From Forest Soil to the Canopy: Increased Habitat Diversity Does Not Increase Species Richness of Cercozoa and Oomycota in Tree Canopies

Abstract

Tree canopies provide habitats for diverse and until now, still poorly characterized communities of microbial eukaryotes. One of the most general patterns in community ecology is the increase in species richness with increasing habitat diversity. Thus, environmental heterogeneity of tree canopies should be an important factor governing community structure and diversity in this subsystem of forest ecosystems. Nevertheless, it is unknown if similar patterns are reflected at the microbial scale within unicellular eukaryotes (protists). In this study, high-throughput sequencing of two prominent protistan taxa, Cercozoa (Rhizaria) and Oomycota (Stramenopiles), was performed. Group specific primers were used to comprehensively analyze their diversity in various microhabitats of a floodplain forest from the forest floor to the canopy region. Beta diversity indicated highly dissimilar protistan communities in the investigated microhabitats. However, the majority of operational taxonomic units (OTUs) was present in all samples, and therefore differences in beta diversity were mainly related to species performance (i.e., relative abundance). Accordingly, habitat diversity strongly favored distinct protistan taxa in terms of abundance, but due to their almost ubiquitous distribution the effect of species richness on community composition was negligible.

On the phenology of protists: Recurrent patterns reveal seasonal variation of protistan (Rhizaria: Cercozoa, Endomyxa) communities in tree canopies

“…Illumina sequencing were performed as described in Jauss et al (2020a), the used primer and barcode combinations are provided in Supplementary Table S1 and S2.…”

A parasite’s paradise: Biotrophic species prevail oomycete community composition in tree canopies

“…autumn (October) 2017 and 2018 and spring (May) 2018 and 2019 in cooperation with the Leipzig Canopy Crane (LCC) Facility in a floodplain forest in Leipzig,Germany (51.3657 N,12.3094 E). Samples were obtained and processed as described in Jauss et al (2020b). Briefly, seven microbial microhabitat compartments related to tree surface were sampled in the canopy at 20-30m height: Fresh leaves, dead wood, bark, arboreal soil and three cryptogam epiphytes (lichen and two moss genera, Hypnum and Orthotrichum).…”

“…DNA extraction was performed with the DNeasy PowerSoil kit (QIAGEN, Hilden, Germany) according to the manufacturer's instruction. This procedure was performed on four sampling dates: October 2017 (Jauss et al, 2020b), May 2018, October 2018 and May 2019 (this study). Oomycete-specific PCRs and sequencing were performed as described in Jauss et al (2020b) with tagged primers designed by Fiore-Donno & Bonkowski (2021); the used primer tag combinations are provided in Supplementary Table 1. 2.2 Sequence processing Sequence processing and bioinformatics analyses followed the pipeline described in Jauss et al (2020b).…”

“…This procedure was performed on four sampling dates: October 2017 (Jauss et al, 2020b), May 2018, October 2018 and May 2019 (this study). Oomycete-specific PCRs and sequencing were performed as described in Jauss et al (2020b) with tagged primers designed by Fiore-Donno & Bonkowski (2021); the used primer tag combinations are provided in Supplementary Table 1. 2.2 Sequence processing Sequence processing and bioinformatics analyses followed the pipeline described in Jauss et al (2020b). Briefly, raw reads were merged using VSEARCH v2.10.3 (Rognes et al, 2016) and demultiplexed with cutadapt v1.18 (M. Martin, 2011).…”

“…The infamous oomycete Phytophthora infestans causes one of the most destructive plant diseases, the potato late blight, and initiated the great Irish famine in the late 1840's with a million deaths and massive emigration (Mizubuti & Fry, 2006). The ecological and economic impact of oomycetes has led to an increased research interest on their community structures (Robideau et al, 2011;Riit et al, 2016;Singer et al, 2016;Jauss et al, 2020bJauss et al, , 2020a, and, correspondingly, their pathogenicity and infection strategies (Rizzo & Garbelotto, 2003;Rizzo et al, 2005;Thines & Kamoun, 2010).…”