Long-term Fertilization Structures Bacterial and Archaeal Communities along Soil Depth Gradient in a Paddy Soil

Abstract

Soil microbes provide important ecosystem services. Though the effects of changes in nutrient availability due to fertilization on the soil microbial communities in the topsoil (tilled layer, 0–20 cm) have been extensively explored, the effects on communities and their associations with soil nutrients in the subsoil (below 20 cm) which is rarely impacted by tillage are still unclear. 16S rRNA gene amplicon sequencing was used to investigate bacterial and archaeal communities in a Pup-Calric-Entisol soil treated for 32 years with chemical fertilizer (CF) and CF combined with farmyard manure (CFM), and to reveal links between soil properties and specific bacterial and archaeal taxa in both the top- and subsoil. The results showed that both CF and CFM treatments increased soil organic carbon (SOC), soil moisture (MO) and total nitrogen (TN) while decreased the nitrate_N content through the profile. Fertilizer applications also increased Olsen phosphorus (OP) content in most soil layers. Microbial communities in the topsoil were significantly different from those in subsoil. Compared to the CF treatment, taxa such as Nitrososphaera, Nitrospira, and several members of Acidobacteria in topsoil and Subdivision 3 genera incertae sedis, Leptolinea, and Bellilinea in subsoil were substantially more abundant in CFM. A co-occurrence based network analysis demonstrated that SOC and OP were the most important soil parameters that positively correlated with specific bacterial and archaeal taxa in topsoil and subsoil, respectively. Hydrogenophaga was identified as the keystone genus in the topsoil, while genera Phenylobacterium and Steroidobacter were identified as the keystone taxa in subsoil. The taxa identified above are involved in the decomposition of complex organic compounds and soil carbon, nitrogen, and phosphorus transformations. This study revealed that the spatial variability of soil properties due to long-term fertilization strongly shapes the bacterial and archaeal community composition and their interactions at both high and low taxonomic levels across the whole soil profile.

Organic Farming Improves Soil Microbial Abundance and Diversity under Greenhouse Condition: A Case Study in Shanghai (Eastern China)

“…Most of the studies to date have suggested that organic farming systems increase soil pH when compared to conventional farming in acidic soils by buffering from bicarbonates and organic acids in manure [32], while chemical fertilizer addition decreased soil acidity by acidification and nitrification [21]. However, opposite trends were observed here in a moderate alkaline soil in both open-field and plastic-tunnel cultivations.…”

“…Furthermore, high microbial diversity has been linked to high functional diversity in soil [5], which may cause the important ecological processes mentioned above. In addition, most researchers studied the microbial community under different agricultural management practices with field crops such as rice [3,21] and wheat [10], whereas little research has focused on vegetable cultivations [22]. Specifically, we still have a limited understanding of the long-term effects of organic and conventional management on soil microbial communities under open-field and protected conditions.…”

The effects of soil depth on the structure of microbial communities in agricultural soils in Iowa, USA

“…The differences of microbial community composition between surface soils and subsurface soils have been attributed to the drastic differences in soil nutrients, extracellular enzyme activities, soil organic carbon, and microbial biomass [22,23]. However, most of these studies focused on the microbial diversity variation between the surface and subsurface soils at a depth range of 0 - 100 cm in natural soils [24], in very specific environments, such as Alaskan soil cores or in a paddy soils [11,19]. The subsurface soil microbial communities are also very important to characterize because they have greater impact on soil forming processes than surface soils [25].…”

Effect of Long-Term Cropping Systems on the Diversity of the Soil Bacterial Communities

“…Long-term fertilization and cultivating methods have a significant effect on soil microbial community composition. The relative abundance of several bacterial genera alters with the use of fertilizer, also different fertilizer types induce different changes [8,9]. Not only bacterial, but also fungal communities are altered by fertilizer use, method of tillage and crop rotations.…”