A regional scale soil microbial biodiversity study across the Windmill Islands, eastern Antarctica in 2019 - DNA sequencing, A16S, 18S, 16S, ITS

In the 2019 austral summer, up to 93 surface and subsurface soil samples was collected from three remote locations (Browning Peninsula, Mitchell Peninsula, Robinson Ridge) in the Windmill Islands, Eastern Antarctica. Archaeal 16S rRNA gene, Bacterial 16S rRNA gene, Micro-eukaryotes 18S rRNA gene, and Fungal ITS1- 4 diversity data were obtained using Illumina sequencing combined with comprehensive soil physiochemical data.A previously used geospatial sampling design was re-applied at these locations to allow for a comparison to soil biodiversity data obtained for the original polar soil archive which was first sampled in 2005 (Siciliano et al 2014). In this case, up to 93 soils were collected from all three locations and soils were collected at two soil depths: surface or biocrust = 0-3 cm and subsoil = 3-10 cm. At each location, soils were sampled from three parallel 300-m-transects, 2 m apart, with samples taken at variable lag distances of 0, 0.1, 0.2, 0.5, 1, 2, 5, 10, 20, 50, 100, 100.1, 100.2, 100.5, 101, 102, 105, 110, 120, 150, 200, 200.1, 200.2, 200.5, 201, 202, 205, 210, 220, 250 and 300 m. The transects were divided into three groups based on their distances along the transect (Start: 0-50m; Mid: 100-150m; End: 200 – 300m). In this record, a subsample of 18 subsoil and surface soil samples (at 6 x distance points 0, 2, 100, 102, 200, 202m of all three transects) were selected for analysis at all three locations. The goal was to understand what abiotic or biotic drivers were correlated to the natural environmental gradient across the three different landscapes and thus determine what factors were shaping the local microbial community structure. All soils (0.25 g) were extracted in triplicates using the FastDNA SPIN kit, gDNA was subjected to Illumina sequencing (16S, A16S, 18S, ITS) and a suite of physicochemical data (AAS_4406_Windmill_Islands_2019) was obtained for all 18 subsoils for all three sites that were analysed. This biodiversity study was designed to be able to be used as part of a long-term monitoring capability across the region. With the 16S, A16S, and 18S dataset derived from 2005 soils (ITS not available), we aim to use this 2019 dataset to determine shifts in microbial communities and associated environmental parameters after 14 years of change at these locations. We also aim to examine the differences in microbial biodiversity in the above-surface-biocrust soil and below-ground (subsoil) microbial communities. Details on Illumina sequencing can be found here: https://www.ramaciotti.unsw.edu.au/services/next-generation-sequencing/microbiome-custom-target. The four primer sets used to target specific hypervariable gene regions to cover the soil microbiome in this study were the:27F/519R - Bacterial 16S V1-V31391F/EukBr - Eukaryotic 18S V9A2F/519R - Archaeal A16SITS1F-ITS2/fITS7-ITS4 - Fungal ITS1- ITS4Except for A16S data, all primer sequences were not retained in the raw DNA files.