Date of Defense


Date of Graduation



Biological Sciences

First Advisor

Kathryn Docherty

Second Advisor

Kristina Lemmer

Third Advisor

Todd Barkman


Microorganisms are known to be highly abundant and diverse in the atmosphere and are distinct from those found in soil, plant, and aquatic environments (Barberán et al. 2014, Bowers et al. 2011a, Bowers et al. 2011b, Mhuireach et al. 2016, Fierer et al. 2008). Until recently, atmospheric microbial communities were thought to have little influence on ecosystem function. Recently, scientists have begun to think of the atmosphere as an important vector for dispersal of atmospheric microbial communities across all the surface habitats on Earth. Microorganisms are responsible for important steps in the carbon, nitrogen and hydrologic cycles in terrestrial and aquatic systems (Deguillaume et al. 2008), yet very little is known about the mechanisms that control microbial dispersal to these systems (Womack et al. 2010). Traditional microbial theory suggests that, because of their small size, microbial populations are not limited by dispersal the way larger organisms are, leading to the theory that “everything is everywhere, the environment selects” (Baas Becking, 1934). However, this theory has never conclusively been tested, because sampling of microbial populations higher in the atmosphere has not been conducted. Furthermore, some studies suggest that the atmosphere may even serve as a native habitat for specific types of microorganisms, where they are not only dispersed, but are actively interact with abiotic and biotic components of the air (e.g. Womack et al. 2010, Bowers et al. 2011b, Klein et al. 2016).

Despite the potential importance of airborne microbial communities to the global ecosystem, our understanding of their global distribution is limited. The few studies that have examined microorganisms in the atmosphere have sampled near the surface. These studies indicate that airborne bacterial and fungal diversity is high. For example, previous studies have found that abundance of microbial cells ranges from 10# to 10$ cells·m−3 in the atmosphere (Bowers et al. 2009).

The composition of these communities can be influenced temporally, by underlying terrestrial systems and by changes in land-use (Bowers et al. 2011a, Bowers et al. 2012, Barberan et al. 2015). However, most published studies that have examined airborne microbial communities thus far only sampled air 2 m above the ground (Bowers et al. 2011, Fierer et al. 2007, Mhuireach et al. 2016, Whon et al. 2012), and the effect of altitude on the dispersal of airborne microbial communities upward has not been examined. The question remains: Are near-surface airborne microorganisms transported up into the atmosphere, leading to widespread dispersal?

The goal of my honors thesis was to help design and test novel airborne microbial community samplers to conduct measurements of microbial communities from higher altitudes. I worked with a multi-disciplinary team of biologists and aerospace engineers at Western Michigan University for nearly two years to accomplish this goal. The team chose helium-filled helikites as the mechanism for launching samplers into various altitudes. As opposed to manned aircraft or drones, balloons are easy to implement and act as completely passive sampler vehicles that will not disturb collection of air samples. In addition, balloons can target specific altitude ranges and remain at those altitudes for long sampling periods required to collect enough microbial biomass to conduct downstream testing. The engineers on the team designed and built a system to collect airborne microbial samples at different altitudes (Figure 1). To do this, they met several design challenges: 1) the sampler collects sufficient microbial biomass to conduct DNA extractions and amplicon-based sequencing; 2) the sampler remains sterile when closed; 3) the sampler weighs under 6 lbs. to meet FAA regulations; 4) the sampler is made of aluminum and plastic materials that can be sterilized; 5) the sampler opens and closes using a remote control or altitude-based system, to prevent contamination from non-target altitudes.

The biologists on the project were responsible for determining how to collect airborne microbial samples within the sampler and to troubleshoot several aspects of sample collection. In previous work, it was determined that an array of petri dishes coated in silica gel provided a range of sterile surfaces that could passively collected airborne microorganisms (Figure 1). In this study, we asked several troubleshooting-related questions prior to implementing full-scale sampling of atmospheric microbial communities. The questions we address are: 1) Do open boxes collect sufficient biomass to yield extracted microbial DNA suitable for 16S rRNA-based amplicon sequencing, while closed boxes have negligible amounts of contamination? 2) How long do boxes need to be UV-sterilized to remove any contaminants that may have been introduced before sampling? 3) How many coated dishes are required to collect sufficient amounts of DNA for airborne microbial community analyses? 4) Does storing samples under different conditions alter the microbial communities present in the samples? The results of this work inform best practices for airborne microbial community sampling from different altitudes in the upcoming field season.

Access Setting

Honors Thesis-Restricted