The goal of this MicroEducation series is to demonstrate the remarkable importance of microorganisms in our day-to-day lives. I believe that many people don’t realize just to what extent microbes are involved in our everyday activities. Some aspects of microbial life are more widely known than others. For example, it is common knowledge that we extensively use microbes in the food industry. Indeed, all fermentation processes are controlled by bacteria and yeast. This biological activity provides us with an impressive list of foods and beverages including bread, yogurt, cheese, kefir, beer, wine, and vinegar, just to name a few. Of course, microbes also bring us coffee, through a process that we covered in our previous post. It is also relatively well known that the microbes that live inside our bodies support and maintain our health but may also cause serious diseases. We will discuss these more obvious but undoubtedly important topics in further detail in future articles of this series.
In this post, you are going to read about another microbially mediated process that contributes significantly to the well-being of our biosphere - biodegradation. The official definition of this term may sound a bit intimidating - the biologically catalyzed reduction in complexity of chemical compounds. However, all it means is that biodegradation is the process by which complex organic molecules are broken down into smaller compounds by microbes. When we talk about biodegradable products, we usually mean various natural organic materials of plant/animal origin or artificially produced organic compounds - all of which can be broken down by microorganisms. Some microbes have a remarkable metabolic potential and can degrade a vast range of organic compounds, such as polychlorinated biphenyls (PCBs), pesticides, industrial solvents, hydrocarbon containing products (e.g. petroleum based), and many others.
Which ecologically relevant processes employ biodegradation?
The ability to degrade organic matter naturally allows microbes to play important roles in a variety of ecologically relevant processes, some of which we will discuss in this post.
Composting and soil formation.
One of the most useful but often overlooked processes mediated by microorganisms allows us to put food scraps in those special garbage bins, labelled “Compost”. Strictly speaking, what is composting? It is an aerobic process by which various groups of microorganisms degrade complex organic materials in succession (one after another) into more simple compounds. These simple organic compounds contribute to the richness of soil whose importance for life on Earth is obvious but is often overlooked. Hence, microbes are actively involved in two processes, they help us get rid of organic waste material via composting and they are a vital part of the soil formation by creating organic nutrients necessary for the soil productivity.
We are all so used to the fact that soil seems to be everywhere, that it’s vastly available and there’s no shortage of it. In fact, the truth is quite the opposite. The earth’s soil layer is rapidly eroding (disappearing) because we don’t take good care of it, i.e. we often don’t follow ecologically sound agricultural practices and we simply overuse soil to produce as much food as possible without letting the soil layer rest and retain its strength. As an example, let’s think about what soil and a smartphone have in common. Among other things, they both need to be rested/charged. If we use our phones for too long without charging it, the battery will eventually die. Something similar is taking place with our planet’s soil layer. We have been watching metaphorical YouTube on it for way too long without recharging it.
Degradation of pesticides
Another biodegradation example that we are going to talk about today is about pesticides and how vital microorganisms are in the process of their degradation. Let’s start by defining what exactly pesticides are. A pesticide is any poisonous substance that negatively affects target organisms and is harmless to non-target organisms. Pesticides can have very different targets, both from the animal and plant kingdoms, including rats, mites, a wide variety of insects but also weeds and other undesirable fauna representatives. Hence, different types of -cides exist, including insecticide, herbicide, fungicide, etc. Even though the use of pesticides is undoubtedly beneficial in managing pest populations, their continued widespread application has led to the increased concentrations of dangerous pesticide residues in soils, waters, and even foods. Furthermore, inhabitants of the surrounding areas where pesticides are heavily used face higher risks of being exposed to dangerously high concentrations of poisonous chemicals.
Where do pesticides come from? Well, as for the majority of things that are bad for the environment, people are involved. Overall, we produce and release in air and water more than 450 million kilograms (1 billion pounds) of toxic materials per year. We synthesize around a thousand new chemical products every year, some of which are extensively used in agriculture to increase crop yields and the product quality as well as to minimize negative pest impacts.
Which microbes are involved and what can they do?
Certain soil microorganisms can use pesticides as their source of carbon and energy, in simpler terms, their food. Some microbes are better at degrading pesticides than others which allows them to proliferate even in heavily contaminated soils. It depends among other reasons on their metabolic flexibility, their ability to live in a range of environmental conditions, and their willingness to create collaborations with other organisms. Some microorganisms have a very specific environmental niche where they feel comfortable. It means that they can grow well only under very specific conditions (temperature, salinity, pH level, etc) and that they can eat only a narrow range of compounds. Whereas other microbes are not as picky, they feel comfortable and active in a variety of conditions and they can eat n’importe quoi. Another parallel with people is quite straightforward here. Those human individuals who are more flexible in their professional and social lives, e.g. those who can work (and work hard) under varying conditions -under stress, if necessary-, with colleagues from various backgrounds, tend to be more successful in their respective fields than their less adapted peers.
Overall, we produce and release in air and water more than 450 million kilograms (1 billion pounds) of toxic materials per year.
So who are these well adapted microbes who are willing to live under different environmental conditions, eat whatever is available, while helping us restore the soil layer? And what pesticides can they degrade? A schematic figure below shows a few examples of bacteria, algae, and fungi that can eat up a long list of nasty chemicals that contaminate our soils.
Wastewater treatment
Microbes also play an important role in neutralizing harmful organic wastes at wastewater treatment plants. How much waste exactly are we talking about? Well, actually a lot! Hundreds of cubic kilometers of wastewater is generated worldwide each year. It was estimated that in North America alone, this number reaches 85 cubic kilometers.
To give you an idea of how much one cubic kilometer of wastewater is, try to imagine the famous Pyramid of Cheops in Egypt, that monumental structure almost 150 metres (492 ft) high. So imagine that and multiply it by 390 - and you will roughly get one km3, which is about 1% of water wastes that only the United States produces in one year. Impressive and unsettling, to say the least.
However, not all countries provide these data so it is challenging to accurately calculate these numbers. A study led by the United Nations reported that out of 181 countries, 55 had information on three key aspects of wastewater: generation, treatment, and reuse. Another 69 countries had data on one or two aspects and 57 countries did not collect or share any information. However, it is safe to assume that the total volume of wastewater that we generate every year is staggering and we can definitely use all the help we can get to treat it in a way that will allow us to reuse it.
This is where, yet again, microorganisms come to the rescue since they can remove a lot of organic compounds from the wastewater. It’s important to remember that often what is dangerous and harmful for us, is useful and desirable for microbes. Like everyone else, microbes like to eat well, and for them fine dining actually means sewage -yes, sewage- because it contains all of the necessary organic compounds including carbohydrates, fats, and proteins as well as a variety of inorganic molecules including nitrogen, phosphorus, sodium, potassium, and many others.
A waste water treatment plant works like a Michelin Star restaurant.
So how exactly do microorganisms help us clean the wastewater? Microbes are involved in every step of the water purification process at wastewater treatment plants (WWTP), also known as Water Resource Recovery Facilities. A WWTP is a complicated engineering structure that employs multiple steps to clean the water. These steps include physical separation of solid particles from the liquid as well as a variety of chemical and biological processes aimed at completely degrading or effectively reducing harmful organic compounds. To remove various contaminants from the water, WWTP researchers use different microbes, and more importantly, they introduce these microbes to the cleaning process at different stages and not all at once. The process of microorganisms replacing one another in a common task is called a microbial community succession and it represents one of the most powerful features of any microbial process including biodegradation.
To better understand how this succession of microbes works at a WWTP, think about a trendy Michelin Star restaurant. To achieve the best results, certain tasks at these establishments are strictly divided between their employees. Dishwashers clean the plates, a line of cooks prepare different dishes and usually one person is responsible for only one or a few dishes. Rarely -almost never- a person who is in charge of a vegetarian soup would be asked to prepare a salmon steak, because the skill sets needed to prepare these two dishes are too different. Then the chef assesses the quality of the ready to be served plates at the pass and fixes something if needed (here, this would be the researchers who monitor water quality at the plant). And finally a member of the waiting staff brings the dish to the customer. To sum it up, for the best results, many different professionals will perform tasks that they are best at in a strict and well determined sequence. You can’t imagine a waitress bringing a plate to a customer until the plate is ready! Work at a WWTP is organized similarly to a fancy restaurant. Certain organisms consume/degrade a number of compounds while growing under the environmental conditions that they prefer, e.g. temperature that they like, salinity, pH, concentration of oxygen and many others. Then, when they are done with their task, they step away and another group of organisms takes over to degrade metabolites produced by the previous group. This goes on until the water reaches the acceptable quality point, after which microbes themselves are removed from the system and we are left with clean water. Of course, the actual process at a real WWTP isn’t quite as straightforward but the overall microbial workflow at a regular WWTP resembles the one we describe here.
Take home message
I hope that yet again we managed to demonstrate that microorganisms are vital to the well being of our planet. They don’t just make us food and beverages. Although we can’t underestimate the importance of that aspect either. Imagine where we would be without coffee, wine, beer, kombucha, bread, and cheese? What’s there left to live for? They also support agriculture by forming rich in nutrients soil matter and by degrading harmful pollutants. They take our recycling efforts to the next level by helping us compost our leftovers that would otherwise get dumped to a landfill. They clean our water that we manage to pollute at an ever increasing pace. In other words, microbes help us fix problems that we create ourselves, hence it is of high importance to know them well, to understand their preferences and their physiology to be able to help them help us best.
The next installment of the MicroEducation series is not far off, stay tuned. Let us know what you would like to read about next, we love hearing from you.
You can reach us by email at prettylightscience@gmail.com or on social media via twitter or instagram.
Glossary:
Biosphere - (from Greek βίος bíos "life" and σφαῖρα sphaira "sphere") is the zone of life on Earth, i.e. a sum of all ecosystems occupied by living organisms.
Organic compounds are generally any chemical compounds that contain carbon-hydrogen (C-H) bonds.
Inorganic compounds are typically chemical compounds that lack carbon-hydrogen (C-H) bonds.
Aerobic - relating to, involving, or requiring free oxygen.
Biodegradation - the naturally-occurring breakdown of materials by microorganisms.
Composting - a human-driven process in which biodegradation occurs under a specific set of conditions.
Ecological succession - the process by which the structure of a biological community evolves over time.
Wastewater treatment plant is a facility in which a combination of various processes are used to treat industrial wastewater and remove pollutants.
Erosion is the action of surface processes (such as water flow or wind) that removes material (soil, rock etc) from one location on the Earth's crust, and then transports it to another location.
Environmental niche - the position or function of an organism in the environment.
References:
McGuinness M, Dowling D. Plant-associated bacterial degradation of toxic organic compounds in soil. International journal of environmental research and public health. 2009;6(8):2226-47. - https://doi.org/10.3390/ijerph6082226
Timmis K, Cavicchioli R, Garcia JL, Nogales B, Chavarría M, Stein L, McGenity TJ, Webster N, Singh BK, Handelsman J, Lorenzo V. The urgent need for microbiology literacy in society. Environmental Microbiology. 2019;5(21):1513-28. - https://doi.org/10.1111/1462-2920.14611
Wirsching J, Pagel H, Ditterich F, Uksa M, Werneburg M, Zwiener C, Berner D, Kandeler E, Poll C. Biodegradation of Pesticides at the Limit: Kinetics and Microbial Substrate Use at Low Concentrations. Frontiers in microbiology. 2020;11:2107. - https://doi.org/10.3389/fmicb.2020.02107
Huang Y, Xiao L, Li F, Xiao M, Lin D, Long X, Wu Z. Microbial degradation of pesticide residues and an emphasis on the degradation of cypermethrin and 3-phenoxy benzoic acid: a review. Molecules. 2018;23(9):2313. - https://doi.org/10.3390/molecules23092313
Nakasaki K, Idemoto Y, Abe M, Rollon AP. Comparison of organic matter degradation and microbial community during thermophilic composting of two different types of anaerobic sludge. Bioresource technology. 2009 Jan 1;100(2):676-82. - https://doi.org/10.1016/j.biortech.2008.07.046
Nakasaki K, Nag K, Karita S. Microbial succession associated with organic matter decomposition during thermophilic composting of organic waste. Waste Management & Research. 2005;23(1):48-56. - https://doi.org/10.1177/0734242X05049771
UN: Rising Reuse of Wastewater in Forecast but World Lacks Data on “Massive Potential Resource” - https://unu.edu/media-relations/releases/rising-reuse-of-wastewater-in-forecast-but-world-lacks-data.html
Living Soils: The Role of Microorganisms in Soil Health - https://www.futuredirections.org.au/publication/living-soils-role-microorganisms-soil-health/
Written by Alexey Vorobev
Pretty Lightly Edited by Courtney Thomas
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