Mineral vs. Organic Amendments: Microbial Community Structure, Activity and Abundance of Agriculturally Relevant Microbes Are Driven by Long-Term Fertilization Strategies

Abstract

Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially to the impressive increases in food production. Despite the pivotal role of soil microorganisms in agro-ecosystems, we still have a limited understanding of the complex response of the soil microbiota to organic and mineral fertilization in the very long-term. Here, we report the effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization), carried out for more than a century, on the structure and activity of the soil microbiome. Organic matter content, nutrient concentrations, and microbial biomass carbon were significantly increased by mineral, and even more strongly by organic fertilization. Pyrosequencing revealed significant differences between the structures of bacterial and fungal soil communities associated to each fertilization regime. Organic fertilization increased bacterial diversity, and stimulated microbial groups (Firmicutes, Proteobacteria, and Zygomycota) that are known to prefer nutrient-rich environments, and that are involved in the degradation of complex organic compounds. In contrast, soils not receiving manure harbored distinct microbial communities enriched in oligotrophic organisms adapted to nutrient-limited environments, as Acidobacteria. The fertilization regime also affected the relative abundances of plant beneficial and detrimental microbial taxa, which may influence productivity and stability of the agroecosystem. As expected, the activity of microbial exoenzymes involved in carbon, nitrogen, and phosphorous mineralization were enhanced by both types of fertilization. However, in contrast to comparable studies, the highest chitinase and phosphatase activities were observed in the solely mineral fertilized soil. Interestingly, these two enzymes showed also a particular high biomass-specific activities and a strong negative relation with soil pH. As many soil parameters are known to change slowly, the particularity of unchanged fertilization treatments since 1902 allows a profound assessment of linkages between management and abiotic as well as biotic soil parameters. Our study revealed that pH and TOC were the majors, while nitrogen and phosphorous pools were minors, drivers for structure and activity of the soil microbial community. Due to the long-term treatments studied, our findings likely represent permanent and stable, rather than transient, responses of soil microbial communities to fertilization.

Effects of Subsurface Banding and Broadcast of Poultry Litter and Cover Crop on Soil Microbial Populations

“…4C, fertilizer as either BC, BD, or STD yielded elevated richness levels over UTC plots, indicating that simply applying fertilizer changed the microbial population. This contradicts the findings of Francioli et al (2016), which indicated that manure significantly increased estimates over STD.…”

“…For example, Toyota and Kuninaga (2006) demonstrated that cultivated heterotrophic plate count bacteria (HPC) were two to six times greater in soils treated with manure + STD than with STD alone; however, total bacterial numbers were not different, indicating that STD alone may enrich total soil microbiota. Others have shown that STD treatments alone can increase soil microbial parameters (Gong et al, 2009; Francioli et al, 2016). Nevertheless, the intricacies of measurable soil biology and the effect of agronomic practices may be soil, crop, region, and/or climate specific.…”

Effect of long‐term organic and mineral fertilization strategies on rhizosphere microbiota assemblage and performance of lettuce

“…Long-term soil fertilization strategies play a significant role in the alteration of soil biological properties, and thus may affect soil functioning and quality (Bünemann et al, 2018). Several studies showed that soil microbial communities are influenced by long-term fertilization strategies (Hartmann et al, 2015;Francioli et al, 2016;Lupatini et al, 2017). The use of mineral fertilizers in conventional agriculture has contributed to increased crop productivity over the last decades (Robertson and Vitousek, 2009).…”

“…These compounds do serve not only the plants but also the soil microbiota as nutrient source and increase the soil organic matter content (Mäder et al, 2002;Liang et al, 2012). Accordingly, it has been reported that soils under long-term organic fertilization strategies harbour higher microbial biomass , higher microbial species richness (Esperschütz et al, 2007;Hartmann et al, 2015;Schmid et al, 2017), enhanced microbial activity (Lori et al, 2017) and an increased abundance of plant beneficial microbes (Francioli et al, 2016). However, the effect of agricultural practices on the soil microbiota is not consistent across published reports and greatly depends on the pedoclimatic context and the overall agricultural strategy applied at the site.…”

Decomposition of Fertilizer Use Intensity and Its Environmental Risk in China’s Grain Production Process

“…In the long run, it has been proven that fertilizer use can directly or indirectly affect the physical, chemical, and biological characteristics of the soil as well as the soil fertility and crop productivity [2][3][4][5][6]. In order to meet the food demand of an ever-increasing world population, most countries have shown an overload use of inorganic fertilizer in agricultural production [7,8].…”