Dynamics of rhizosphere bacterial communities and soil physiochemical properties in response to consecutive ratooning of sugarcane

Effect of applying oyster shell powder on soil properties and microbial diversity in the acidified soils of pomelo garden

The application of oyster shell has recently been used to increase soil pH in Southern China. However, little is known about causal shifts in the rhizosphere microbial community of pomelo trees, especially in orchards that have experienced natural accumulation of heavy metals over many years due to continuous fertilization and soil acidification. This study evaluated the effects of oyster shell powder applied for 1 year (T1), 2 years (T2) and 3 years (T3), alongside a control group with no soil amendments (Control; CK), on soil acidification and microbial diversity. Our findings demonstrated that the application of oyster shell significantly increased soil pH and reduced the concentrations of heavy metals such as thallium (Tl), chromium (Cr), and manganese (Mn). Illumina sequencing-based community analysis revealed that oyster shell application significantly increased the alpha diversity indices of both bacterial and fungal communities and influenced their distribution in the soil. Notably, all oyster shell-treated groups (T1-T3) showed significantly higher relative abundances of beneficial microbes (e.g., Nitrolancea, Vicinamibacterales) and those involved in carbohydrate degradation and nitrogen fixation compared to the control. Conversely, the relative abundances of Acidibacter and Chujaibacter (associated with heavy metal degradation and soil-borne diseases), Trichoderma and Acremonium (plant-beneficial fungi), as well as functionally annotated groups linked to nitrogen assimilation and pathotrophic modes (predicted via FUNGuild analysis), decreased significantly. Our results suggest that the application of oyster shell powder amendments contributes to improved soil properties and microbial environments; however, the effects on soil nitrogen cycling and fungal function are complex, warranting further research.

Soil-dependent responses of bacterial communities, phosphorus and carbon turnover to uranium stress in different soil ecosystems

Uranium (U) can impact microbially driven soil phosphorus (P) and carbon (C) cycling. However, the response of microbial P and C turnover to U in different soils is not well understood. Through the quantitative assay of P pools and soil organic C (SOC) quantitative assay and sequencing of 16S rRNA gene amplicons and metagenomes, we investigated the effect of U on P and C biotransformation in grassland (GL), paddy soil (PY), forest soil (FT). U (60 mg kg-1) impacted the diversity, interaction and stability of soil bacterial communities, leading to a decrease in available P (AP). Under U stress, organophosphate mineralization substantially contributed to the AP in GL and FT, whereas intracellular P metabolism dominated the AP in PY. Also, the reductive citrate cycle (rTCA cycle) promoted the content of SOC in GL, while the rTCA cycle and complex organic C degradation pathways enhanced the SOC in PY and FT, respectively. Notably, functional bacteria carrying organic C degradation genes could decompose SOC to enhance soil AP. Bacteria developed various resistance strategies to cope with U stress. This study reveals soil-dependent response of microbial P and C cycling and its ecological functions under the influence of radioactive contaminants in different soil systems.

Unveiling potential roles of earthworms in mitigating the presence of virulence factor genes in terrestrial ecosystems

Earthworms can redistribute soil microbiota, and thus might affect the profile of virulence factor genes (VFGs) which are carried by pathogens in soils. Nevertheless, the knowledge of VFG profile in the earthworm guts and its interaction with earthworm gut microbiome is still lacking. Herein, we characterized earthworm gut and soil microbiome and VFG profiles in natural and agricultural ecosystems at a national scale using metagenomics. VFG profiles in the earthworm guts significantly differed from those in the surrounding soils, which was mainly driven by variations of bacterial communities. Furthermore, the total abundance of different types of VFGs in the earthworm guts was about 20-fold lower than that in the soils due to the dramatic decline (also by approximately 20-fold) of VFG-carrying bacterial pathogens in the earthworm guts. Additionally, five VFGs related to nutritional/metabolic factors and stress survival were identified as keystones merely in the microbe-VFG network in the earthworm guts, implying their pivotal roles in facilitating pathogen colonization in earthworm gut microhabitats. These findings suggest the potential roles of earthworms in reducing risks related to the presence of VFGs in soils, providing novel insights into earthworm-based bioremediation of VFG contamination in terrestrial ecosystems.

Peanut-based intercropping systems altered soil bacterial communities, potential functions, and crop yield

Intercropping is an efficient land use and sustainable agricultural practice widely adopted worldwide. However, how intercropping influences the structure and function of soil bacterial communities is not fully understood. Here, the effects of five cropping systems (sole sorghum, sole millet, sole peanut, sorghum/peanut intercropping, and millet/peanut intercropping) on soil bacterial community structure and function were investigated using Illumina MiSeq sequencing. The results showed that integrating peanut into intercropping systems increased soil available nitrogen (AN) and total nitrogen (TN) content. The alpha diversity index, including Shannon and Chao1 indices, did not differ between the five cropping systems. Non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) illustrated a distinct separation in soil microbial communities among five cropping systems. Bacterial phyla, including Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi, were dominant across all cropping systems. Sorghum/peanut intercropping enhanced the relative abundance of phyla Actinobacteriota and Chloroflexi compared to the corresponding monocultures. Millet/peanut intercropping increased the relative abundance of Proteobacteria, Acidobacteriota, and Nitrospirota. The redundancy analysis (RDA) indicated that bacterial community structures were primarily shaped by soil organic carbon (SOC). The land equivalent ratio (LER) values for the two intercropping systems were all greater than one. Partial least squares path modeling analysis (PLS-PM) showed that soil bacterial community had a direct effect on yield and indirectly affected yield by altering soil properties. Our findings demonstrated that different intercropping systems formed different bacterial community structures despite sharing the same climate, reflecting changes in soil ecosystems caused by interspecific interactions. These results will provide a theoretical basis for understanding the microbial communities of peanut-based intercropping and guide agricultural practice.