Microbial Communities Associated With Long-Term Tillage and Fertility Treatments in a Corn-Soybean Cropping System

Abstract

Tillage and fertilization are common practices used to enhance soil fertility and increase yield. Changes in soil edaphic properties associated with different tillage and fertility regimes have been widely examined, yet, the microbially mediated pathways and ecological niches involved in enhancing soil fertility are poorly understood. The effects of long-term conventional tillage and no-till in parallel with three fertility treatments (No fertilization, N-only, and NPK) on soil microbial communities were investigated in a long-term field study that was established in the 1970's. Here, we used highthroughput sequencing of bacterial, fungal and oomycetes markers, followed by community-level functional and ecological assembly to discern principles governing tillage and fertility practices' influence on associated soil microbiomes. Both tillage and fertilizer significantly altered microbial community structure, but the tillage effect was more prominent than the fertilizer effect. Tillage significantly affected bacteria, fungi, fusaria, and oomycete beta-diversity, whereas fertilizer only affected bacteria and fungi beta-diversity. In our study different tillage and fertilizer regimes favored specific networks of metabolic pathways and distinct ecological guilds. No-till selected for beneficial microbes that translocate nutrients and resources and protect the host against pathogens. Notably, ecological guilds featuring arbuscular mycorrhizae, mycoparasites, and nematophagous fungi were favored in no-till soils, while fungal saprotrophs and plant pathogens dominated in tilled soils. Conventional till and fertilizer management shifted the communities toward fast growing competitors. Copiotrophic bacteria and fusarium species were favored under conventional tillage and in the presence of fertilizers. The analysis of the metagenomes revealed a higher abundance of predicted pathways associated with energy metabolism, translation, metabolism of cofactors and vitamins, glycan biosynthesis and nucleotide metabolism in no-till. Furthermore, no specific pathways were found to be enriched under the investigated fertilization

Microbial Shifts Following Five Years of Cover Cropping and Tillage Practices in Fertile Agroecosystems

“…This may owe to chisel tillage being less aggressive than typical conventional tillage methods, thus the microbial responses to tillage could be more clear-cut under practices like moldboard plowing [24]. The CT-favored oligotrophs in PC2 and PC3 responding positively to chisel tillage contradicts past studies [27,90], yet these analyses were limited to the phyla level, thereby highlighting the discrepancy between the collective microbial behaviors at higher taxonomic ranks and those of individual microbes.…”

“…Community-level inferences, however, only superficially explain how the soil microbiome responds to CC and tillage. New metagenomics research allows for a closer look into the soil microbial composition and function and the changes brought about by agricultural practices [ 25 , 26 , 27 ]. This usually involves using β-diversity measures to detect shifts in the microbial community structure between samples [ 28 ], interpreting the changes with further analyses targeting specific functional genes, such as amo A, involved in nitrification [ 29 ], and characterizing the compositional shifts that identify the responsive taxa [ 30 , 31 ].…”

Temporal Soil Bacterial Community Responses to Cropping Systems and Crop Identity in Dryland Agroecosystems of the Northern Great Plains

“…Tillage can act as a selective pressure leading to a difference in soil microbial community composition under contrasting soil disturbance regimes (Navarro-Noya et al, 2013). Breaking apart soil aggregates exposes previously protected soil organic matter to oxidizing conditions (Six et al, 2000;Van Groenigen et al, 2010) favorable to fast growing copiotrophic bacteria (Srour et al, 2020). However, findings on the effects of tillage on soil microbial communities are not consistent.…”

Plant Microbiota Beyond Farming Practices: A Review

“…A fall in α-diversity under conservation tillage practices is common and attributable to a reduction in evenness as much as in richness (Degrune et al, 2016;Piazza et al, 2019;Tyler, 2019). Nevertheless, conservation tillage and no-till practices favor slower organic matter degradation and the establishment of less diverse but more oligotrophic, complex, and stable microbial communities (Degrune et al, 2017;Song et al, 2017;Wang et al, 2017;Tyler, 2019;Srour et al, 2020). Babin et al (2019) consistently observed a higher abundance of predicted genes involved in oligotrophic lifestyles under low tillage conditions.…”

“…From a metagenomic perspective, the impact of tilling on soil microbial diversity is usually investigated through αor β-diversity indexes describing respective differences within and between communities. Conventional tillage has a low impact on fungal α-diversity, while increasing prokaryotic αdiversity has a significant impact on prokaryotic β-diversity favoring opportunistic commensal and copiotroph microbes (Degrune et al, 2017;Hartman et al, 2018;Sommermann et al, 2018;Babin et al, 2019;Banerjee et al, 2019;Piazza et al, 2019;Srour et al, 2020). Tilling facilitates fast organic matter decomposition resulting in a sudden nutrient release that is homogeneously distributed in tilled soil columns, thus increasing the abundance of r-strategists or fast-growing microorganisms (Degrune et al, 2017;Schmidt et al, 2018).…”