Polycarbonate filter membrane

The water samples (1000 mL) were sequentially filtered through 0.45 and 0.22 µm GE® polycarbonate filter membrane. The membranes from 0.22 µm were cut into small pieces in sterilized condition and DNA extraction was performed using an optimized CTAB method (Zhou et al. 1996 (link)). The DNA extractions were performed in triplicates and replicates were later pooled prior to metagenome sequencing. DNA quality and quantity was examined with a Thermo Scientific NanoDrop 3300 Fluorospectrometer (Thermofisher Scientific, USA). The extracted DNA was randomly sheared into short fragments and ligated with Illumina adapters to construct a library. The libraries were pooled, barcoded and subsequently shotgun sequenced on one lane of a flow cell using a 150 bp paired-end run on a NovaSeq PE150 instrument (Illumina) at Novo-gene (Hong Kong). The sequences were de-multiplexed using Cassava v.2.0 and FastQC was used for quality control checks on the sequence composition of paired-end raw reads. Trimmomatic v0.36 (Q-value ≤ 38; N >10 bp; reads overlap with adapter >15 bp) was employed to remove low quality bases and any adapter contamination.

Water and sediment samples were collected from three soda lakes in the East African Rift Valley: Lakes Abijata (7°37′0″N, 38°36′0″E), Chitu (7°24′14″N, 38°25′15″E), and Shala (7°25′29″N, 38°36′57″E), using sterile Niskin bottles (Ocean Scientific International Ltd., Hampshire, United Kingdom) and polyethylene bags, respectively. The water samples were filtered within 24 h of sample collection, using a polycarbonate filter membrane (0.22 μm pore size, 47 mm diameter; GE, IL, United States) to harvest the biomass for metagenomic DNA extraction.