Garden Soil Bacteria in Central Oregon and the Willamette Valley, Oregon
Abstract
Soil microbes play critical roles in both soil health (e.g. water and nutrient cycling, soil structure) and crop health/productivity, but very little is known about the ecology of many soil bacterial microbes. Many cannot be cultured and studied in a laboratory, and thus are only known from their genetic code. To improve our understanding of the abundance and diversity of bacterial microbes in urban garden soils, we collected soil samples from 40 gardens (mostly vegetable) across Central Oregon and the Willamette Valley. We included gardens with different management practices and, within a garden, we sampled soil from beds with different crops. We prepared and analyzed two technical replicates from each soil core, using amplicon (16S) sequencing. Bioinformatic processing of raw 16S reads was performed in R using the DADA2 package for filtering, merging, cleaning, and assigning taxonomy to paired-end reads. Amplicon sequence variants (ASVs) resulting from the DADA2 pipeline were assigned taxonomy down to genus level using the Ribosomal Database Project (RDP) Bayesian Classifier. We assigned ecological roles, based upon information gleaned from the published literature, microbiology textbooks, and also inferred possible ecological roles based upon phylogenetic relationships and population dynamics of microbes in different soil types. Fifty percent of the most common bacterial microbes act to remediate soils, by breaking down metals, concentrated nutrients, pesticides, or other environmental toxins. We did not measure pesticide applications or chemical markers in our study, but the abundance of bacteria capable of degrading environmental pollutants suggests that pesticides may have been in use.
Garden Soil Bacteria in Central Oregon and the Willamette Valley, Oregon
Soil microbes play critical roles in both soil health (e.g. water and nutrient cycling, soil structure) and crop health/productivity, but very little is known about the ecology of many soil bacterial microbes. Many cannot be cultured and studied in a laboratory, and thus are only known from their genetic code. To improve our understanding of the abundance and diversity of bacterial microbes in urban garden soils, we collected soil samples from 40 gardens (mostly vegetable) across Central Oregon and the Willamette Valley. We included gardens with different management practices and, within a garden, we sampled soil from beds with different crops. We prepared and analyzed two technical replicates from each soil core, using amplicon (16S) sequencing. Bioinformatic processing of raw 16S reads was performed in R using the DADA2 package for filtering, merging, cleaning, and assigning taxonomy to paired-end reads. Amplicon sequence variants (ASVs) resulting from the DADA2 pipeline were assigned taxonomy down to genus level using the Ribosomal Database Project (RDP) Bayesian Classifier. We assigned ecological roles, based upon information gleaned from the published literature, microbiology textbooks, and also inferred possible ecological roles based upon phylogenetic relationships and population dynamics of microbes in different soil types. Fifty percent of the most common bacterial microbes act to remediate soils, by breaking down metals, concentrated nutrients, pesticides, or other environmental toxins. We did not measure pesticide applications or chemical markers in our study, but the abundance of bacteria capable of degrading environmental pollutants suggests that pesticides may have been in use.