This collection pertains to the data collected for the purpose of PhD research, under Research Project UNE1601. Data is organised in line with thesis entitled "Subsoil microbial processes under Australian rotational cotton systems" - for example, data relating to Chapter 2, is organised in folders under this heading and with file names indicating thesis sections. Data includes both raw and analysed sets, most of which are in excel spreadsheets. Metagenomic data has a range of file types, however the raw data can be accessed through CSV or excel file types. Data were collected at the Australian Cotton Research Institute, New South Wales, Australia.