Table 2 Data coding
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) |