Skip to main content

Table 2 Data coding

From: What is the impact of aminoglycoside exposure on soil and plant root-associated microbiota? A systematic review protocol

Code Variable Description
Bibliographic information Author Only last name of the first author and et. al, for the other colleagues
  Publication year Year the paper was published
  Title Full title of the paper
  Source of publication Nature of the publication e.g., journal article, report, etc
Study location Country The country where the study was conducted
Study site Field/laboratory If the study is based in the field or laboratory
Soil type Sandy/clay/silt/loamy Taxonomic unit used in soil science to categorize soil characteristics
Plant species Name Taxonomic unit used to describe plants
Soil use Agricultural/natural Primary purpose of soil for crop use (agricultural) or no use (natural)
Experimental conditions Light/dark Light conditions for incubation period after exposure
  Temperature Temperature in Celsius
  Duration The length of time in days that soil was exposed to antibiotic before outcomes were measured
Properties of soil pH pH of soil
  Organic matter content Proportion of organic matter of soil consisting of plants and animals in various stages of composition expressed as a percentage
  Moisture Water content of soil expressed in terms of volume or weight
  Oxygen status Oxygen present in the atmosphere in the soil expressed as concentrations
  Compost use The use of compost to amend the soil
Antibiotic characteristics Name Name of aminoglycoside used for exposure
  Chemical formula Formula describing chemical proportions of atoms making up aminoglycoside
  Concentration Concentration of antibiotic expressed in terms of volume or weight
  Method of application The way the microbiome was exposed to antibiotic (ex. manure, direct application, etc.)
  Limit of detection Lowest concentration of antibiotic able to be detected in soil expressed in terms of volume or weight
  Duration of detection
Frequency of application
Length of time in days that antibiotic is able to be detected in the soil
The number of antibiotic exposures
Method for estimating microbial composition PFLA/T-RFLP/DGGE Experimental method used to determine the impact of aminoglycoside on microbial community
Reported levels of microbial composition Reported levels of microbial composition Biomass reported as mg/kg; changes in banding patterns, or richness expressed as H' and S' indices
Method for estimating resistance genes Shotgun/high throughput Meta-genomic sequencing method used to estimate resistance genes
Reported levels of resistance genes Reported levels of resistance genes Similarity or abundance reported as percentage
  Reported levels of resistance genes Similarity or abundance reported as percentage
Method for estimating soil suppression Shotgun/high throughput Genomic sequencing method used to identify suppressive pathogens
Reported levels of suppressive pathogen Reported levels of biological control agents Similarity or abundance reported as percentage
Comparator Control Nature of the study/experiment control (i.e., no aminoglycoside)
Type of tillage Depth of tillage used in agricultural practices No-till, deep (deeper than 10 inches), medium-depth (5–10 inches), shallow (1–4 inches)