Commentary on De Gannes et al. (2013): "Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety".

Abstract

NEXT-GENERATION COMPOST FUNGAL ECOLOGY 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. (2013a) provides one of the first in-depth studies into the microbial ecology of compost fungal communities using NGS and demonstrates its usefulness in addressing basic ecological questions, such as those relating diversity to resource limitation through time under dynamic environmental conditions. A sister publication by the same authors (De Gannes et al., 2013b) showed that prokaryotic diversity in different composts (from wastes derived from bagasse, coffee, and rice) increases as resources become limited, i.e., consumed by microbes. This is generally in line with classical ecological theory, which predicts that diversity is directly proportional to the number of resources at limiting levels within a system (Tilman, 1982). The relationship holds true for prokaryotes through progressive disturbances. i.e., early stage acidification from fermentation of labile organics; intermediate stage heat from intense microbial activity; and late stage production of antibiotics often associated with actinomycetes. Compared to prokaryotes, the diversity-resource relationship of certain fungal communities in the same composts were more constrained by prolonged compost temperatures exceeding 60◦C, which is a known limitation of fungal growth (Tansey and Brock, 1978). Similar NGS-based surveys targeting microbial predators and parasites will provide a more complete view of the entire compost trophic structure. Studies such as these across different composting recipes and management schemes will contribute to the synthesis of microbial knowledge grounded on ecological principles. However, these studies also raise questions that NGS-based rRNA gene surveys alone cannot answer, i.e., questions regarding the relationship between community structure and function. Composting is essentially a process of biodegradation and humification. Since mature compost that has undergone sufficient heating is often considered safe to handle, how do humic substances affect microbial functions in general, and virulence of potential pathogens in particular? 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., 2012). Therefore, it makes sense to confirm the viability of potential pathogens and to determine how consistently they are detected in composts of different types. Despite the sequencing power of NGS, 454 sequencing only provides presence/absence data