Contrasting responses of protistan plant parasites and phagotrophs to ecosystems, land management and soil properties

Abstract

Highlights  Protistan plant parasites of worldwide importance (Phytomyxea) are absent from forest  Protistan plant parasites are enhanced by land use intensification in grassland  Opposite responses of protistan trophic guilds to environmental conditions in forest  Drastic differences in protistan community composition between grassland and forest Abstract Functional traits are increasingly used in ecology to link the structure of microbial communities to ecosystem processes. We investigated two important protistan lineages, Cercozoa and Endomyxa (Rhizaria) in soil using Illumina sequencing and analysed their diversity and functional traits along with their responses to environmental factors in grassland and forest across Germany. From 600 soil samples, we obtained 2,101 Operational Taxonomy Units representing ~18 million Illumina reads (region V4, 18S rRNA gene). All major taxonomic and functional groups were present, dominated by small bacterivorous flagellates (Glissomonadida). Endomyxan plant parasites were absent from forest. In grassland, they were promoted by more intensive land use management. Grassland and forest strikingly differed in community composition. Relative abundances of bacterivores and eukaryvores were contrastingly influenced by environmental factors, indicating bottom-up regulation by food resources. These patterns provide new insights into the functional organization of soil biota and indications for a more sustainable land-use management.

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

“…This study aimed to identify seasonal changes in the community composition of Cercozoa and Endomyxa in tree canopies, over two consecutive years. A total number of 783 OTUs were detected in the temperate floodplain forest, which is 43% of the cercozoan OTU richness that Fiore-Donno, Richter-Heitmann and Bonkowski ( 2020 ) retrieved with the same method from mineral soil of 150 different forest sites across Germany. The thorough recovery of the diversity, including even rare taxa due to the taxon-specific primers (Fiore-Donno et al .…”

“…2016 ; Fiore-Donno et al . 2018 ; Fiore-Donno, Richter-Heitmann and Bonkowski 2020 ). Especially the small and bacterivorous flagellates in the order Glissomonadida dominated in all canopy microhabitats throughout all four sampling periods (Figs 1 and 5 ; Figure S7, Supporting Information).…”

“…For subsequent PCR amplification, all four replicates of each microhabitat per tree were pooled. Semi-nested PCRs with tagged group-specific primers (Fiore-Donno, Richter-Heitmann and Bonkowski 2020 ) and Illumina sequencing were performed as described in Jauss et al . ( 2020 ), the used primer and barcode combinations are provided in Tables S1 and S2 (Supporting Information).…”

“…Sequence processing followed the pipeline described in Fiore-Donno, Richter-Heitmann and Bonkowski ( 2020 ). Briefly, paired reads were assembled using MOTHUR v.39.5 (Schloss et al .…”

“…Therefore, four samplings were conducted in two consecutive spring and autumn seasons, over a period of 2 years. We applied a MiSeq Illumina sequencing protocol using taxon-specific primers, which target the hypervariable V4 region within the 18S rRNA gene of the protistan phyla Cercozoa and Endomyxa (Rhizaria; Fiore-Donno, Richter-Heitmann and Bonkowski 2020 ). Cercozoa are a highly diverse phylum, with many taxa encompassing a broad variety of functional traits (Dumack et al .…”