Distribution Patterns of Benthic Protist Communities Depending on Depth Revealed by Environmental Sequencing—From the Sublittoral to the Deep Sea

Abstract

Protists are key components of the microbial food web in marine pelagic systems because they link algal and bacterial production to higher trophic levels. However, their functioning and bathymetric distribution in benthic deep-sea ecosystems are still only poorly understood. However, biogeographical patterns of communities can be coupled to the functioning of ecosystems and are therefore important to understand ecological and evolutionary processes. In this study, we investigated the diversity and distribution of benthic protist communities from the sublittoral down to the deep seafloor (50–2000 m) around three islands of the Azores in the North Atlantic Ocean. Using amplicon sequencing of the V9 region (18S rDNA) of 21 samples, we found that protist community compositions from different depths were significantly different. Three assemblages were separated along the following depths: 50 m, 150–500 m and 1000–2000 m, which indicate that deep-sea areas surrounding islands might act as isolating barriers for benthic protist species. A limited gene flow between the communities could favor speciation processes, leading to the unique protist communities found at the different investigated islands.

Protist communities of microbial mats from the extreme environments of five saline Andean lagoons at high altitudes in the Atacama Desert

“…The correct identification of the eight strains in the mock communities additionally supported the classification method for the study of our environmental samples. With these results, we confirm the use of mock community-deduced thresholds as the backbone of studies on protist communities in different environments through metabarcoding (e.g., Fiore-Donno et al, 2019 ; Dünn and Arndt, 2023 ; Sachs et al, 2023 ).…”

The dilemma of underestimating freshwater biodiversity: morphological and molecular approaches

“…ASVs in the sample dataset with read counts lower than this calculated proportion (0.057%) were excluded. Similar thresholds were calculated in previous studies using the same mock community [ 56 , 57 ]. Bridge amplification and paired-end (2 × 150 bp) sequencing of the amplified fragments were performed using a NovaSeq 6000 system at the Cologne Center of Genomics (CCG) in Germany.…”

“…Amplicons were then pooled and purified using the FastGene Gel/PCR Purification Kit (Nippon Genetics Europe, Düren, Germany). For subsequent quality measures during data analysis for protists, we used an in vitro community (“mock community”) comprising DNA of nine different protist cultures belonging to representatives of the main protist supergroups [ 56 ]. We used this mock community to correct for the occurrence of non-reliable sequences.…”

“…Moreover, we removed Metazoa, Archaeplastida and Fungi for the protist dataset. As described by Dünn and Arndt [ 56 ], as a last filtering step, we used a minimum threshold of the previously described mock community by calculating the proportion of the lowest read number of an ASV in the mock community data set that could be assigned to the cultured species with a pairwise identity of 100%. ASVs in the sample data sets with a smaller read number than this calculated proportion were discarded.…”

The dilemma of underestimating freshwater biodiversity: morphological and molecular approaches

“…Amplicons were then pooled and purified using the FastGene Gel/PCR Purification Kit (Nippon Genetics Europe, Düren, Germany). For subsequent quality measures during data analysis for protists, we used an in vitro community ("mock community") comprising DNA of nine different protist cultures belonging to representatives of the main protist supergroups [57]. We used this mock community to correct for the occurrence of non-reliable sequences.…”