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Algivorous Cercozoa shape the community composition of cryptogamic covers, the dominant vegetation in Polar Regions

Soil algae are the most important primary producers where vascular plants are absent, as in the Arctic and Antarctica. They give rise to species-rich microbial food webs in biological soil crusts (biocrusts). The terrestrial snow- and ice-free areas are in permanent expansion as glaciers retreat, leaving behind extensive areas of uncovered rock and new soil. Biocrusts stabilize the soil surface and have an important role in soil development. However, the microbial food webs and the nutrient and energy flow to higher trophic levels remain largely unexplored. Here, we characterized the microbial predator-prey dynamics of polar soils by combining molecular and traditional culturing techniques. Using high-throughput sequencing of environmental samples, we assessed the biodiversity and function of soil protists, applying a trait-based approach for acquiring and describing functional traits, i.e., the feeding behavior of heterotrophic protists in relation to microalgae. The study encompasses the analysis of biocrust samples of three polar regions. In the Arctic, one region was sampled - Svalbard in the Arctic Ocean (78°N) in July 2021. In Antarctica, two regions were studied, i.e. King George Island (62°S) in the South Shetland archipelago of Maritime Antarctica and the Thala Hills oasis in Enderby Land, East Antarctica (67°S), between January and March 2022.

Predator-prey interactions between the heterotrophic protist Polykrikos kofoidii and prey mixtures of three Alexandrium strains (A. catenella, A. limii, A. pseudogonyaulax)

The ingestion rates of the heterotrophic protist Polykrikos kofoidii feeding on three different species of Alexandrium were determined by means of incubation experiments in well-plates. In this experiment P. kofoidii was subjected to prey mixtures consisting of A. pseudogonyaulax (strain L4-B9) and A. catenella (strain Alex 5) or A. limii (strain Atay99Shio-02), whereby one prey was dyed with the fluorescent dye CMAC. The dye had no influence on the feeding behaviour of P. kofoidii and thus dye combinations of the same prey mixtures were combined. This dataset contains all data collected within this experiment including cell counts and ingested prey cells of P. kofoidii. The experiments were carried out on January 18, 2023 in the laboratories at the Alfred-Wegener-Institute in Bremerhaven, Germany.

Predator-prey interactions between the heterotrophic protist Polykrikos kofoidii and strains of three dinoflagellate species of Alexandrium (A. catenella, A. limii, A. pseudogonyaulax)

The ingestion rates of the heterotrophic protist Polykrikos kofoidii feeding on different species of Alexandrium were determined by means of incubation experiments in well-plates. In the first experiment P. kofoidii was subjected to monoalgal prey consisting of either lytic goniodomin producing A. pseudogonyaulax (Limfjord, Denmark, strain L4-B9) or a non-lytic paralytic shellfish toxin producing Alexandrium catenella (Scottish east coast North Sea, strain Alex 5). In the second experiment P. kofoidii was subjected to prey mixtures consisting of A. pseudogonyaulax (strain L4-B9) and A. catenella (strain Alex 5) or goniodomin producing non-lytic A. limii (Shioya Bay, Japan, strain Atay99Shio-02), whereby one prey was dyed with the fluorescent dye CMAC. The experiments were carried out between December 2 and 5, 2022 and on January 18, 2023 in the laboratories at the Alfred-Wegener-Institute in Bremerhaven, Germany.

Eukaryotic microbial community at the LTER site Helgoland Roads from March 2016 to March 2019

Water samples were collected from the long-term ecological research (LTER) site at Helgoland and the eukaryotic microbial community was assessed. 18S V4 region was amplified using the primer set 528iF /964iR and amplicon sequencing was performed on an Illumina MiSeq™ sequencer in a 2 × 300 bp paired-end run. Sequence data have been deposited in the European Nucleotide Archive (ENA) at the European Bioinformatics Institute (EMBL-EBI) under accession number PRJEB37135 using the data brokerage service of the German Federation for Biological Data (GFBio). 21 million sequences remained after bioinformatic processing and were clustered into Operational Taxonomic Units (OTUs). The Protist Ribosomal Reference database (PR2), version 4.11.1 was used as reference database.

Amplicon sequence variant table of benthic heterotrophic protists of the southern Baltic Sea sampled in 2020-2022

We aimed to explore the community compostion of benthic heterotrophic protists in three different regions of the southern Baltic Sea - Fehmarnbelt, Oderbank and Roennebank. Sediment samples where collected with a multicorer system and sliced into layered depth profile during three cruises in 2020, 2021 and 2022 with research vessels Elisabeth Mann Borgese (2020, EMB238 and 2021, EMB267) and Alkor (2022, AL570). We performed a paired-end NovaSeq sequencing (2 × 150 bp) run of the amplified V9 region of the 18S rDNA. For subsequent quality measures during data analysis, we created an in vitro community, called a "mock community", comprising DNA of nine different protist cultures, adding this mixture to each individual sequencing run. After sequencing, the raw reads were demultiplexed and the barcode and primer sequences were clipped using cutadapt (Martin 2011). The data was further processed using the the dada2 package in R (Callahan et al. 2016). For taxonomic assignment we used the PR2 database (Protist Ribosomal Reference database, Guillou et al. 2012, https://pr2-database.org/ ) updated with 150 sequences obtained from our own collection using usearch_global (v2.18.0, Rognes et al. 2016). We discarded all Metazoa, fungi, autotrophic protists (determined on the basis of taxonomic assignment) and retained only heterotrophic protists' amplicon sequence variants (ASVs) with a pairwise identity of >80% to a reference sequence. For the main dataset of samples, we then chose individual minimum thresholds per sample according to the accompanying mock community on the respective sequencing lane. For calculation of these thresholds, we used the proportion of the lowest read number of an ASV in the mock community data set that could be assigned to the cultured species.

Environmental data related to amplicon sequencing of benthic heterotrophic protists of the southern Baltic Sea, in 2020-2022

We aimed to explore the community compostion of benthic heterotrophic protists in three different regions of the southern Baltic Sea - Fehmarnbelt, Oderbank and Roennebank. Sediment samples where collected with a multicorer system and sliced into layered depth profile during three cruises in 2020, 2021 and 2022 with research vessels Elisabeth Mann Borgese (2020, EMB238 and 2021, EMB267) and Alkor (2022, AL570). We performed a paired-end NovaSeq sequencing (2 × 150 bp) run of the amplified V9 region of the 18S rDNA. This dataset includes the environmental data related to the sequencing study including sample IDs, region, sediment depth, station data, salinity and median grain size.

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