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.

Similar articles

SEM images of different types of bioaerosols. @Sachin Patade / Uni Lund

Bioaerosols may act as cloud condensation nuclei and ice nuclei, thereby influencing the formation of clouds and precipitation. But so far there is less knowledge about the ice nucleation activity of each bioaerosol group and atmospheric models hitherto have not differentiated between them. Patade et al. created a new empirical parameterization for five groups of bioaerosols, based on analysis of the characteristics of bioaerosols at ATTO: fungal spores, bacteria, pollen, plant/animal/viral detritus, and algae. This makes it possible for any cloud model to access the role of an individual group of bioaerosols in altering cloud properties and precipitation formation.

Air inlet tube at the top of the ATTO tall tower. © Eva Pfannerstill / MPI-C

Biogenic volatile organic compounds remove OH from the atmosphere through chemical reactions, which affects processes such as cloud formation. In a new study, Pfannerstill et al. reveal the important contributions of previously not-considered BVOCs species and underestimated OVOCs to the total OH reactivity.

Sampling set-up for bioaerosols near the forest floor

Felipe Souza, Price Mathai and their co-authors published a new study analyzing the diverse bacterial population in the Amazonian atmosphere. The composition varied mainly with seasonal changes in temperature, relative humidity, and precipitation. On the other hand, they did not detect significant differences between the ground and canopy levels. They also identified bacterial species that participate in the nitrogen cycle.

GRAEGOR detector unit for measuring trace gases like nitrogen in the laboratory container. © Robbie Ramsay / University of Edinburgh

Ramsay et al. measured inorganic trace gases such as ammonia and nitric acid and aerosols in the dry season at ATTO. They are to serve as baseline values for their concentration and fluxes in the atmosphere and are a first step in deciphering exchange processes of inorganic trace gases between the Amazon rainforest and the atmosphere.

Smoke from biomass burning rises into the atmosphere over the central Amazon basin. © NASA

Soot and other aerosols from biomass burning can influence regional and global weather and climate. Lixia Liu and her colleagues studied how this affects the Amazon Basin during the dry season. While there are many different interactions between biomass burning aerosols and climate, they found that they overall lead to fewer and weaker rain events in the Amazon rainforest.

large tropical fungi

Fungal spore emissions are an important contributor to biogenic aerosols, but we have yet to understand under what conditions fungi release their spores. Nina Löbs and co-authors developed a new technique to measure emissions from single organisms and tested this out at ATTO and with controlled lab experiments. They published their results in the Open Access Journal Atmospheric Measurement Techniques.

Graphical Abstract

In a new study, Dr. Haijie Tong and co-authors studied a subset of PM2.5, the so-called highly oxygenated molecules (HOMs) and its relationship with radical yield and aerosol oxidative potential. They analyzed fine particulate matter in the air in multiple locations. This including the highly polluted megacity Bejing and in the pristine rainforest at ATTO. They wanted to get insights into the chemical characteristic and evolutions of these HOM particles. In particular, they wanted to find out more about the potential of HOMs to form free radicals. These are highly reactive species with unpaired electrons.

Felipe Souza and co-authors now collected bioaerosols at our ATTO site. Then they extracted and analyzed the DNA to determine the communities present. This is the first study that described the community of microorganisms within aerosols in the Amazon. They found many different types of bacteria and fungi. Some were cosmopolitan taxa, but they also identified many that are specific to certain environments such as soil or water. This suggests that the atmosphere may act as an important gateway for bacteria to be exchanged between plants, soil, and water.

Wu et al. collected and analyzed aerosols in two locations: the city of Manaus, a large urban area in Brazil, and the ATTO site in the heart of the forest. The aerosol compositions varied largly. At ATTO most aerosols were emitted by the forest itself, while in Manaus, anthropogenic aerosols were very common. The results were published in ACP.

Mira Pöhlker and her team continuously measured aerosols and their properties in the atmosphere at the 80 m tower at ATTO, thereby created the first such long-term record in the Amazon. They analyzed the data in two subsequent paper. The second was now published in ACP.