*Correspondence:
This article was submitted to Microbiotechnology, Ecotoxicology and Bioremediation, a section of the journal Frontiers in Microbiology.
Edited by: Belinda Ferrari, University of New South Wales, Australia
Reviewed by: Matthias E. Kaestner, Helmholtz-Centre for Environmental Research, Germany
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Composting reduces the volume of and transforms spent organic wastes into a valuable soil amendment. In certain situations, composting can literally save lives: during the aftermath of the 2010 earthquake in Haiti, chaos reigned and it didn't take much for sewage and drinking water streams to intermingle, producing tragic results. In this situation, composting of human wastes helped prevent the wider spread of waterborne diseases such as cholera. When properly undertaken, composting contributes to sanitation and the end product is a humus-rich, value-added material that improves the soil. A compost pile supports complex, staged microbiological processes carried out at temperatures that can range from ambient to extremely thermophilic, with important functions carried out by both prokaryotes and eukaryotes. The complex microbiology of compost is ideal for the application of next-generation DNA sequencing (NGS) technology, which offers the needed depth to investigate relationships between composting stages, changes in diversity and succession of abundant and rare microbial populations.
The recent article by De Gannes et al. (
The article highlights the detection of potentially pathogenic fungi in compost. Assuming that different types of potential fungal pathogens are present in compost, how does their presence as detected by NGS relate to viability? Composting is a good source of bioaerosols—airborne particles that contain microbes or parts of microbes including endotoxins and mycotoxins. For those constantly exposed to compost dust, there is a significantly higher risk for respiratory, gastrointestinal, and skin problems (Hambach et al.,
Potentially pathogenic fungi in compost may be a cause of concern. Among the potential pathogens detected in this study, compost-derived
There are few microbial-based processes that can be undertaken from household to community scales using simple to high technology equipment. Like any process dependent on diverse microbial communities, there is an element of risk that needs to be considered. We cannot totally eliminate potential pathogens from these communities. Individuals with compromised immune systems or who are exposed to the composting environment for prolonged periods need to exercise caution. However, composting is an overall benefit to society—including a good educational and research system to study basic ecological questions that can now be better addressed with NGS as well as an expanded array of “-omics” tools.
The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.