Pairwise comparison of qPCR results for values of 16s rRNA copies per g FW rhizosphere or bulk soil (NS = Non “sterile” and soils were not autoclaved before experimentation S = Sterile and soils were autoclaved before experimentation).

(XLSX)</p

Mean crop fresh-weight (FW) biomass (a) grown in organic soil (b) conventional soil and (c) diseased soil (n = 10 / treatment, ± standard deviation).

Significant increases in biomass of each crop are denoted by “*”, “**” or “***” above each. Siddak’s multiple comparison test using GraphPad (Vers 8.2.1). (TIF)</p

Shared and unique significant abundance increases of genus-level bacteria, prompted by each crop in all undisrupted agroecosystems (FDR: False discovery rate).

Gray highlighting indicates the genus was not significantly altered within the crop rhizosphere).</p

Mean dry-weight (DW) biomass measurements for each crop in each soil treatment (n = 10 per crop per soil treatment, ± standard deviation).

(a) DW biomass results from crops grown in organic soil (b) DW biomass of crops grown in conventional soil (c) DW biomass of all crops grown in diseased soil. Red or blue bars represent the mean DW biomass for each crop in undisrupted or disrupted soil respectively. Significant differences between mean. DW biomass of crops grown in disrupted or undisrupted soils are denoted by “*”, “**”, “***” or “****”. Figure created using GraphPad’s Prism (Vers. 8.2.1).</p

Bacterial genera observed to significantly increase in abundance after corn growth across all disrupted soils, compared to abundances of the same genera across undisrupted soils growing corn.

If any abundance increases were observed from taxa listed in the NPCKs (S9 Table), they were removed from this table so included taxa may be attributed to corn presence. Unclassified genera increased in abundance after disruption are listed with their lowest classification level (k: kingdom, p: phylum, etc.) (FDR: False discovery rate). (XLSX)</p

Pairwise comparison between values of Shannon’s alpha diversity assigned to each treatment.

(Above) Comparison of Shannon’s α-diversity values between disrupted and undisrupted treatments. (Below) Comparison of Shannon’s α-diversity values between communities detected in disrupted no plant treatments and disrupted plant treatments (e.g. Crop: Autoclaved = disrupted, Crop: Unautoclaved = undisrupted). (XLSX)</p

Crop-specific and crop-shared bacterial abundance increases resulting from growth in disrupted agroecosystems.

(XLSX)</p

Principal coordinate analyses (PCoA) of rhizobacterial communities after crop growth in undisrupted and disrupted organic agroecosystem soils.

Colored circles indicate samples treated with disruption, whereas hollow circles indicate undisrupted samples, respectively. Purple, teal, green, yellow, or red color represents rhizospheric samples from beet, corn, lettuce, NPCKs or tomato samples, respectively. Figure created using GraphPad’s Prism (Vers. 8.2.1).</p

Bacterial genera observed to significantly increase in abundance after beet growth across all disrupted soils, compared to abundances of the same genera across undisrupted soils growing beet.

If any abundance increases were observed from taxa listed in the NPCKs (S9 Table), they were removed from this table so included taxa may be attributed to beet presence. Unclassified genera increased in abundance after disruption are listed with their lowest classification level (k: kingdom, p: phylum, etc.) (FDR: False discovery rate). (XLSX)</p

Bacterial genera observed to significantly increase in abundance after tomato growth across all disrupted soils, compared to abundances of the same genera across undisrupted soils growing tomato.

If any abundance increases were observed from taxa listed in the NPCKs (S9 Table), they were removed from this table so included taxa may be attributed to tomato presence. Unclassified genera increased in abundance after disruption are listed with their lowest classification level (k: kingdom, p: phylum, etc.) (FDR: False discovery rate). (XLSX)</p