Microbes and climate change: In agriculture, infectious disease, and biotech
Updated: Apr 22, 2020
Welcome back to this two-part Microbial Mondays series on microbes and climate change! Two weeks ago, we dove into the roles of microbes in climate change on land and in the water. Today, we're turning to microbes and climate change in agriculture, infectious disease, and microbiotechnology!
Just as agriculture usually leads to a loss of biodiversity in plants and animals that we can see (i.e. no buffalo crazing in the corn fields), it also reduces biodiversity in microbes that are invisible to the naked eye. This in itself can cause some problems. Just like a low-diversity microbial community in your gut can cause problems, and lead to only one microbe ruling them all - and wreaking havoc - the same can happen in soil. The soil ends up being "tired": less fertile, and reduced in its nutrient value. On top of this, such "tired", microbially-poor soil is also less able to suck out carbon from the air.
Luckily, there are a few changes that we as humans can make to improve this situation. Land usage involving growing the same single crop for years in the same field without any crop rotation, pumping nitrogen-rich fertilizer into the ground, and heavily tilling the land can tire out soil more quickly. Conversely, rotating crops, inputting less nitrogen, and not tilling can improve the functioning of the microbial community. Another strategy that I found pretty cool, was using a "donor" soil microbiome - just like a poop transplant in humans! Scientists found that introducing some "donor" microbes from healthy soil helped to restore tired out, degraded soil ecosystems.
All this nitrogen used in fertilizers can also lead to other problems, aside from tiring out the soil and reducing microbial diversity. As a result of all this excess nitrogen in agricultural sites, agriculture has actually become the largest emitter of the greenhouse gas nitrous oxide! But why does the nitrogen in the soil get changed into a greenhouse gas? You guessed it - microbes! Just like plants, microbes in the soil will also eat up the nitrogen. However, unlike most plants, microbes can produce nitrous oxide after eating up the nitrogen, which is then released into the skies.
In terms of agriculture, growing crops like corn or wheat in soil is by no means the only type of growing we do. For example, rice is a main source of calories for about half of Earth's population! Unfortunately, warm, soggy soil in rice paddies are also the perfect place for methane-producing microbes, or "methanogens", to grow. To make matters even worse, as atmospheric carbon dioxide (CO2) and temperature go up, rice paddies are predicted to become even more potent sources of methane. This is at least partially because under these wamer, CO2-richer conditions, the rate of methane emissions goes up much faster than the yield of rice per paddy.
Of course, plant agriculture is not the only culprit in terms of greenhouse gas emissions. Ruminant animals, like cows, are the largest single source of human-associated methane emissions. But where exactly does all this methane in cow farts come from? Ruminant animals as a group are defined as mammals that get their nutrients by fermenting plant-based foods in a specialized stomach, before they digest the food in a completely separate stomach. And, if you've been following Microbial Mondays for long enough, you know exactly who is responsible for fermentation: microbes! Indeed, it's the microbes in cow stomachs that are producing all of this methane. They're at it again!
In infectious disease
In terms of infectious disease, there are many, many ways that climate change is expected to affect the spread of pathogenic (disease-causing) viruses, bacteria, and other microbes. Today, I'm just zooming in on a few of them.
First, let's take a look at diseases in the water. Most likely, you've already heard about rising water temperatures being associated with coral bleaching. Coral is actually only coloured because of their symbiotic algae (microbes again!!) that live within them. Corals and algae depend on each other for survival, but unlike the more stationary coral, the coral's algae friends are able to pick up and leave if the water surrounding these buddies becomes too nasty for the algae's taste. If the water gets too warm or too polluted, the algae will evacuate, leaving the coral not only colourless, but also without it's major food source: the algae. And, if the coral is left for too long without any algae friends, it will die, kickstarting the crumbling of complex coral ecosystems.
Interestingly, a paper from this year found that warm waters don't only put corals at risk of bleaching: they also put corals at risk of infectious disease, although it's not yet known exactly what pathogen causes this "white syndrome". To take a broader look, warmer water temperatures can generally change the functioning of some water-bourne pathogens. For example, warmer temperatures can cause these microbes to express more so-called "virulence genes", i.e. to start shooting out toxins, putting on new costumes that help them better infect their plant or animal 'prey', or even getting better at surviving antibiotics. Indeed, increased temperature has been found to make common human-infected bacteria like E. coli, Klebsielle pneumoniae, and Staphylococcus aureus more antibiotic resistant as a population.
What about climate change on land? One of the microbial challenges we are likely to face is with a subset of diseases that microbiologists classify as "vector-bourne". To a microbiologist, a vector is simply any living thing that carries a disease-causing microbe (pathogen) to another living thing. For instance, in the case of Dengue virus, the Aedes aegypti mosquito is a vector that carries the virus to humans. If the mosquito drink human blood from somebody with Dengue virus, it will become infected itself as a result. It takes a little while for the virus to start making copies of itself within the mosquito, so if that mosquito bites another human within a few hours, the human might be lucky and escapes uninfected. However, once the virus has gotten into full swing in the mosquito and made lots of little copies of itself, it is much more likely that all the new humans bitten by this infected mosquito will be infected with the virus too.
For vector-bourne diseases like Dengue virus, climate change is expected to have a particularly big impact because the habitats of the vectors, like the Aedes aegypti mosquito, will be changed. Normally, this mosquito lives in more equatorial areas like Egypt, as its name implies. However, climate change has already been expanding the range of areas where this mosquito is capable of surviving - they have even been found as far north as the Netherlands! As the range of the mosquito gets larger, so does the range of Dengue virus - as well as yellow fever and chikungunya virus, which the same Aedes aegypti mosquito also carries.
On top of the expanding habitat ranges of vectors, warmer temperatures can also change how efficient vectors are at passing on their carried microbe to another animal, including humans. As I mentioned above, there is a window of time between when the Aedes aegypti mosquito first encounters Dengue virus by biting an infected human, and when that same mosquito will be infectious and able to transmit the virus to humans. In slightly warmer temperatures, the time it takes for the mosquito to become infectious actually reduces. That means that in warmer temperatures, one mosquito will have the potential to give more people Dengue virus during its lifetime. Combine this with more mosquitos in extended habitats, plus human overpopulation, and the picture gets a bit grim.
But, let's not end on that note. Now, we'll move on to a more optimistic topic. Since microbes have so many roles to play in climate change, can we also use them as tools to punch back?
Microbes as tools
In this section, I just picked three topics outlined in this paper to talk through with you. If you're interested in more ways that we might be able to use microbes to mitigate effects of climate change, and climate change itself, I'd encourage you to check out the original paper, although does have more scientific jargon than Microbial Mondays.
Mirroring the rest of this series, let's start in the water. One interesting topic that is still under investigation is iron seeding. As we discussed in part one of this series, marine phytoplankton pull out carbon from the air, making them an excellent carbon 'sink'. The whole idea behind iron seeding is that phytoplankton pull out carbon dioxide (CO2), and phytoplankton grow more where there is iron. Therefore, why not add iron to the oceans to induce phytoplankton blooms, and suck out some CO2?
Indeed, there have already been some studies indicating that iron seeding is pretty effective in reducing CO2 in the area nearby the location of seeding. However, some scientists have also expressed concerns about inducing plankton blooms. For example, some plankton whose growth would be stimulated by iron seeding might produce other greenhouse gases, which would limit the effectiveness of this strategy. As more iron seeding experiments are developed, we'll learn more and more about how biologically effective this strategy is, as well as its ecological impacts and whether it is economically feasible.
Back on land, scientists have also designed plants to use the ability of soil microbes to capture carbon from the air. More specifically, some scientists have begun designing soil-plant-microbe combinations that fit perfectly together to maximize carbon 'sinking' and minimize production of carbon dioxide and other greenhouse gases by microbial decomposition. The same concept, of designing the best possible symbiotic relationships between the soil, its microbes, and the plants growing there, can also be used to help plants grow under the types of stressful conditions expected to become more common due to climate change, such as drought.
Finally, bacteria and plankton are not the only microbes that we can use as tools to deal with climate change: viruses can be used, too! You might remember hearing the concept of 'phage cocktails' before on Microbial Mondays. As a refresher, a phage is simply a virus that infects bacteria, and a phage cocktail is a mixtures of several different phages designed to kill specific target bacteria. Just like this technology could prove useful in targeting 'bad bacteria' for elimination (James Bond viruses!) in the guts of animals or humans, phage cocktails also might be useful for 'treating' environments. By adding a cocktail of phages to thawing permafrost for example, scientists might be able to specifically kill microbes that emit methane when they eat up the thawing biomass. Some studies have already indicated that phage cocktails could be useful for controlling infectious diseases of crops, indicating that this could indeed be a promising strategy for mitigating the methane-producing effects of permafrost thawing.
On that positive note, we'll conclude this two-part series on microbes and climate change. Until next time - think like a microbe! What can you do to act on climate change?