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It has been documented that beneficial plant-associated bacteria have contributed to disease suppression, growth promotion, and tolerance to abiotic stresses. Advances in high-throughput sequencing have allowed an increase in research regarding bacterial endophytes, which are microbes that colonize the interior of plants without causing disease. Practices associated with minimizing the use of off-farm resources, such as reduced tillage regimes and crop rotations, can cause shifts in plant-associated bacteria and its surrounding agroecosystem. Integrated crop–livestock systems are an option that can provide environmental benefits by implementing diverse cropping systems, incorporating perennial and legume forages and adding animal manure through grazing livestock. It has been found that crop-livestock systems can increase soil quality and fertility, reduce cost of herbicide use and improve sustainability, especially for farmers in poorer areas of the world. This work explores how crop-livestock systems that integrate chicken rotations can impact tomato plant growth, as well as soil and endophytic bacterial communities. Tomato plants were subjected to greenhouse and field studies where biomass was assessed, and bacterial communities were characterized through culture-dependent and -independent approaches.In greenhouse experiments, the greater percent of chicken grazed soil incorporated in the planting substrate, the greater the stunting of tomato seedlings. In the field study, bacterial communities differed significantly by sample origin and plant development stage, regardless of chicken grazing history. Our findings suggest stronger contribution of agricultural management practices during early plant stages on endophytic microbiome, as opposed to later on in the host lifecycle. Taxonomic composition of dominant groups of recovered endophytic bacterial isolates were consistent with those found by amplicon sequencing. Plots with history of chicken grazing had a significant increase of soil fertility and differentially abundant ASVs. Dominant phyla (Actinobacteria, Proteobacteria, Bacteroidetes and Firmicutes) of bacterial taxa identified were uniform between culture-dependent and -independent approaches from both greenhouse and field experiments. Most of the recovered isolates were found to be phylogenetically similar to formerly cultured plant endophytes and bacteria found in soil. However, some isolates were similar to bacteria recovered in human clinical settings. Further directions should focus on identification and elucidation of transmission of possible plant growth promoting bacteria, as well as human pathogens, found in crops grown in this type of agricultural management strategy. Moreover, the influence of stage in plant lifecycle on bacterial community composition under specific management strategies remains to be explored. This work provides insight into the influence of crop-livestock rotations on soil- and tomato plant-associated bacterial communities. |
