Remarkably Complex Microbial Community Composition in Bromeliad Tank Waters Revealed by eDNA Metabarcoding

Abstract

To investigate patterns of biotic community composition at different spatial scales and biological contexts, we used environmental DNA metabarcoding to characterize eukaryotic and prokaryotic assemblages present in the phytotelmata of three bromeliad species (Aechmea gamosepala, Vriesea friburgensis, and Vriesea platynema) at a single Atlantic Forest site in southern Brazil. We sampled multiple individuals per species and multiple tanks from each individual, totalizing 30 samples. We observed very high levels of diversity in these communities, and remarkable variation across individuals and even among tanks from the same individual. The alpha diversity was higher for prokaryotes than eukaryotes, especially for A. gamosepala and V. platynema samples. Some biotic components appeared to be species‐specific, while most of the biota was shared among species, but varied substantially in frequency among samples. Interestingly, V. friburgensis communities (which were sampled at nearby locations) tended to be more heterogeneous across samples, for both eukaryotes and prokaryotes. The opposite was true for V. platynema, whose samples were more broadly spaced but whose communities were more similar to each other. Our results indicate that additional attention should be devoted to within‐individual heterogeneity when assessing bromeliad phytotelmata biodiversity, and highlight the complexity of the biotic assemblages gathered in these unique habitats.

Illuminating protist diversity in pitcher plants and bromeliad tanks

“…This could be due to the species level morphological differences of tank forming bromeliads as differences in the shape of the tank likely contribute to dispersal patterns and water flow, perhaps leading to the observed variation in SAR communities. Previous work investigating eukaryotic and bacterial communities from wild bromeliads has demonstrated that extensive variation exists within and between bromeliad species [ 19 , 30 , 32 ], supporting our findings of variation in SAR communities within bromeliads found within 3 feet of one another in the Lyman Conservatory.…”

“…Bittleston et al [ 5 ] used an amplicon approach with “universal” eukaryotic primers to demonstrate that communities in two highly diverged pitcher plant genera were strikingly similar, and that pitcher plant communities represent a distinct subset of the community found in the background habitat. Simão et al [ 4 , 32 ] used a different primer set and found that ciliates were the most abundant protists in bromeliad phytotelmata. These approaches are advantageous in that a large portion of eukaryotic diversity may be captured, but problematic as members of certain eukaryotic lineages (e.g.…”

Diversity and putative metabolic function of prokaryotic communities in tank bromeliads along an elevation gradient in tropical Mexico

“…This study revealed rich prokaryotic communities in tank bromeliads along an elevation gradient in tropical Mexico, confirming these plants as extremely diverse micro-habitats for bacteria and archaea in the Neotropics (Goffredi et al, 2015;Louca et al, 2017b;Rodriguez-Nuñez et al, 2018;Giongo et al, 2019;Simão et al, 2020). Consistent with previous studies based on amplicon sequencing of 16S rRNA genes (Goffredi et al, 2011;Louca et al, 2017b;Rodriguez-Nuñez et al, 2018;Simão et al, 2020), Proteobacteria, Verrucomicrobia, Planctomycetes, Acidobacteria and Bacteroidetes were among the top 10 most abundant prokaryotic groups in these plants, comprising 85% of the ASVs in our samples. Interestingly, a similar composition was found in soils, where ca.…”

“…For example, an analysis of 16S rRNA and 18S rRNA genes showed that communities of bacteria and fungi differed between terrestrial soil and litter accumulated in the leaf axils of epiphytic tank bromeliads, with lower bacterial cell numbers in the terrestrial habitat (Pittl et al, 2010). Other studies based on amplicon sequencing of 16S rRNA genes revealed a high diversity of bacteria inhabiting these plants, with Proteobacteria, Acidobacteria, Bacteroidetes, Verrucomicrobia, and Firmicutes as dominant groups (Louca et al, 2017a;Giongo et al, 2019;Simão et al, 2020). Furthermore, it has been shown that an acidic environment in bromeliad tanks favored the abundance of Acidobacteria and Alphaproteobacteria (similar to those found in acidic, waterlogged and peat bog habitats), while Betaproteobacteria and Firmicutes dominated in bromeliads with higher tank pH (Goffredi et al, 2011).…”

“…However, associated microbes used to be virtually unknown, but with the advent of next-generation sequencing technology in the last two decades, diverse microbial communities have been described. These communities are distinct from the surrounding environment and present a remarkable variation among and within bromeliad species ( Goffredi et al, 2011 ; Carmo et al, 2014 ; Louca et al, 2017b ; Simão et al, 2020 ). For example, an analysis of 16S rRNA and 18S rRNA genes showed that communities of bacteria and fungi differed between terrestrial soil and litter accumulated in the leaf axils of epiphytic tank bromeliads, with lower bacterial cell numbers in the terrestrial habitat ( Pittl et al, 2010 ).…”