Table 1.
qPCR primers and probes used in this study.
Fig 1.
Average relative abundances of phyla among sample types.
Included in “Other” are phyla that individually make up less than 1% of total abundance: Nitrospirae, Armatimonadetes, Spirochaetes, Synergistetes, Latescibacteria, BRC1, Parcubacteria, Microgenomates, Chlamydiae, Deferribacteres, Fibrobacteres, Candidatus Saccharibacteria, Elusimicrobia, candidate division WPS-2, SR1, Lentisphaerae, Hydrogenedentes, Cloacimonetes, Ignavibacteriae, Deinococcus-Thermus, and Fusobacteria.
Fig 2.
Alpha diversity indices of microbiome samples.
Boxplots represent 25th to 75th percentiles and whiskers showing a maximum of 1.5x the interquartile range (IQR). Different letters indicate significant differences within the alpha diversity indexes (P<0.05).
Fig 3.
Comparison of community composition between soil and manure line samples.
Community composition varied significantly between all samples except between the spring samples. Spring time 1 and spring time 2 soil are combined as spring soil. Clustering is based on nonmetric multidimensional scaling analysis of samples according to Bray-Curtis distances. Manure was excluded from the NMDS plot to show variation of soil samples.
Fig 4.
Average relative abundance of manure associated OTUs.
OTUs are classified as manure associated if abundances were significantly greater (P<0.05) in manure compared to fall pre-manure soil.
Fig 5.
Relative abundance of target genes to 16S rRNA copy number.
Different letters indicate significant differences (P<0.05). n = 10 for manure. n = 20 for soil samples.