Table 1.
Prevalence of non-O157 STEC in pre- and post-grazing fecal samples from sheep (CA) and goats (MN) collected from field trials of integrated crop-livestock systems (2020–2022).
Fig 1.
Alpha diversity (Chao1, Shannon, Simpson, and Faith’s phylogenetic diversity (PD)) in fecal samples collected from field trials of integrated crop-livestock systems in California (CA) and Minnesota (MN).
Comparisons between (A) sheep (CA) and goat (MN) fecal samples, (B) years (2020–2022) and the presence of non-O157 STEC in sheep feces, and (C) years (2021–2022) and pre- and post-grazing status in goat feces (**p < 0.01, * p <0.05).
Fig 2.
Beta diversity with Bray-Curtis dissimilarity using principal coordinate analysis (PCoA) of fecal samples collected from field trials of integrated crop-livestock systems in California (CA) and Minnesota (MN).
Comparisons between (A) sheep (CA) and goat (MN) fecal samples, (B) sheep feces from different years (2020–2022), and (C) pre- and post-grazing status in goat feces.
Fig 3.
Differential abundance analysis between sheep and goat fecal samples collected from field trials of integrated crop-livestock systems in California (CA) and Minnesota (MN).
(A) Observed relative abundance at the phylum level, (B) log fold changes in differential abundance at the phylum level using ANCOM-BC2. (Bar plots highlighted in green indicate significant differences between two groups with a significance level of p < 0.05).
Fig 4.
Differential abundance analysis within sheep and goat fecal samples collected from field trials of integrated crop-livestock systems in California (CA) and Minnesota (MN).
Log fold changes in differential abundance using ANOCM-BC2 (A) at the phylum level comparing non-O157 STEC positive and negative groups in sheep, (B) at the family level comparing grazing and control groups in sheep, (C) at the phylum level, and (D) at the family level comparing pre- and post-grazing groups in goats. (Blue-colored and green-colored bar plots depict taxa showing significantly different abundance between the compared groups, p < 0.05).
Table 2.
Presence (%) of generic E. coli in soil samples+ in each treatment group (fallow, non-graze CC, and graze CC) collected from field trials of integrated crop-livestock systems in California (CA) and Minnesota (MN) (2020–2022).
Fig 5.
Alpha diversity (Chao1, Shannon, Simpson, and Faith’s phylogenetic diversity (PD)) in soil samples collected from field trials of integrated crop-livestock systems in California (CA) and Minnesota (MN).
(A) Sampling day (i.e., day post-grazing (DPG)) effect in the CA Trial 1 tomato field, (B) State effect in spinach/cucumber fields (CA Trial 2 and MN Trial 3) (2021–2022) (**p < 0.01, * p <0.05).
Fig 6.
Beta-diversity with Bray-Curtis dissimilarity using principal coordinate analysis (PCoA) of soil samples collected from field trials of integrated crop-livestock systems in California (CA) and Minnesota (MN).
(A) Sampling day (i.e., day post-grazing (DPG)) effect in the CA Trial 1 tomato field (2020–2021), (B) state and year effects in spinach/cucumber fields (CA Trial 2 and MN Trial 3, 2021–2022).
Fig 7.
Observed relative abundance and differential abundance analysis of soil samples collected from spinach/cucumber field trials (CA Trial 2 and MN Trial 3) (2021–2022) of integrated crop-livestock systems between California (CA) and Minnesota (MN).
(A) The observed relative abundance at the phylum level by treatment group in each state; (B) log fold changes in differential abundance using ANOCM-BC2 at the phylum level; and (C) the family level comparing two states. (Bar plots highlighted in orange indicate significant differences between the two groups, p < 0.05). *Relative abundance less than 1% is not depicted in the bar plots.
Table 3.
Core microbiomes in (A) post-grazing fecal samples and (B) graze CC soil collected from field trials of integrated crop-livestock systems in California (CA) and Minnesota (MN) (2020–2022).