old traditional form of collecting or transferring a liquid in a laboratory setting. Even though this is a rare practice today we still have to remind students that it is not allowed and is particularly dangerous in a microbiology lab. Now know that microorganisms are all around us playing important parts in our lives a lot of the research is going to the general public (as citizen science) to collect samples from the environment or their bodies, it’s for science!
Many science presentations happened through the week and there were many concurrent sessions! I chose extreme environments (traditionally thought of as not supporting life) as my starting point. This was because microorganisms in deep-sea hydrothermal vents was a first science crush for me. There are other extreme environments and I enjoyed two talks about them and their microbes: saline lakes in eastern Europe with Nitrospira bacteria learning to live with the salt as well as the strong influence from pH (Daebeler) then a ‘science rockstar’ presentation about dirt actually being an extreme environment for microorganisms (I’m not so convinced yet, Fierer). Regardless of calling dirt as extreme, it does host a complex community of microorganisms that is awesome and is even better to study when it is old frozen dirt such as the deep in the tundra (Mackelprang).
One of the challenges of studying microorganisms in the setting of the surrounding environment and plants or animals is that the ideas that organize similar work for plants or animals were developed before we knew about microorganisms (they were just a ‘black box’ in concepts or formulas). Therefore, another set of presentations I went to were focused on making the connection between microorganisms and the early ecology ideas. However, the challenge for any ecologist, is still to think out of the ‘box’ (Curtis) of any existing ideas. An example of big ideas at the small scale, is how the Neutral Theory does not apply to marine microbial communities in many cases (Furhman). When looking for new ideas or applying these old ideas in new ways, often the simplest answer is the best answer, parsimony (Curtis). This is true when trying to figure out how the power house of our own cells, mitochondria, have their own genome or set of genetic instructions. If the mitochondria left it up to the nucleus then the materials it needs to run may be delivered to the wrong area in a cell, so their genome is a way for them to make sure they get what they need (instead of the greedy endoplasmic reticulum; Anderson).
Many techniques to understand microorganisms focus on knowing the genes and what genes do. Such as how core genes revealed more about the bacteria and additional genes clarify the role in the environment (Young). The diversity and abundance of antibiotic resistance genes in microorganisms suggests selective roles (pressure from exposure that only allows microorganisms that can resist the pressure to survive) of antibiotics on all microbes (Wright). Sometimes the loss, rather than gain, of some genes can also make bacteria more dangerous to other organisms (Anderson). Antibiotics produced by microorganisms are ‘at the end of the day’ more of a weapon than a form of communicating (Wright). Applying these weapons microorganisms are predators and when preferred prey overlap, the predator that has a variety of preferred prey lessens the impact on the community from another predator that has specific prey (Chantinotas). Then something to think about for microorganism communities is that most (91%) of the world’s best predators, viruses, infect a specific host and 84% live in a specific area (Kyrpides). These dynamics illustrate how microorganisms are highly diverse and scaling models, or formulas that describe all the elements that promote diversity, predict >1 trillion microbial species on earth (Lacey).
To understand more about this potential trillion species sampling technology is improving. Often the traditional method of travel, sailing, can support innovative methods, such as the Tara expedition. This expedition traveled the world and has now contributed to finding 80% of the marine microorganisms we know (in the genome catalog; Bower). Some of their conclusions are interesting in the context of community ecology – they found that in the plankton network that the neighbors were more important than the neighborhood (environment) and cooperating with them is more important than competing with them (Bower). Additionally, having equipment move through the ocean the same exact way the water is moving keeps the equipment with the same marine bacteria. Then this equipment can regularly sample and learn what the bacteria are doing in their environment (by looking at which genes are being used, transcriptome; Delong).
One important role of bacteria in the environment can be bioremediation. After the Deep Water Horizon oil spill in the gulf much research has been in progress and completed on the best way to remove the oil. A common response to oil spills is to apply dispersants to disperse or reduce the visible sheets/globs of oil. With some ideas that these now smaller particles would be more available to bacteria to breakdown the oil then removing the oil from the environment. However, there is counter evidence that while the oil is invisible to us it is not gone, the bacteria are not consuming it, which creates a greater risk of our exposure (Joye). While the marine microbes have a minimal natural role of oil bioremediation they are essential for moving nutrients through the system, such as Nitrogen. Though where there is limited oxygen at great depths in the ocean, there are only a few microorganisms that can move the Nitrogen around, which increases their environment or system to be vulnerable to changes in climate (Sachdeva). In shallower environments, like wetlands, microorganisms have a mixed roll in influencing climate changes. The methane, a ‘greenhouse gas’, produced in wetlands is directly related to the amount and type of microorganisms producing methane (Tinge). In environments with less water, drought or long periods without rain or snow can alter what the microorganisms do in the environment, such as decomposition. Overall microorganisms are highly resilient and are back to their normal roles after a 1-3 years of change (such as drought; Allison).
In the theme of scaling up from what microorganisms are to what they are doing there are also the symbioses of microorganisms living with other macro-organisms (plants/animals). My favorite of these symbioses is the microorganisms that live with corals and sponges. These symbioses, particularly with coral, is so interwoven that the term holobiont is used to describe all the living organisms as a single unit. The bacteria are essential to the survival of coral and the bacterial community regulates the algal symbiosis (Medina). The genes of the algae (a dinoflagellate, symbiobinium genome) are connected with physiological or the way it lives affects its symbiosis with the coral (Aranda-Lastra). This complicated, intimate symbiosis of macro- and microorganisms regulating each other while supporting the growth of each other is why the term holobiont is necessary. Then not all bacteria are welcome to live with corals or sponges, especially for sponges they are food. Therefore, there are bacteria that create proteins, which sponge cells produce, to fool the sponge into ignoring or not eating them (Thomas).
Thank you for reading to the end. I hope there was some science points that were a fun ‘take-away’ for you too.