Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

Abstract

High animal and plant richness in tropical rainforest communities has long intrigued naturalists. It is unknown if similar hyperdiversity patterns are reflected at the microbial scale with unicellular eukaryotes (protists). Here we show, using environmental metabarcoding of soil samples and a phylogeny-aware cleaning step, that protist communities in Neotropical rainforests are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, too few operational taxonomic units (OTUs) of Oomycota were found to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model. Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that protists play a large role in tropical terrestrial ecosystems long viewed as being dominated by macroorganisms.S ince the works of early naturalists such as von Humboldt and Bonpland 1 , we have known that animal and plant communities in tropical rainforests are exceedingly species rich. For example, one hectare can contain more than 400 tree species 2 and one tree can harbour more than 40 ant species 3 . This hyperdiversity of trees has been partially explained by the Janzen-Connell model 4,5 , which hypothesizes that host-specific predators and parasites reduce plant population growth in a density-dependent manner 6,7 . Sampling up in the tree canopies and below on the ground has further led to the view that arthropods are the most diverse eukaryotes in tropical rainforests 8,9 .The focus on eukaryotic macroorganisms in these studies is primarily because they are familiar and readily observable to us. We do not know whether the less familiar and less readily observable protists-microbial eukaryotes that are not animals, plants or fungi 10 -inhabiting these same ecosystems exhibit similar diversity patterns. To evaluate if macroorganismic diversity patterns are reflected at the microbial scale with protists, we conducted an environmental DNA metabarcoding study by sampling soils in 279 locations in a variety of lowland Neotropical forest types in La Selva Biological Station, Costa Rica, Barro Colorado Island, Panama and Tiputini Biodiversity Station, Ecuador. This metabarcoding approach has the power to uncover known and new taxa on a massive scale 11 . By amplifying DNA extracted from the soils with broadly targeted primers for the V4 region of 18S rRNA and sequencing it using the Illumina MiSeq platform, we were able to detect most eukaryotic lineages, and assess the diversity and relative dominance of free-living and parasitic lineages.

Consistent patterns of high alpha and low beta diversity in tropical parasitic and free‐living protists

“…Details of sampling and sequencing can be found in Mahé et al. (). In brief, soil samples were collected from La Selva Biological Station (Costa Rica) and Barro Colorado Island (Panama) in October 2012 and June 2013, and from Tiputini Biodiversity Station (Ecuador) in October 2013 (Supporting information Figure ).…”

“…Details of bioinformatic processing can be found in Mahé et al. (). In brief, reads were pair‐ended with pear v0.9.8 (Zhang, Kobert, Flouri, & Stamatakis, ) and filtered with filtered with cutadapt v1.9 (Martin, ).…”

“…Mahé et al. () recently looked at the biodiversity of soil‐inhabiting protists in lowland rainforests in Costa Rica, Panama and Ecuador using general primers amplifying the V4 hypervariable region of the 18S rRNA. They found that similar to macro‐organisms, the microbial eukaryotes were exceedingly species rich and that there was low similarity in community composition between samples.…”

“…Here, we evaluated the taxa–area and distance–decay relationships of the three most abundant protist taxa in Mahé et al. () data: the Apicomplexa, which are parasites of animals that disperse by vectors or cysts; and the Cercozoa and Ciliophora, which are largely free‐living bacterivores that disperse by active movements or cysts (Bass & Cavalier‐Smith, ; Grattepanche et al., ; Lynn, ; Votýpka, Modrý, Oborník, Šlapeta, & Lukeš, ). These taxa together represented 85.9% of the protist reads and 74.2% of the protist OTUs amplified with the V4 primers, and they allowed for robust statistical comparisons at both the OTU and phylogenetic diversity levels.…”

Effects of intragenomic polymorphism in the SSU rRNA gene on estimating marine microeukaryotic diversity: A test for ciliates using single‐cell high‐throughput DNA sequencing

“…The advent of high‐throughput DNA sequencing has revolutionized the study on the diversity of microbial eukaryotes. The application of deep‐sequencing techniques in combination with genetic barcode markers, such as the widely preferred hypervariable V4 and V9 fragments of the 18S rRNA gene, revealed extensive diversity of microeukaryotes in various marine environments (de Vargas et al ; Kammerlander et al ; Massana et al ; Forster et al ; Filker et al ; Mahé et al ). The extremely high diversity of the 18S rRNA gene largely exceeded species diversity detected by morphological methods.…”