Fungi Identify the Geographic Origin of Dust Samples

Abstract

There is a long history of archaeologists and forensic scientists using pollen found in a dust sample to identify its geographic origin or history. Such palynological approaches have important limitations as they require time-consuming identification of pollen grains, a priori knowledge of plant species distributions, and a sufficient diversity of pollen types to permit spatial or temporal identification. We demonstrate an alternative approach based on DNA sequencing analyses of the fungal diversity found in dust samples. Using nearly 1,000 dust samples collected from across the continental U.S., our analyses identify up to 40,000 fungal taxa from these samples, many of which exhibit a high degree of geographic endemism. We develop a statistical learning algorithm via discriminant analysis that exploits this geographic endemicity in the fungal diversity to correctly identify samples to within a few hundred kilometers of their geographic origin with high probability. In addition, our statistical approach provides a measure of certainty for each prediction, in contrast with current palynology methods that are almost always based on expert opinion and devoid of statistical inference. Fungal taxa found in dust samples can therefore be used to identify the origin of that dust and, more importantly, we can quantify our degree of certainty that a sample originated in a particular place. This work opens up a new approach to forensic biology that could be used by scientists to identify the origin of dust or soil samples found on objects, clothing, or archaeological artifacts.

Dimensions of biodiversity in the Earth mycobiome

“…For example, the results of a study that sequenced fungi from approximately 600 soil samples across North American Pinaceae forests were highly consistent with dispersal limitation (BOX 3), as statistical ordinations showed strong geographical clustering of fungal communities 3 , and community similarity decreased with increasing distance between samples, even after controlling for climate and environment. In fact, the geographical signal of fungal communities in soil is so strong that fungal community composition can be used to identify the origin of dust samples 43 . Although fungal communities overall show strong patterns of regional endemism and dispersal limitation, long-distance dispersal can occur over short timescales through the aerial movement of spores or, over longer timescales, alongside the migration of vegetation during climatic change (see below).…”

Fungal DNA barcoding

“…In a large-scale survey of outdoor dust samples, Grantham et al (2015) found evidence for geographic endemism for many dust fungi. Specifically, they obtained the ITS-1 sequences directly through high-throughput metabarcoding from nearly 1000 dust samples collected from the top edges of doors opening to the outside environment, from across the continental US.…”

“…Many of these taxa exhibited a high degree of geographic specificity, with 72% of the observed OTUs found in less than 10 dust samples. Based on the geographic endemism in dust fungal diversity, the authors developed a statistical learning algorithm via discriminant analysis that allowed correct identification of dust samples to within a few hundred kilometers of their geographic origin with high probability (Grantham et al 2015). This work also opened up a new approach to forensic biology where fungal barcodes could be used to identify the potential origins of dust samples found on a variety of objects.…”

“…The rapid increase in fungal barcoding studies has been significantly benefited from the availability of affordable DNA sequencing technologies in many parts of the world. These studies have revealed tremendous undescribed fungal diversity across a broad-spectrum of ecological niches (e.g., Osmundson et al 2013;Tedersoo et al 2014;Grantham et al 2015; see also below).…”

The ecology of microscopic life in household dust

“…temperature, humidity) that select for certain taxa in certain regions. We expect that indoor fungi will exhibit particularly strong variability across geographical regions, given that most fungal taxa found indoors come from outside the home [27] and the fungi found in outdoor air can exhibit a high degree of geographical endemism [31,32]. Yet, the biogeography of indoor microbial life remains largely unstudied with the exception of a single study of 72 buildings, in which strong effects of climate were found on indoor fungal taxa [25].…”