Soil Depth Significantly Shifted Microbial Community Structures and Functions in a Semiarid Prairie Agroecosystem

Bacterial community composition and function vary with farmland type and soil depth around a mining area

Heavy metal pollution can have adverse impacts on microorganisms, plants and even human health. To date, the impact of heavy metals on bacteria in farmland has yielded poor attention, and there is a paucity of knowledge on the impact of land type on bacteria in mining area with heavy metal pollution. Around a metal-contaminated mining area, two soil depths in three types of farmlands were selected to explore the composition and function of bacteria and their correlations with the types and contents of heavy metals. The compositions and functions of bacterial communities at the three different agricultural sites were disparate to a certain extent. Some metabolic functions of bacterial community in the paddy field were up-regulated compared with those at other site. These results observed around mining area were different from those previously reported in conventional farmlands. In addition, bacterial community composition in the top soils was relatively complex, while in the deep soils it became more unitary and extracellular functional genes got enriched. Meanwhile, heavy metal pollution may stimulate the enrichment of certain bacteria to protect plants from damage. This finding may aid in understanding the indirect effect of metal contamination on plants and thus putting forward feasible strategies for the remediation of metal-contaminated sites. MAIN FINDINGS OF THE WORK: This was the first study to comprehensively explore the influence of heavy metal pollution on the soil bacterial communities and metabolic potentials in different agricultural land types and soil depths around a mining area.

Soil depth exerts a stronger impact on microbial communities and the sulfur biological cycle than salinity in salinized soils

The distribution of microbial communities along salinity gradients in the surface layer of salinized soils has been widely studied. However, it is unknown whether microbial communities exhibit similar distribution patterns in surface and deep soils. Additionally, the relationship between soil depth, salinity, and sulfur metabolism remains unclear. Herein, bulk soils in the surface (S, 5-10 cm) and deep (D, 20-25 cm) layers from high- and low-salinity soils were analyzed using metagenomic and physicochemical analyses. Soil depth was significantly correlated to the concentration of sulfur compounds in the soil and exerted a stronger effect than salinity. Non-metric multidimensional scaling analysis revealed significant differences in microbial community structure with varying soil depths and salinities. However, soil depth clearly influenced microbial community abundance, homogeneity, and diversity, while salinity had a limited effect on microbial abundance. Archaea and bacteria were enriched in the surface and deep soils, respectively. Gene abundance analysis revealed significant differences in the abundance of sulfur-related genes at different soil depths. The abundance of sulfur oxidation genes was lower in deep soil than in surface soil, whereas the abundance of other sulfur-related genes showed the opposite trend. Redundancy analysis (RDA) showed that environmental factors and sulfur compounds have a significant impact on sulfur metabolism genes, with sulfide significantly affecting low-salinity soils in the surface and deep layers, whereas salinity and sulfane sulfur had a greater correlation with high-salinity soils. Correlation analysis further showed that Euryarchaeota clustered with Bacteroidetes and Balneolaeota, while Proteobacteria clustered with many phyla, such as Acidobacteria. Various sulfur metabolism genes were widely distributed in both clusters. Our results indicate that microorganisms actively participate in the sulfur cycle in saline soils and that soil depth can affect these processes and the structure of microbial communities to a greater extent than soil salinity.

The soil microbiome: An essential, but neglected, component of regenerative agroecosystems

Regenerative agriculture (RA) is gaining traction globally as an approach for meeting growing food demands while avoiding, or even remediating, the detrimental environmental consequences associated with conventional farming. Momentum is building for science to provide evidence for, or against, the putative ecosystem benefits of RA practices relative to conventional farming. In this perspective article, we advance the argument that consideration of the soil microbiome in RA research is crucial for disentangling the varied and complex relationships RA practices have with the biotic and abiotic environment, outline the expected changes in soil microbiomes under RA, and make recommendations for designing research that will answer the outstanding questions on the soil microbiome under RA. Ultimately, deeper insights into the role of microbial communities in RA soils will allow the development of biologically relevant monitoring tools which will support land managers in addressing the key environmental issues associated with agriculture.

Elevated CO2 and biochar differentially affect plant C:N:P stoichiometry and soil microbiota in the rhizosphere of white lupin (Lupinus albus L.)

Biochar application is a potent climate change mitigation strategy in agroecosystems. However, little is known about the interactive effects of elevated CO₂ (eCO₂) and biochar on plant nutrient uptake and soil microbial processes. A pot experiment was conducted to investigate the effects of eCO₂ and biochar addition on plant C:N:P stoichiometry and rhizobacterial community for better management of nutrient balance and use efficiency in a future climate scenario. White lupin (Lupinus albus L.) was grown for 30 days in topsoil and subsoil with or without 2% corn-stubble biochar under ambient CO₂ (aCO₂: 390 ppm) or eCO₂ (550 ppm). Elevated CO₂ increased, but biochar decreased, plant biomass and shoot N and P uptake, with no interactions in either soil layer. Elevated CO₂ decreased shoot N concentration by 16% and biochar decreased shoot P concentration by 11%. As a result, eCO₂ increased shoot C:N ratio by 20% and decreased the N:P ratio by 11%. Biochar decreased shoot C:N ratio by 8% in the subsoil under eCO₂. However, biochar increased shoot C:P ratio by an average of 13% and N:P ratio by 23% in the subsoil. Moreover, plants grown in the subsoil showed lower shoot N (35%) and P (70%) uptake compared to the topsoil. The results indicate that N and P are the more limiting factors that regulate plant growth under eCO₂ and biochar application, respectively. Elevated CO₂ and biochar oppositely affected dominant rhizobacterial community composition, with the eCO₂ effect being greater. The microbiota in the subsoil held a greater diversity of contrasting species than the topsoil, which were associated with nutrient cycling, hydrocarbon degradation and plant productivity. These results enrich our understanding of potential soil nutrient cycling and plant nutrient balance in future agroecosystems.