Abstract
Environmentally friendly agricultural production necessitates manipulation of microbe–plant interactions, requiring a better understanding of how farming practices influence soil microbiota. We studied the effect of conventional and organic treatment on soil bacterial richness, composition, and predicted functional potential. 16S rRNA sequencing was applied to soils from adjacent plots receiving either a synthetic or organic fertilizer, where two crops were grown within treatment, homogenizing for differences in soil properties, crop, and climate. Conventional fertilizer was associated with a decrease in soil pH, an accumulation of Ag, Mn, As, Fe, Co, Cd, and Ni; and an enrichment of ammonia oxidizers and xenobiotic compound degraders (e.g., Candidatus Nitrososphaera, Nitrospira, Bacillus, Pseudomonas). Soils receiving organic fertilization were enriched in Ti (crop biostimulant), N, and C cycling bacteria (denitrifiers, e.g., Azoarcus, Anaerolinea; methylotrophs, e.g., Methylocaldum, Methanosarcina), and disease-suppression (e.g., Myxococcales). Some predicted functions, such as glutathione metabolism, were slightly, but significantly enriched after a one-time manure application, suggesting the enhancement of sulfur regulation, nitrogen-fixing, and defense of environmental stressors. The study highlights that even a single application of organic fertilization is enough to originate a rapid shift in soil prokaryotes, responding to the differential substrate availability by promoting soil health, similar to recurrent applications.
Highlights
Advances in irrigation and soil management techniques, along with the application of chemical fertilizers and pesticides introduced by the Green Revolution in farming, resulted in a substantial increase in food production over the last 50 years [1]
Irrespective of the impacts on food quality, the potential for organic farming to impact soil health has been expounded as a significant benefit
Synthetic fertilizers can result in disrupted soil health, and may negatively impact plant growth as well as soil and plant microbial diversity and structure [7]
Summary
Advances in irrigation and soil management techniques, along with the application of chemical fertilizers and pesticides introduced by the Green Revolution in farming, resulted in a substantial increase in food production over the last 50 years [1]. Organic systems have previously been associated with either an increase in soil microbial richness [8] or no significant change [6,13,15,16] Some of this variance may be explained by differences in the composition of the organic amendment, the time of harvesting, the studied time span, the rotation of crops planted, and so on. Proteobacteria and Firmicutes dominate organic farming systems in long-term field experiments, with plant growth-promoting genera enriched (e.g., Rhizobium, Bradyrhizobium, Burkholderia, Pseudomonas, Rhodoplanes), while Actinobacteria and Acidobacteria predominate in conventionally managed lands [18,19]
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