Terrestrial and marine influence on atmospheric bacterial diversity over the north Atlantic and Pacific Oceans

Regional distribution of airborne and surface water bacterial phyla in the Pacific and Atlantic oceans

The two open ocean sailing transects examined in this study included the western Pacific path, sampled in May 2017 from Keelung, Taiwan, towards Fiji (Fig. 1a and Supplementary Data 1), and the Atlantic crossing, sampled in June 2016 from Lorient, France, to Miami, USA (Fig. 1b and Supplementary Data 1). In the water, we found a higher homogeneity in phyla distribution within each transect (significantly lower Euclidean distances between centered log-ratio (CLR)-converted phyla counts (betadispar): Atlantic: 0.3212 compared to 0.4229 in the air, ANOVA (with Tukey’s post hoc), p < 0.0001; Pacific: 0.1865 compared to 0.3891 in the air, ANOVA (Tukey’s post hoc), p < 0.0001; Tables S1–S4), with Proteobacteria dominating both oceans (58 ± 3% in the Pacific and 66 ± 4% in the Atlantic; Fig. 1c, d, respectively). Cyanobacteria (29 ± 2% and 9 ± 4%) and Bacteroidetes (9 ± 1% and 17 ± 2%) were the next two most abundant phyla. When compared to other marine microbiome studies, the phyla distribution of the near-surface water environment was similar^2,13. For example, the Cyanobacteria to Proteobacteria ratios in our study are 0.49 ± 0.06 and 0.14 ± 0.07 in the Pacific and Atlantic surface water, respectively. Similarly-calculated ratios characterized in these oceanic regions were 0.43 and 0.16, for the Pacific¹³ and Atlantic² regions, respectively.

In the AMBL, Proteobacteria was also the most dominant airborne bacterial phylum in both the Pacific and Atlantic oceans, with 69 ± 12% and 64 ± 8% average percentile abundance, respectively (Fig. 1e, f). However, we found a more heterogeneous distribution of bacterial phyla than in ocean surface water samples (Fig. S1), even when considering air masses spending at least 120 h over an oceanic path prior to sampling (Fig. 1a, b, colored lines). Other abundant phyla in the Pacific AMBL included Cyanobacteria (11 ± 9%), Bacteroidetes (8 ± 3%), Firmicutes (8 ± 3%), Actinobacteria (4 ± 3%), and Planctomycetes (2 ± 1%). In the Atlantic AMBL, the abundant phyla included Actinobacteria (11 ± 5%), Firmicutes (10 ± 6%), and Bacteroidetes (6 ± 3%; Fig. 1f), while Cyanobacteria was observed with an average abundance of less than 0.5%. In general, while Proteobacterial abundance is high in both air and water, there is a distinct difference in Bacteroidetes (higher in oceanic samples, Two-sample t-test, performed on CLR values, equal variance (F = 1.174, p = 0.341), t = 14.889; p = 1.91 × 10⁻²²).

Firmicutes were predominantly observed in the air samples (8 ± 3% and 10 ± 6% in the Pacific and Atlantic AMBL, respectively), with low (<1% in average) to non-significant abundance in the water samples (unequal variance t-test on CLR values (F = 5171.823, p = 1.2 × 10⁻⁸³), t = 25.716; p = 2.1 × 10⁻³⁶). Actinobacteria abundance was also significantly higher in the Atlantic AMBL compared to the water (unequal variance t-test on CLR values (F = 68.383, p = 4.6 × 10⁻³⁵), t = 17.117, p = 1.2 × 10⁻²⁶). Airborne Actinobacteria and Firmicutes have been previously connected to desert dust samples in the Eastern Mediterranean^14,15,16, and detected in different studies of airborne bacteria^17,18,19. In addition, Firmicutes are usually more abundant in soils than in marine surface water^2,20, where specifically the Bacillus genus was detected²⁰. Sul et al. found marine Firmicutes in low relative abundance (<6% on average) across latitudes with little latitudinal dependence²¹. Therefore, the airborne Firmicutes most likely represent a terrestrial source.

Members of the airborne-detected Fusobacteria, Deinococcus-Thermos, and Acidobacteria phyla (Fig. 1e, f) exhibit high physiological diversity in cell shapes and sizes^20,22. Their presence in remote locations, such as Antarctica²³, airborne dust¹⁴, and precipitation over the alpine²⁴, together with their detection in the current study above the western Pacific Ocean, after 120 h transport above the ocean, suggests that they are ubiquitous in the atmospheric environment.

The local primary production impact on the AMBL was estimated by calculating the ratio of known autotrophic to heterotrophic bacterial amplicon sequence variant (ASV; as listed in Table S5)²⁵ in the atmospheric and oceanic samples (Fig. S2). The ratios in the Pacific AMBL were more than an order of magnitude higher than those measured in the Atlantic AMBL (mean values ± SE: 0.186 ± 0.029 and 0.005 ± 0.002, respectively, Wilcoxon rank test, p = 7.44 × 10⁻⁰⁶; Fig. S2a, b). Additionally, the average ratio in the Pacific surface water is approximately four times higher than in the Atlantic (0.406 ± 0.010, compared to 0.104 ± 0.010, respectively; Wilcoxon rank test, p = 2.98 × 10⁻⁰⁸). Similarly, a significantly higher relative abundance of cyanobacterial 16S rRNA gene to total bacterial 16S rRNA gene was observed in the Pacific compared to the Atlantic air samples (mean values ± SE: 0.171 ± 0.016 and 0.001 ± 0.000, respectively, Wilcoxon rank test, p = 1.863 × 10⁻⁰⁹; Fig. S2c, d and Table S6) based on qPCR analysis (Supplementary Note 8). The observed difference in oceanic cyanobacterial abundance is consistent with results reported by Flombaum et al., showing a higher abundance of marine Synechococcales in the Pacific compared to the Atlantic²⁶.

Similarities and differences in the atmospheric and oceanic microbiomes

The marine and atmospheric microbiomes were further analyzed at higher taxonomic resolution. We found the airborne bacterial diversity to be significantly higher compared to the water samples (Fig. 2a; DivNet for Shannon diversity, Wilcoxon rank test, p = 2.98 × 10⁻⁰⁸ for the Atlantic, and p = 2.587 × 10⁻⁰⁵ for the Pacific), as well as the airborne bacterial composition distances (Fig. 2b; ANOSIM R = 0.7519, p = 0.01). In addition, both mean Euclidean distances (Fig. 2c; Kruskal–Wallis chi-squared = 1321.9, df = 1, p < 2.2 × 10⁻¹⁶; Wilcoxon rank test, p < 2.2 × 10⁻¹⁶ for both Atlantic and Pacific environments) show that for each environment, the surface water sample distances are significantly smaller compared to the AMBL samples, indicating a more homogeneous and stable community structure in the marine surface water.

The surface water environments shared 166 taxa between the Atlantic and Pacific oceans, and the AMBL biomes shared 341 taxa (comprising 28% of all ocean taxa vs. 25% of all airborne taxa; Fig. 2d). Only 78 taxa in the Atlantic and 134 in the Pacific (7% of all Atlantic taxa vs. 15% of all Pacific taxa) were shared between an ocean and its corresponding atmosphere. The ubiquity of shared species found only in the atmospheric samples of the Atlantic and Pacific oceans suggests a potentially higher pool of air-resident bacteria with efficient long-range transport in the atmosphere. In addition, different oceans are found to have a greater resemblance to one another than to their overlaying AMBL, and atmospheric samples from distinct locations (at least 13,000 km apart from each other) share more common taxa than the ocean beneath. This suggests that the proximity of the sampled biomes is second in significance to the type of sampled environment.

A phylogenetic tree based on the bacterial 16S amplicon sequences provides an overview of the bacterial community and genetic distances between them in the observed marine environment (Fig. S3). Among the shared groups in the Atlantic and Pacific atmospheric biomes, the main phyla occurrences included 44% Proteobacteria, 19% Actinobacteria, 19% Firmicutes, and 10% Bacteroidetes.

While the wind-driven surface water currents show connectivity between oceans with time scales of years, the atmospheric circulation time scales are in the range of days to weeks^27,28. Therefore, the high diversity and variations between samples of airborne bacteria in both the Atlantic and Pacific is most likely a consequence of a short turnover time of the air mass, leading to continuously changing and dynamic community composition in the AMBL.

Spatial distributions of bacteria across the Pacific and Atlantic environments

To better understand possible nonrandom exchanges between the ocean and the atmosphere, we explored the association between bacterial taxa and geographic locations (Atlantic vs. Pacific), as well as different environments (air vs. water). The differential (CLR-converted) abundance of the marine taxa detected in the pacific AMBL samples was 19.5%, while only 2.6% in the Atlantic AMBL (Fig. 3a). The highest bacterial prevalence in the AMBL samples was observed for Pseudomonas (with 88 and 64% prevalence in air and water, respectively), continuously detected in the two environments. This taxon was significantly classified as associated with the air environment (Taxon 09 in Fig. 3a and Supplementary Data 4, MaAsLin2 Coeff. = 2.570, q < 0.0001). The contribution of bacteria to the formation of water precipitation is of high interest, and studies revealed bacterial proteins e.g., Pseudomonas sp., can promote droplet freezing²⁹ and even detected bacterial activity in clouds¹⁹. Paracoccus, a Proteobacterium detected only in the AMBL, was found in 84% of air samples, with a significant association with the air environment (Taxon 22 in Fig. 3a and Supplementary Data 4, MaAsLin2 Coeff. = 2.457, q < 0.0001). Paracoccus strains have been isolated from different environments including soil³⁰, marine sediments³¹, sewage³², and have been detected in other atmospheric bacterial studies^33,34.

The most observed Firmicutes genus that appeared exclusively in the air samples was Bacillus, found in 81% of air samples, with significant association with the Pacific air environment (Taxon 23 in Fig. 3a and Supplementary Data 4, MaAsLin2 Coeff. = 2.717, and 1.261 for air and the pacific associations, respectively, q < 0.0001 in both cases). This genus is known to contain endospores that can remain dormant for years. Bacillus is a common bacterium found in transported desert dust^14,35, and the deep marine environment³⁶. Some Bacillus species are known for their unique metabolites and antagonistic activity against pathogens³⁷. The rare abundance of marine bacilli in the water may result from the preferential growth environment of the deep sea, coral, and sediments³⁶, and their copiotrophic property (i.e., flourishing in environments with high nutrient availability)³⁸. Notably, additional spore-forming Firmicutes, e.g., Tumebacillus³⁹, were detected in the Atlantic AMBL (Taxon 76 in Fig. 3a and Supplementary Data 5). Endospores can survive harsh and dry conditions and thus might be transported through the air at higher survival rates than others.

The underrepresentation of Firmicutes in the water samples was further explored in a focused phylogenetic analysis targeting only Firmicutes ASVs (Fig. S5a). The few detected water ASVs differed phylogenetically from the atmospheric ASVs. Additionally, in a supportive environmental ontology (ENVO) analysis⁴⁰ on airborne Firmicutes ASVs in the Atlantic and Pacific (Fig. S5b, c and Supplementary Note 7), a higher relative contribution of soil-borne ENVO annotations was observed in both environments.

Since prokaryote concentrations in the atmosphere are orders of magnitude smaller compared to the ocean (~10³–10⁴ m⁻³ in the atmosphere^4,41 vs. ~10¹¹–10¹⁵ m⁻³ in the surface waters^20,41), sedimentation of terrestrial-originated bacteria to the ocean are not expected to induce a significant change in the microbial diversity in the water, unless profound proliferation takes place. Thus, we conjecture that the airborne Firmicutes most probably originate from terrestrial long-range transport, but the extent to which their sedimentation and proliferation occur in the ocean is yet to be determined.

We have detected bacterial genera that are known to include human-associated microbes (i.e., Micrococcus, Actinomyces; Fig. 3a and Supplementary Data 5). Although not detected in the blank filters, we cannot exclude the possibility that those taxa may originate from the human activity onboard Tara. Nevertheless, the prevalence of these genera is low, ranging on average between ~0.1–~2.7% of the ASVs per filter.

The most prevailing Actinobacteria was Actinomarina, a marine bacterium, appearing in all oceanic samples and in the Pacific air samples (Taxon 05, in Fig. 3a and Supplementary Data 5). Its presence suggests that the surface water contributes to the overlying atmosphere, yet to a limited extent. The highest occurring Bacteroidetes genera found in the atmospheric samples were Chryseobacterium and Sediminibacterium (Taxa 82, and 45 in Fig. 3a, found in 43, and 40% of the air samples, respectively; Supplementary Data 4, 5). Sediminibacterium (MaAsLin2 Coeff. = 2.022 and 1.686 for air and the pacific associations, respectively, q < 0.0001 in both cases) was previously found to contribute to the coral microbiome⁴² and detected in air samples over the Great Barrier Reef¹⁷ and the Mediterranean Sea⁴³. In our study, it was detected in 40% of the air samples, and in the water samples of the Pacific Ocean solely, with low relative abundance (<0.01%) and spatial prevalence.

We continuously detected water-borne species, known from the literature, in the air samples, with higher relative abundance in the Pacific AMBL. One such genus is the Cyanobacteria Prochlorococcus (Taxon 01 in Fig. 3a and Supplementary Data 5) considered a key and most abundant autotroph⁴⁴, found mainly in oligotrophic oceans⁴⁵, with 100% prevalence in the ocean compared to 54% in the air, from which 75% were in the Pacific AMBL (Wilcoxon rank test, p = 3.03 × 10⁻⁰⁶).

Terrestrial-associated airborne bacteria

Key species found in our analysis to be significantly dominant in the Atlantic air (e.g., Paracoccus, Methylobacterium, Mesorhizobium, etc.; Fig. 3a), are known as terrestrial-^46,47,48 and specifically, dust-^35,49 associated bacteria. The ENVO annotation (Fig. S6) retrieved from genomic databases corroborates these findings and emphasizes a significantly higher terrestrial-annotated bacteria predicted to be a partial source for the Atlantic AMBL (Wilcoxon rank test, p = 1.49 × 10⁻⁰⁸). Additionally, we detected significantly higher DNA biomass in the Atlantic air samples compared to the Pacific (average of 639.6 ± 468.2 and 128.4 ± 54.4 pg m⁻³, respectively; Two-sample t-test, unequal variance (F = 74.097, p < 0.001), t = 4.7288, p = 0.0002), implying a higher concentration of microbial cells per air volume in this region.

A previous study by Mayol et al.⁴¹ determined that overall, 25% of the airborne bacteria over the ocean originated from the marine environment, and 42% originated from terrestrial sources based on parameterizations of sea spray and deposition flux calculations. Flores et al.^50,51 have found higher concentrations of larger particles related to the deposition of mineral dust in aerosols sampled in the Atlantic compared to the Pacific transect. Together with other studies reporting on massive dust quantities crossing over the Atlantic Ocean^52,53, they support our findings indicating a vast contribution of terrestrial-borne and specifically, dust-associated bacteria into the Atlantic Ocean.

Selectivity in the emission of marine bacteria

While the increased fraction of terrestrial-associated bacteria in the Atlantic AMBL could partially explain the reduction in the relative abundance of the local marine bacteria, marine-associated taxa were absent from a significantly high fraction of the sampled Atlantic AMBL, suggesting other factors may also play a role in the observed difference between the two AMBLs. A clear case of such difference is seen for the Pelagibacterales (SAR-11 clade; (Taxon 03, 06, 08, and others in Fig. 3a and Supplementary Data 5), representing approximately one-third of the oceanic surface water microbial community⁵⁴, and highly abundant in both oceans’ samples. Their prevalence ratio between atmospheric and oceanic samples is significantly lower than Prochlorococcus (Wilcoxon rank test for the Atlantic (p = 0.006), and Pacific (p = 4.847 × 10⁻⁰⁶); Supplementary Data 4). However, while the prevalence is minimal in the Atlantic, the Pacific AMBL shows a 79% prevalence of SAR-11 ASVs in these samples, significantly higher than the Atlantic (Wilcoxon signed-rank test, p = 3.182 × 10⁻⁰⁵; Supplementary Data 4). A reduced aerosolized fraction of SAR-11 compared to the seawater was also observed in the Arctic Sea by Fahlgren et al.⁵⁵. Part of the difference in abundance between the Atlantic and Pacific AMBLs could be related to properties of the sea-surface microlayer, including thickness, concentration, and chemical composition, which was shown to differ according to changes in heat exchanges, microbial composition, oceanic waves, pollution, and dust storms^56,57. However, to fundamentally characterize the causing factors for the reduced detection of marine bacteria in the Atlantic AMBL, further investigation is required.

Possible boundaries between air and water

Environmental associations between air and water (Fig. 3b) were found to be more profound than those between the Atlantic and Pacific environments (Fig. 3c). This strengthens our findings that the type of the environment (air vs. water) is higher in contribution compared to the geographic location (Atlantic vs. Pacific) in influencing the microbial composition. A notable difference in the abundance and prevalence of marine bacteria in the Pacific AMBL compared to the Atlantic AMBL is also seen for different phyla, including Bacteroidetes, Verrucomicrobia, and Planctomycetes (Fig. 3c). Supportive evidence derived from ENVO analysis of the Atlantic and Pacific AMBLs similarly indicates a higher fraction of marine-annotated bacteria in the Pacific (Fig. S6a, b; 47 ± 20% compared to 12 ± 5% in the Atlantic), while the Atlantic aerobiome was dominantly predicted to be from a terrestrial origin (Fig. S6c, d; 59 ± 16% compared to 35 ± 18% in the Pacific).

It seems that boundaries might be drawn between the atmosphere and hydrosphere, allowing a nonrandom distribution of species between them. One case is the underrepresentation of marine bacteria in the Atlantic air, and others are airborne taxa (e.g., Firmicutes species) not detected in the water samples. Zhou & Ning (2017)¹⁰ have reviewed stochastic vs. deterministic mechanisms controlling microbial ecology and environmental processes that impact the balance between the two mechanisms. However, the effect of environmental interphases, such as the sea-surface microlayer on microbial biogeography and their impact on selective transmission from the ocean to the atmosphere, is still underexplored. We, therefore, propose that the chemical and physical properties of the sea-surface microlayers may determine in part the extent of selective transport of different bacteria from the ocean to the atmosphere.

Source: Ecology - nature.com