Distinct communities of Cercozoa at different soil depths in a temperate agricultural field

Abstract

Protists are the most important predators of soil microbes like bacteria and fungi and are highly diverse in terrestrial ecosystems. However, the structure of protistan communities throughout the soil profile is still poorly explored. Here, we used Illumina sequencing to track differences in the relative abundance and diversity of Cercozoa, a major group of protists, at two depths; 10-30 cm (topsoil) and 60-75 cm (subsoil) in an agricultural field in Germany. At the two depths, we also distinguished among three soil compartments: rhizosphere, drilosphere (earthworm burrows) and bulk soil. With increasing depth, we found an overall decline in richness, but we were able to detect subsoil specific phylotypes and contrasting relative abundance patterns between top-and subsoil for different clades. We also found that the compartment effect disappeared in the subsoil when compared to the topsoil. More studies

Soil depth and grassland origin cooperatively shape microbial community co‐occurrence and function

“…, Degrune et al. ). We have expanded upon these studies by examining the whole soil microbiome (fungal and bacterial) in two prairie types and have demonstrated the distinct and unique populations found in different soil depths.…”

What Drives the Diversity of the Most Abundant Terrestrial Cercozoan Family (Rhogostomidae, Cercozoa, Rhizaria)?

“…The sequences of all strains obtained in this study (Table 1) were manually checked for sequencing errors using Chromas (V2.6.5) and assembled in SeaView (V4.6, [31]). Additionally, we added subsets of large-scale environmental survey data marking the hypervariable region V4 of the SSU rDNA (18S rDNA) of Cryomonadida from following published datasets: Degrune et al [9], Fiore-Donno et al [5,6], Heger et al [25] and Jauss et al [24]. Accordingly, an alignment with 752 sequences, containing 501 NCBI database sequences and an additional 251 OTUs from the previously mentioned datasets were used for phylogenetic analysis.…”

“…Environmental sequencing surveys challenge traditional beliefs of protist biodiversity and its environmental drivers. Amplicon-based metagenomics (also called metabarcoding) with different underlying bioinformatic pipelines and various primer sets all report consistent findings: (i) Cercozoa (Rhizaria) are one of the most abundant groups of protists in soils [1][2][3] and (ii) among the cercozoan sequence reads, operational taxonomic units (OTUs) assigned to the Rhogostomidae (Thecofilosea) appear to dominate cercozoan communities in a wide variety of terrestrial and some aquatic habitats [4][5][6][7][8][9][10]. However, aside from such molecular surveys, the Rhogostomidae are hardly mentioned in scientific literature and only a handful of species have been described until today [11][12][13].…”

“…(ii) We measured morphological traits in these strains, which were subjected to ordination techniques to identify the best suited morphological characters for species delimitation of Rhogostomidae. (iii) We extracted all sequences that could be assigned to the Rhogostomidae from the NCBI database and five publicly available environmental sequencing datasets [5,6,9,24,25] to explore genetic diversity on a large scale. (iv) Finally, we delimit edaphic factors that shape the community composition of Rhogostomidae, based on three of the previously mentioned datasets that come with extensive environmental data [6,24,25].…”

“…The bootstrap values are visualized in a colour flow from black (low support) to purple (high support); end nodes are also given in black. Environmental sequences of the in-depth analysed datasets[5,6,9,24,25] are indicated in purple font, NCBI database environmental sequences and sequences derived from isolated strains are indicated in black. Isolation habitats are highlighted and visualized in the outer colour stripe.…”