Cleaning Up Pollution With Fungi

It’s no news that rapid industrialization has caused numerous environmental problems. Our most densely populated areas are cities of concrete and glass, where the sky is coated gray from car exhaust, and man-made lights replace stars for miles. In rural areas, drugs used in farming to treat diseases in the livestock leak into the water and soil, contaminating and negatively affecting all surrounding ecosystems, including the microbial communities (1). Furthermore, our water and soil are becoming increasingly contaminated with toxic metals, which are also detrimental to their respective ecosystems, as well as a high risk to human health (2).

Environmental contamination caused by industrial waste reduces the quality of the environment, and therefore the quality of life for all organisms. Traditionally, the issue of contamination has been approached by moving the contamination elsewhere, generally to landfills. Of course this does not actually fix the problem, it just gets rid of it in its original setting. Another method that has been used is destroying or transforming the contaminants to a harmless form via chemical decomposition (3). It isn’t hard to see how this method isn’t a great approach either; adding more chemicals to the mix causes further contamination.

The best alternative is bioremediation, and particularly mycoremediation. Bioremediation uses microorganisms that are already part of their environments to clean up pollution. Mycoremediation more specifically uses fungi. These fungi eat organic pollutants. Through the use of fertilizers and enhanced conditions, they grow more rapidly, and therefore breakdown the pollutants at a faster rate. This is a considerably better approach to solve the problem of environmental contamination.

Unfortunately, the field of mycoremediation has not been able to expand enough to be applied in practice. This is mainly due to the lack of funding for the field. The few studies that have been conducted on mycoremediation have all yielded successful results, which indicates that this is indeed a promising field of study. Funding for research in mycoremediation is crucial, for it is potentially one of the most preferable solutions to environmental contamination.

Fungi achieve the digestion of the contaminants by secreting extracellular enzymes that breakdown organic waste (4). A good example of the success of mycoremediation is seen in a study by Migliore et al. on the biodegradation of oxytetracycline by Pleurotus ostreatus. Oxytetracycline (OTC) is a drug that is heavily used on livestocks in intensive farming to treat diseases. Due to animal waste disposal, OTC contaminates water, sediments and soil, negatively affecting microbial community structures and natural systems. They cultured Pleurotus ostreatus with exposure to varying concentrations of OTC, and measured mycelial growth, extracellular enzyme secretion, and the degradation of OTC. Their results demonstrated that P. ostreatus survived and successfully grew even when exposed to high concentrations of the drug. While no OTC degradation was observed in the controls, P. ostreatus almost completely degraded the drug in a few days (1).

Valentin et al. conducted a study on the mycoremediation of contaminated wood and soil samples that was similarly successful. In order to really reflect the conditions of the setting their results would have potential use in, they used non-sterile conditions in their experiment. With the intentions of investigating white-rot and litter-decomposing fungi to treat contamination by chlorinated phenols present in sawmills, they inoculated non-sterile soil and wood — meaning the soil and wood had native microbial communities along with contamination — with nine fungi. The litter-decomposing fungus, Stropharia rugosoannulata, mineralized and degraded multiple contaminants at a significantly faster rate than indigenous microbes in soil. Therefore, S. rugosoannulata is a suitable fungus for mycoremediation of soil contaminated with chlorophenols. In wood, white-rot fungi grew and degraded contaminants faster than both indigenous degraders (which were barely present), and litter-decomposing fungi. These results show that S. rugosoannulata has particularly high potential to be used in mycoremediation of specifically sawmills containing chlorophenols (5). This study displays successful fungal growth as well as high degradation success in realistic conditions. It also pushes to further investigate the understudied litter-decomposing fungi for mycoremediation. Funding for more studies of this kind are necessary to improve our understanding of specific fungal interactions with contaminated environments.

Both these studies indicate successful usage of fungi in cleaning pollutants. Because this is a field that leans towards experimentation in rather specific contexts, thorough research must be done in a variety of contexts in order to ensure its applicability to real-life scenarios. However, the experimentation that has been done clearly shows the potential of mycoremediation. Even studies that have been done indicate the necessity for further research in the field in order to start applying their results in real life. Environmental contamination decreases the life quality of all organisms, and using fungi as remedies for our environment is a sustainable, natural, and affordable solution. With sufficient funding, this field could grow and become the number one cure for environmental pollution.

1.     Migliore, L. et al., “Biodegradation of oxytetracycline by Pleurotus ostreatus mycelium: a mycoremediation technique.” Journal of Hazardous Materials. 215-216, 227-232, 2012.

2.     Sharma, A., Sharma, H., “Role Of Vesicular Arbuscular Mycorrhiza In The Mycoremediation of Heavy Toxic Metals From Soil.” International Journal of Life Sciences Biotechnology and Pharma Research. 2, no. 3, 418-427, 2013.

3.    Vidali, M. "Bioremediation. An Overview*." Pure Applied Chemistry 73, no. 7, 1163-172. IUPAC, 2001.

4.     Adenipekun, C. O., Lawal, R. “Uses of mushrooms in bioremediation: A review.” Biotechnology and Molecular Biololgy Review, 7, no. 3, 62-68. Academic Journals, 2012.

5.     Valentin, L. et al., “Mycoremediation of wood and soil from an old sawmill area contaminated for decades.” Journal of Hazardous Materials. 260, 668-675, 2013

The Human Mycobiome ;)

MYCOBIOME

Fungal diversity in the human skin microbiome

A discussion of the importance of fungi in microbial community composition and stability.

by Doğa Tekin

We used to associate bacteria with disease and disease only. In recent years, we’ve been becoming more comfortable with the idea of commensal bacterial presence in different microbial communities throughout our bodies. However, in this effort to accept friendly bacteria, we’ve completely ignored the same role played by fungi. Most of us still think of fungal interactions with humans to be solely pathogenic. Recent research within the up and coming field of the human microbiome has revealed that fungi play just as significant a role in microbial community composition and stability as bacteria do. 

Although most studies on the human microbiome have focused solely on bacteria, a new study performed by Findley et al. showed that our skin microbiome exhibits a vast amount of fungal diversity as well (1). The term ‘microbiota,’ which we are quite familiar with, is primarily used to describe bacterial communities, whereas ‘mycobiota’ can be used to describe the fungal component of our microbiome (2).  

Mycobiota on our skin consist of much more than toenail infections and athlete’s foot. Findley et al. demonstrated that the diversity and composition of microbial communities on our skin depends highly on the topography of the inhabited region. They analyzed 14 regions of the skin in 10 healthy adults to determine the genera and species composition of the mycobiota. Their results indicated the highest level of fungal diversity in the plantar heel, toenail and toe web. All other regions were primarily dominated by the genus Malassezia, which also displayed a higher level of species diversity in the three foot regions (see Fig. 1). This genus contains yeasts that have been known to be part of the natural human flora for over a century. Malassezia yeasts depend on lipids for survival, which is why they are commonly found in skin microbiomes. (3)

To test temporal stability, Findley et al. sampled six of the healthy volunteers one to three months later. Their results showed consistency in topography-based diversity, which indicates structural and temporal stability of the mycobiota. (1)

Furthermore, they investigated the bacterial profile of the same region using genomic sequencing. Their results indicated lower bacterial diversity compared to fungal diversity in foot regions, and higher bacterial diversity compared to fungal diversity in arm regions. This entails a high level of complexity in the composition of the skin microbiome, and suggests that the microbiota and mycobiota form based on different characteristics (1).

While Findley et al. focus on the skin, other studies reveal similar fungal diversity mycobiotic composition in different parts of the human body. For example, in a study of the oral mycobiota, Ghannoum et al. identified a total of 101 species in the oral cavities of 20 healthy individuals (4). This was the first study that identified the oral mycobiota. Although they did not include bacterial communities, the level of fungal diversity alone is sufficient to indicate a highly delicate ecosystem.

 The human microbiome is just like all ecosystems; organisms are linked through multiple layers and networks of interactions. In this sense, to understand changes in our microbiotic ecosystem – especially those with the potential of causing us harm – we must familiarize ourselves with all of the organisms that partake in it. Exploring the diversity of our fungal inhabitants is key to understanding our microbiome, and has potential applications to treat microbial infections. Research in this field has indicated a high level of complexity in fungal and bacterial interactions. The two communities influence each other directly and indirectly (5). Therefore, future implications of these studies are huge. Understanding the commensal inhabitants of our microbiomes and their interactions with each other and the environment can enable us to develop new and more successful therapies for fungal and bacterial pathogenicity. (6) 

REFERENCES

1. K. Findley et al., Nature 498, 367 (2013).

2. D. M. Underhill, I. D. Iliev, Nature Reviews Immunology 14, 405 (2014)

3. A. J. Kindo, J. Kalyani, S. Anandan, Indian Journal of Medical Microbiology, 22, 179 (2004)

4. M. A. Ghannoum et al., PLoS Pathog. 6.1, (2010)

5. A. Y. Peleg, D. A. Hogan, E. Mylonakis, Nature Reviews Microbiology 8, 340 (2010)

6. E. A. Grice et al., Genome Res. 18, 1043 (2008)