Amicon ultra 0.5 3k centrifugal filters

In order to enrich the phage sample, a frozen sample of the Aquamicrobium phage P14 was thawed and incubated for 48 h (30 °C, constant shaking) with the bacteria Aquamicrobium H14 in LB broth. Then, 1.5 mL of the medium were filtered through a 0.22 µm syringe filter (Durapore^® PVDF membrane, Merck Millipore). The biomass was further concentrated using Amicon^® Ultra-0.5 3K Centrifugal Filters (Merck KGaA, Darmstadt, Germany) yielding 150 µL of concentrate.
The DNA from the concentrate was extracted using the UltraClean Microbial DNA Isolation Kit (MO BIO, Carlsbad, CA, USA) according to manufacturer’s instructions with two modifications: the first step where bacterial cells are pelleted and concentrated was skipped and the elution step was done using only 25 µL of the elution buffer. The DNA concentrations were determined by a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and the purified DNA was sequenced using Illumina MiSeq (San Diego, CA, USA), with 250-bp paired-end reads.

Samples (1.5 mL) from the test tubes were filtered through a 0.22 μm syringe filter (Durapore^® PVDF membrane, Merck Millipore, Billerica, MA, USA) and then concentrated 10-fold using Amicon^® Ultra-0.5 3K Centrifugal Filters (Merck KGaA, Darmstadt, Germany). The DNA was extracted from the concentrated 0.15 mL samples using the UltraClean Microbial DNA Isolation Kit by MO BIO (Carlsbad, CA, USA) following the manufacturer’s protocol with two modifications: the first step of the DNA extraction, which concentrates bacterial cells by centrifugation, was omitted, and only 25 µL of elution solution was used. The purified DNA was sequenced on a MiSeq Illumina machine (San Diego, CA, USA) with 150 bp paired-end reads. The raw sequences used in this research are available in the NCBI’s Sequence Read Archive (SRA) under accessions SRX827032 and SRX7412192.