FISH-ing for bioaerosols in the Amazon rainforest

The Amazon rain forest plays a major role in global hydrological cycling. Biogenic aerosols, such as pollen, fungi, and spores likely influence the formation of clouds and precipitation. However, there are many different types of bioaerosols. The particles vary considerably in size, morphology, mixing state, as well as behavior like hygroscopicity (how much particles attract water) and metabolic activity. Therefore, it is likely that not only the amount of bioaerosols affects the hydrological cycle, but also the types of aerosols present.

FISH-ing for data

Maria Prass, Christopher Pöhlker and their colleagues now wanted to find out which types of bioaerosols are present in the atmosphere above the Amazon Rainforest, and in which quantities. For their new study, they sampled air in the wet season of 2018. They utilized the infrastructure at ATTO to sample at three heights: near the ground at 5 m, above the canopy at 60 m and on top of the tall tower at 325 m. Subsequently, they filtered the air for airborne aerosols.

They wanted to distinguish them on a domain level. Specifically, they looked at three groups: bacteria, archaea (single-celled organisms without a cell nucleus), and eukaryotic cells such as fungi and algae. To achieve this, they used the FISH method. FISH (Fluorescence in situ hybridization) is a molecular genetic technique that enables cell identification by characteristic RNA or DNA sequences combined with fluorescence staining. Maria then looked at the stained particles under a microscope and manually counted them.

Schematic overview of the sampling strategy and FISH method.
Schematic overview of the sampling strategy and FISH method. Figure from Prass et al. (2021).

The authors found that more than 70% of the aerosols in the analyzed size range were in fact intact cells. Only the remaining 30% were likely fragmented or degenerated biological material. Out of intact 70%, eukaryotic cells dominated bioaerosol numbers, accounting for more than half of all particles. Bacteria were also abundant, accounting for a quarter of all present cells. Archaea on the other hand were very rare. (The remaining particles could not be identified.)  Beyond that, they noticed a clear day-to-day variability in the concentrations. For example, bacteria are relatively more abundant on 3 of the 7 days following a strong rain event.

In addition to the variability over time, the scientists also looked at changes in bioaerosol distribution with height. They noticed an overall decrease of aerosol abundance with height and a decrease in particle size. This is likely due to the high abundance of sources within and under the canopy in combination with higher sedimentation tendency and lower atmospheric residence times of large particles. This trend is less pronounced for bacterial cells that are often smaller than spores that were more abundant closer to the ground.

Microscopic images of fluorescence signals after DNA staining.
Microscopic images of fluorescence signals after DNA staining. © Maria Prass / MPI-C

Potential for future studies

Specific bioaerosol numbers generated by Maria and colleagues are the first of their kind for a tropical rainforest environment. They represent the wet season when the atmosphere in that region is almost pristine and largely free of anthropogenic pollution. They can now serve as a reference for future modeling and process studies. Here, they will be useful for studies of climate-relevant forest–atmosphere interactions such as precipitation cycles and the specific impact of bioaerosols. Especially the data from 325 m can serve as an estimate for cells that are being convectively lifted to the cloud base, where they potentially impact cloud formation and evolution processes.

Furthermore, the team could demonstrate the potential of the FISH method for targeting organism classes on different taxonomic levels. In theory, this is possible down to species level. They hope to conduct future studies with FISH in close relation to cloud microphysical process studies. Targeted bioaerosol characterizations during periods of climate extremes, such as El-Niño-related droughts in the Amazon, are of great importance to study the response and resilience of the bioaerosol population in the Amazon under warmer and presumably drier climatic conditions in the future.

Prass et. al. published the study “Bioaerosols in the Amazon rain forest: temporal variations and vertical profiles of Eukarya, Bacteria, and Archaea” Open Access in Biogeochemistry.

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