Borehole waters were first flushed with three to five section volumes of water. Planktonic cells >0.22 μm and >0.1 μm were collected on membrane filters and DNA extracted using the MO BIO PowerWater DNA isolation kit as described in Supplementary Files 1 and 2. The cells passing the 0.22 μm filter (that is, the <0.22 μm fraction) were prepared by the iron chloride precipitation method followed by filtration through a 0.8 μm filter based on John et al. (2011) (link). The cells were concentrated with an Amicon Ultra-15 centrifugal device and DNA extracted with the Wizard PCR Preps DNA purification System (Promega, Fitchburg, WI, USA) (Supplementary Files 1 and 2). The 16S rRNA gene tag sequencing was carried out on an Illumina MiSeq(Illumina, San Diego, CA, USA), whereas community DNA was sequenced on an Illumina MiSeq and HiSeq from the >0.22 μm and <0.22 μm borehole fractions, respectively.