The global community of microbial ecologists was invited to submit samples for microbiome analysis, and samples were accepted for DNA extraction and sequencing provided that scientific justification and high-quality sample metadata were provided before sample submission. Standardized sampling procedures for each sample type were used by contributing investigators. Samples were collected fresh and, where possible, immediately frozen in liquid nitrogen and stored at –80 °C. Detailed sampling protocols are described in publications of the individual studies (Supplementary Table 1). Bulk samples (for example, soil, sediment, faeces) and fractionated bulk samples (for example, sponge coral surface tissue, centrifuged turbid water) were taken using microcentrifuge tubes. Swabs (BD SWUBE dual cotton swabs or similar) were used for biofilm or surface samples. Filters (Sterivex cartridges, 0.2 μm, Millipore) were used for water samples. Samples were sent to laboratories in the United States for DNA extraction and sequencing: water samples to Argonne National Laboratory, soil samples to Lawrence Berkeley National Laboratory (pre-2014) or Pacific Northwest National Laboratory (2014 onward), and faecal and other samples to the University of Colorado Boulder (pre-2015) or the University of California San Diego (2015 onward).
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