TABLE 1. Metadata Field Codes Summary
TABLE 1. Metadata Field Codes – A summary table of protocol codes and associated protocols that are listed in this manual and included in the downloadable metadata for Australian Microbiome data.
| Metadata Field Code | Method Name |
| meth_1.1 | Soil Sampling for Biomes of Australian Soil Environments BASE |
| meth_1.2 | Soil Sampling for UTAS Urban Soil and Aerial Microbiome Study |
| meth_1.3 | Marine Sediment Sampling for Marine Microbes Coastal Project |
| meth_1.4 | Pelagic Water Sampling for Integrated Marine Observing System National Reference Stations |
| meth_1.5 | Coastal Seawater Sampling for Australian Coastal Microbial Observatory Network |
| meth_1.5.1 | Botany Bay, NSW, and Port Phillip Bay, VIC |
| meth_1.5.2 | Great Barrier Reef, QLD |
| meth_1.6 | Pelagic Water Sampling for Ocean Voyages |
| meth_1.7 | Coastal Seawater Sampling for Downstream DNA Analyses for Marine Microbes Coastal Project |
| meth_1.8 | Coastal Seawater Sampling for Downstream DNA Analyses for Marine Microbes Coastal UPDATED SEPT 2019 TT |
| meth_1.9 | Coastal Seawater Sampling for Downstream RNA Analyses for Marine Microbes Coastal Project |
| meth_1.10 | Coastal Seawater Sampling for Downstream DIC and TA Analyses for Marine Microbes Coastal Project |
| meth_1.11 | Seagrass Sampling, Marine Microbes Coastal |
| meth_1.11.1 | Surficial Sediment Sampling |
| meth_1.11.2 | Seagrass Sampling |
| meth_1.12 | Sponge Sampling for Marine Microbes Coastal Project |
| meth_1.13 | Seaweed Ecklonia radiata Sampling for Marine Microbes Coastal Project |
| meth_1.14 | Coral Sampling for Marine Microbes Coastal Project |
| meth_1.15 | Water Sampling from Acidic Saline Lakes |
| meth_1.16 | Water Sampling from Brisbane River Estuary |
| meth_1.17 | Plant Sampling including leaf root and soil |
| meth_1.18 | Coastal Water Sampling and Filtering for DNA Analysis in the Derwent Estuary |
| meth_1.19 | National Geochemical Survey of Australia Field Manual Geoscience Australia |
| meth_1.20 | Northern Australian Geochemical Survey Geoscience Australia |
| meth_1.21 | Regional geology and mineral systems of the Stavely region in western Victoria Geoscience Australia |
| meth_1.22 | Water sampling for Bush Blitz DNP |
| meth_1.23 | Soil Sampling and Processing AM0024 |
| meth_2.1 | CSBP Laboratory Procedures for Soil and Water Biomes of Australian Soil Environments BASE |
| meth_2.2 | Integrated Marine Observing System National Reference Stations Biogeochemical Operations Manual |
| meth_2.2int | IMOS sample metadata produced from integrated water column measurements |
| meth_2.3 | CSIRO RV Southern Surveyor Metadata Procedures SS2010_V09 |
| meth_2.4 | CSIRO RV Southern Surveyor Metadata Procedures SS2012_T06 |
| meth_2.5 | CSIRO RV Southern Surveyor Metadata Procedures SS2012_T07 |
| meth_2.6 | CSIRO RV Southern Surveyor Metadata Procedures SS2012_V04 |
| meth_2.7 | CSIRO RV Southern Surveyor Metadata Procedures SS2013_T03 |
| meth_2.8 | CSIRO RV Investigator Metadata Procedures IN2014_E03 |
| meth_2.9 | CSIRO RV Investigator Metadata Procedures IN2015_C02 |
| meth_2.10 | CSIRO RV Investigator Metadata Procedures IN2015_V03 |
| meth_2.11 | CSIRO RV Investigator Metadata Procedures IN2016_T01 |
| meth_2.12 | CSIRO RV Investigator Metadata Procedures IN2016_V03 |
| meth_2.13 | CSIRO RV Investigator Metadata Procedures IN2016_V04 |
| meth_2.14 | Sediment Grain Size Fractionation percent fines in marine sediments Marine Microbes Coastal Project |
| meth_2.15 | Sediment Grain Size Fractionation percent fines in marine seagrass sediments Marine Microbes Coastal |
| meth_2.16 | Total Organic Carbon TOC in marine sediment Marine Microbes Coastal Project |
| meth_2.17 | Total Organic Carbon TOC in marine seagrass sediment Marine Microbes Coastal Project |
| meth_2.18 | Porewater nutrients from marine sediment Marine Microbes Coastal Project |
| meth_2.19 | PAM Fluorometry in situ measurements of seagrass Marine Microbes Coastal Project |
| meth_2.20 | Analytical Services Tasmania Laboratory Procedures Derwent Estuary Program, Ambient Water Quality Program |
| meth_2.21 | In situ water measurements using a YSI EXO 3 multiparameter sonde Derwent Estuary Program Ambient Water Quality Program |
| meth_2.22 | CSIRO RV Investigator Laboratory Procedures IN2021_V04 |
| meth_2.23 | CSIRO RV Investigator Laboratory Procedures IN2019_V03 |
| meth_2.24 | Contextual Metadata for Sediment Sampling in East Coast Australian Estuaries |
| meth_2.25 | AIMS Marine Monitoring Program for Inshore Water Quality QAQC Manual |
| meth_2.26 | Soil visible-near infrared vis-NIR spectra for BASE samples |
| meth_2.27 | In silico analysis of Australian Soil Classification |
| meth_2.28 | Vegetation Assessment AM0024 |
| meth_2.29 | Environment Protection Agency Victoria Water Quality Monitoring Methods AM0001 |
| meth_2.30 | Nutrient Analysis via Flow Injection Analysis (University of Technology, Sydney) |
| meth_2.31 | In situ water measurements using a WTW Multi 3630 IDS Multi-Parameter Portable Meter (University of Technology, Sydney) |
| meth_3.1.1 | Qiagen DNeasy PowerLyzer PowerSoil Kit for BASE at AGRF |
| meth_3.1.2 | Qiagen DNeasy PowerSoil Kit for soil and rhizosphere and sediments |
| meth_3.1.3 | Qiagen DNeasy PowerSoil modified for marine sediments Marine Microbes Coastal Project |
| meth_3.1.4 | Qiagen DNeasy PowerSoil modified for coastal seawater Marine Microbes Coastal Project |
| meth_3.1.5 | Qiagen DNeasy PowerSoil modified for seagrass Marine Microbes Coastal Projects |
| meth_3.1.6 | MoBio PowerPlant Pro DNA Isolation Kit for coral Marine Microbes Coastal Project |
| meth_3.1.7 | Qiagen DNeasy PowerWater Sterivex Kit |
| meth_3.1.8 | Qiagen DNeasy PowerWater Sterivex Kit modified for removal of filter from sterivex |
| meth_3.1.9 | Qiagen DNeasy PowerWater Sterivex Kit modified IMOS NRS ACMON and voyages CSIRO Hobart Genetics Laboratories |
| meth_3.1.10 | MP Biomedicals FastDNA Spin Kit for Soil modified for soil crust and filtered water samples from acidic saline lakes |
| meth_3.1.11 | Omega BioTek Inc Mag-Bind Plant DNA DS Kit M1130-00 |
| meth_3.1.12 | Qiagen DNeasy PowerSoil Kit for marine sponges |
| meth_3.2.1 | Qiagen RNeasy PowerSoil Total RNA Kit |
| meth_3.2.2 | Qiagen RNeasy PowerSoil Total RNA Kit modified for marine sediments Marine Microbes Coastal Project |
| meth_3.2.3 | PureLink RNA Mini Kit modified for seagrass Marine Microbes Coastal Project |
| meth_3.2.4 | PureLink RNA Mini Kit modified for sponges Marine Microbes Coastal Project |
| meth_3.3.1 | DNA Quantification using NanoDrop Spectrophotometer Thermo Scientific |
| meth_3.3.2 | Fluorometric Nucleic Acid Quantification at AGRF |
| meth_3.3.3 | DNA Quantification using the Invitrogen Qubit Flex Fluorometer |
| meth_4.1.1 | Bacterial 16S rRNA gene (27F and 519R) 1-step using Immolase™ DNA Polymerase (Bioline) |
| meth_4.1.2 | Bacterial 16S rRNA gene (27F and 519R) 1-step using KAPA HiFi Hot Start ReadyMix (Roche) |
| meth_4.1.3 | Archaeal 16S rRNA gene (A2F and 519R*) 2-step using Immolase™ DNA Polymerase (Bioline) |
| meth_4.1.4 | Eukaryotic 18S v4 rRNA gene (TAReuk454FWD1 and modified TAReukREV3) 1-step |
| meth_4.1.5 | Eukaryotic 18S V9 rRNA gene (1391F and EukBR) 1-step (5 PRIME HotMasterMix) |
| meth_4.1.6 | Fungal ITS gene (ITS1F and ITS4) 1-step |
| meth_4.1.7 | Illumina TruSeq Nano Library Preparation for Metagenomics (BASE) |
| meth_4.1.8 | Illumina Nextera XT Library Preparation for Metagenomics (Marine Microbes 2015-2017) |
| meth_4.1.9 | Metagenomics Library Preparation (Australian Microbiome) |
| meth_4.1.10 | Illumina Ribo-Zero rRNA Removal Kit for Metatranscriptomics (Marine Microbes 2015-2017) |
| meth_4.1.11 | Illumina TruSeq Stranded mRNA Library Preparation for Metatranscriptomics (Marine Microbes 2015-2017) |
| meth_4.2.1 | Illumina MiSeq 2 x 300 bp paired reads |
| meth_4.2.2 | Illumina MiSeq 2 x 250 bp paired reads |
| meth_4.2.3 | Illumina MiSeq 2 x 150 bp paired reads |
| meth_4.2.4 | Illumina HiSeq 2500 Rapid v2 (BASE metagenomics sequencing) |
| meth_4.2.5 | Illumina HiSeq 2500 Rapid SBS 500-cycle v2 (Marine Microbes metagenomics sequencing 2015-2017) |
| meth_4.2.6 | Illumina HiSeq 2500 SBS v4 (Marine Microbes transcriptomics sequencing 2015-2017) |
| meth_4.2.7 | Illumina NovaSeq 6000 (Australian Microbiome 2017 – ongoing) |
| meth_5.1 | Amplicon Analysis |
| meth_5.2 | Metagenome Analysis |
| meth_6.1.1 | Microbial Niche Indices |