Pollen Monitoring by Optical Microscopy and DNA Metabarcoding: Comparative Study and New Insights

Abstract

Environmental samples collected in Brindisi (Italy) by a Hirst-type trap and in Lecce (Italy) by a PM10 sampler were analysed by optical microscopy and DNA-metabarcoding, respectively, to identify airborne pollen and perform an exploratory study, highlighting the benefits and limits of both sampling/detection systems. The Hirst-type trap/optical-microscopy system allowed detecting pollen on average over the full bloom season, since whole pollen grains, whose diameter vary within 10–100 μm, are required for morphological detection with optical microscopy. Conversely, pollen fragments with an aerodynamic diameter ≤10 μm were collected in Lecce by the PM10 sampler. Pollen grains and fragments are spread worldwide by wind/atmospheric turbulences and can age in the atmosphere, but aerial dispersal, aging, and long-range transport of pollen fragments are favoured over those of whole pollen grains because of their smaller size. Twenty-four Streptophyta families were detected in Lecce throughout the sampling year, but only nine out of them were in common with the 21 pollen families identified in Brindisi. Meteorological parameters and advection patterns were rather similar at both study sites, being only 37 km apart in a beeline, but their impact on the sample taxonomic structure was different, likely for the different pollen sampling/detection systems used in the two monitoring areas.

A primer on pollen assignment by nanopore-based DNA sequencing

“…The DNeasy Plant Mini Kit from Qiagen is the most commonly used kit for pollen DNA extraction (Galimberti et al, 2014;Hawkins et al, 2015;Baksay et al, 2020;Bänsch et al, 2020;Vaudo et al, 2020;Gous et al, 2021;Jones et al, 2021), closely followed by the NucleoSpin Food Kit from Macherey-Nagel (Bell et al, 2017a;Voulgari-Kokota et al, 2019;Arstingstall et al, 2021;Swenson and Gemeinholzer, 2021). But there are also other column-based DNA extraction kits provided by Qiagen and Macherey-Nagel that are applied (Leontidou et al, 2021;Oliver et al, 2021;Fragola et al, 2022).…”

“…Besides in agricultural sciences, it also plays a major role in, e.g., aerobiology, a discipline that investigates the passive transport of bioaerosols through air. Here, pollen is mostly studied in the context of allergen monitoring (Fragola et al, 2022;Khan et al, 2022;Polling et al, 2022). In forensic palynology, pollen, which easily attaches to many surfaces such as skin and clothes, which is insensitive to chemical reactions, and that is incredibly durable, provides information about the potential timing and location of a crime scene (Alotaibi et al, 2020).…”