Predicting Species Boundaries and Assessing Undescribed Diversity in Pneumocystis, an Obligate Lung Symbiont

Far more biodiversity exists in Fungi than has been described, or could be described in several lifetimes, given current rates of species discovery. Although this problem is widespread taxonomically, our knowledge of animal-associated fungi is especially lacking. Fungi in the genus Pneumocystis are obligate inhabitants of mammal lungs, and they have been detected in a phylogenetically diverse array of species representing many major mammal lineages. The hypothesis that Pneumocystis cospeciate with their mammalian hosts suggests that thousands of Pneumocystis species may exist, potentially equal to the number of mammal species. However, only six species have been described, and the true correspondence of Pneumocystis diversity to host species boundaries is unclear. Here, we use molecular species delimitation to estimate the boundaries of Pneumocystis species sampled from 55 mammal species representing eight orders. Our results suggest that Pneumocystis species often colonize several closely related mammals, especially those in the same genus. Using the newly estimated ratio of fungal to host diversity, we estimate approximate to 4600 to 6250 Pneumocystis species inhabit the 6495 currently recognized extant mammal species. Additionally, we review the literature and find that only 240 (similar to 3.7%) mammal species have been screened for Pneumocystis, and many detected Pneumocystis lineages are not represented by any genetic data. Although crude, our findings challenge the dominant perspective of strict specificity of Pneumocystis to their mammal hosts and highlight an abundance of undescribed diversity.

Automated summary

There is far more biodiversity in Fungi than we can currently describe, especially in regards to animal-associated fungi. Pneumocystis fungi, which inhabit mammal lungs, have been found in a diverse range of mammal species, suggesting the existence of thousands of Pneumocystis species. However, only six species have been described so far. Using molecular species delimitation, this study suggests that Pneumocystis species often colonize multiple closely related mammal species. Based on the estimated fungal to host diversity ratio, it is estimated that there are approximately 4600 to 6250 Pneumocystis species inhabiting the currently recognized 6495 mammal species.