Biology and Fertility of Soils最新文献

Understanding the impact of agricultural land use on the soil prokaryotic communities in connected downslope sites is crucial for developing sustainable strategies to preserve ecosystem properties and mitigate agriculture’s environmental impacts. In this study, we investigated topsoil samples collected at three time points in 2022 (March, June, and November) from two adjacent catenas, reaching from hillslope to floodplain. The catenas differed in land use (extensive grassland vs. extensive cropland) at the top and middle parts, while the floodplain remained an extensive grassland due to legal restrictions. Using quantitative real-time PCRs and metabarcoding, we assessed prokaryotic abundance and prokaryotic community composition. Results show higher bacterial abundance in the cropland-influenced floodplain part across all time points compared to the grassland-influenced floodplain part. Temporal dynamics revealed a progressive decrease in the shared prokaryotic communities of the floodplain parts, peaking at the summer sampling time point, indicating a significant influence of the respective management type of the agricultural sites over the bacterial and archaeal communities of the floodplain parts. Differential abundance analyses identified several nitrifying taxa as more abundant in the cropland-influenced floodplain. Upstream land use also influenced the prokaryotic network of the cropland-floodplain, with some cropland taxa becoming keystone taxa and altering network morphology, an effect not observed in the grassland-influenced floodplain. These findings suggest that upstream agricultural land use practices have exerted a long-term influence on the floodplain prokaryotic communities over the past three decades. Moreover, there is evidence suggesting that these prokaryotic communities may undergo a potential reset during winter, which requires further investigation.

The root-associated type II methanotrophs significantly contribute to CH₄ oxidation-dependent N₂ fixation. However, it is unclear whether type I methanotrophs are involved in CH₄ oxidation and N₂ fixation, especially in natural wetlands. So far, limited attention has given to root-associated active microorganisms. Here, metatranscriptomic analysis of root-associated microbes has been proposed to reveal the aerobic methanotrophs contributing to CH₄ and nitrogen cycles in the roots of Phragmites australis grown in a natural wetland. Results showed Methylocystaceae (type II methanotrophs) and Methylococcaceae (type I methanotrophs) as major taxa (relative abundance, 14%) at transcription level. However, based on 16S rRNA gene sequencing, contribution of these taxa was < 1% at DNA level. Genes encoding methane monooxygenase (enzyme responsible for the first step of CH₄ oxidation) were detected in Methylomonas (pmoCBA) and Methylosinus (mmoXYZCB). Furthermore, genes related to methanol dehydrogenase, formaldehyde dehydrogenase, and formate dehydrogenase were also detected in Methyosinus and Methylomonas, while mcrA gene was observed in Methanospirillum and Methanofollis. Moreover, nitrogenase structural genes, such as nifHDK, were found in Methylosinus (Methylocystaceae) and Methylomonas (Methylococcaceae). Minor nitrogenase genes were detected in Cyanothece, Lyngbya, Pelobacter and Smithella of Cyanobacteriaceae family. In addition, N₂ fixing activity of P. australis was determined by analyzing the natural abundance of δ¹⁵N from June to August. The N₂ fixing activity of P. australis increased in presence of CH₄ in root system under ¹⁵N-N₂ feeding. Metatranscriptomic analysis revealed that not only type II methanotrophs, but also type I methanotrophs oxidize CH₄ and fix N₂.

In the absence of an appropriate formulation, the population of plant growth-promoting bacteria (PGPB) inoculated into soil may be significantly reduced. These unprotected introduced bacteria must compete with the often-more adapted native microflora and are susceptible to predation by soil microfauna. This opinion paper addresses the significance of proper formulation in creating an effective inoculant, discusses the primary challenges associated with current liquid and dry formulations, and emphasizes the rationale for bioencapsulation as the optimal approach for protecting PGPB in a successful inoculant.

Using two kinds of microbial inoculations extracted from soil cropped to rice and peanut, we conducted a swap-inoculation experiment to explore the relative importance of microbial inoculation and soil properties on CO₂ emissions from soil. Inoculated microorganisms into a soil different from their origin (swap inoculation) were partially successful and reduced CO₂ emissions, namely according to home-field advantage (HFA); The success of invasive microorganisms depended on molecular composition of soil organic matter (SOM) compared to inoculation of native microbes (inoculated microorganisms into origin soil). The different habits screened the fewer microorganisms to undergo respiration for energy and life-sustaining activities, thus decreasing CO₂ emissions from SOM. However, the effect of HFA diminished with incubation time, as the invasive microorganisms reshaped SOM molecular diversity and composition during microbial community assemblage, which fits with the Gaia effect (GE). Specific microbial communities, such as Bacteroidetes and Actinobacteria, drove the conversion of persistent molecules to labile molecules, thereby increasing the chances of SOM mineralization by microorganisms. We found there was positive correlation between labile SOM molecules and SOM mineralization. In addition, MBC increased in swap inoculation compared to native inoculation after 60 days, which also resulted in higher CO₂ emissions from SOM. HFA and GE provide new perspectives to help decipher the interaction between microorganisms and the habitat under microbial invasion, and the mechanism of influence on CO₂ emissions from SOM.

Soil gross mineral N production and consumption processes are crucial regulators of plant productivity and N loss from croplands. Substituting synthetic fertilizers by integrating legumes in cultivation systems is common in organic farming, but research on its long-term impact on dynamics of gross soil N transformation and associated environmental N loss is scarce. In particular, studies at a temporal resolution that allows for a mechanistic understanding of long-term effects of organic farming are missing. Therefore, we determined gross N turnover rates of ammonification, nitrification, and ammonium and nitrate immobilization at monthly temporal resolution during a full green rye-maize cropping sequence. Measurements were carried out at sites with same pedo-climatic background but organic farming (OF) and integrated farming (IF) history. During green rye growing, N turnover rates for OF and IF were low and not significantly different, likely owing to low temperatures. During silage maize growing, IF exhibited significantly higher average N turnover rates of 1.86, 4.46, and 5.57 mg N kg⁻¹ dry soil d⁻¹ for gross ammonification, ammonium immobilization, and nitrate immobilization, respectively, compared to OF values of 1.11, 1.80, and 2.90 mg N kg⁻¹ dry soil d⁻¹. The significantly higher N turnover rates were likely due to higher soil organic C, N and microbial biomass which result from different long-term management practices. Especially the increased immobilization potential on the IF site contributed to significantly lower area-scaled N₂O emissions (1.45 vs. 4.36 kg N ha⁻¹) during periods of high nitrification. This shows that for low SOC soils, integrated farming history with high C return enhances soil N cycling and reduces the risk of N losses in the form of N₂O emission.

Acetochlor (ACE), one of the widely used herbicides in northeastern China, has raised concerns due to its residual presence in the soil. In this study, a pot experiment was conducted to investigate the effects of adding vermicompost on the degradation efficiency and pathways of acetochlor in black soil under dark conditions. The results showed that the vermicompost addition increased the degradation rate of acetochlor, shortened its degradation half-life, and altered the composition of the bacterial community. The influence of vermicompost on bacterial community diversity is minimal, but it can increase the relative abundance of acetochlor degradation bacteria, promoting the collaboration between exogenous and indigenous bacteria to enhance acetochlor utilization. GC-MS analysis revealed the formation of seven metabolites during the acetochlor degradation process, including 2-chloro-N-(2-ethyl-6-methylphenyl) acetamide, 2-ethyl-6-methylaniline, 4-amino-3-ethyl-5-methylpheno, 2-ethyl-6-methylcychexa-2,5-diene-1,4-diol, 2-ethyl-6-methylcychexa-2,5-diene-1,4-dione, N-(2-ethyl-6-methylphenyl)hydroxylamine and 1-ethyl-3-methyl-2-nitrobenzene. The synergistic action of Sphingomonas, Rhodococcus, Bacillus, Arthrobacter, Methylobacillus, and Streptomyces probably lead to the gradual decomposition of acetochlor into H₂O and CO₂. Comparative analysis of functional genes in the KEGG metabolic pathways showed upregulation of hyaB/hybC, hyaA/hybO, nfsA, nfnB/nfsB, and nemA in the soil treated with vermicompost. These functional genes could promote -NHOH conversion to -NO₂. Additionally, redundancy analysis revealed that soil organic matter and pH were the main driving factors for bacterial community variation. These findings suggest that vermicompost can be used as a bioremediation measure to reduce acetochlor in black soil.

Despite the crucial role of microbial communities in agroecosystem functioning, a clear picture of how nitrogen shapes rhizosphere microbial complexity and community structure across diverse maize lines remains elusive. To address this gap, we conducted 16S amplicon sequencing of the rhizosphere microbial communities across a diverse range of maize inbred lines (305 genotypes) and their F1 hybrids (196 genotypes) cultivated in both low-nitrogen (unfertilized) and high-nitrogen (fertilized) soils. Our findings reveal that N fertilizer treatment had contrasting effects on the rhizosphere microbial communities of inbreds and hybrids. N fertilization increased alpha diversity but decreased the abundance of Pseudomonas taxa in inbred lines, while the opposite was true for hybrids. The proportion of variance determined by plant host factors was also better explained under low-N, demonstrating that N fertilization reduced the influence of the host over the rhizosphere microbial community. Microbial networks revealed significant differences in the number of nodes and clustering coefficients between the rhizosphere microbial communities of inbred and hybrid maize, with these differences being further differentiated by changes in nitrogen levels. Overall, our study reveals the interplay among rhizosphere microbiomes, abiotic stress induced by low soil nitrogen, and plant host factors facilitating the identification of stable microbial communities in response to environmental stress. These findings contribute to the potential engineering of resilient microbial consortia highlighting the importance of the influence of plant genotype and the environment on the rhizosphere microbiome.

Nitrous oxide (N₂O) is one of the most important climate-forcing gases, and a large portion of global anthropogenic N₂O emissions come from agricultural soils. Yet, how contrasting global change factors and agricultural management can interact to drive N₂O emissions remains poorly understood. Here, conducted within a rice–wheat cropping system, we combined a two-year field experiment with two pot experiments to investigate the influences of elevated atmospheric carbon dioxide (eCO₂) and crop straw addition to soil in altering N₂O emissions under wheat cropping. Our analyses identified consistent and significant interactions between eCO₂ and straw addition, whereby eCO₂ increased N₂O emissions (+ 19.9%) only when straw was added, and independent of different N fertilizer gradients and wheat varieties. Compared with the control (i.e., ambient CO₂ without straw addition), eCO₂ + straw addition increased N₂O emission by 44.7% and dissolved organic carbon to total dissolved nitrogen (DOC/TDN) ratio by 115.3%. Similarly, eCO₂ and straw addition significantly impacted soil N₂O-related microbial activity. For instance, the ratio of the abundance of N₂O production genes (i.e., nirK and nirS) to the abundance of the N₂O reduction gene (i.e., nosZ) with straw addition was 26.0% higher than that without straw under eCO₂. This indicates an increased denitrification potential and suggests a change in the stoichiometry of denitrification products, affecting the balance between N₂O production and reduction, leading to an increase in N₂O emissions. Taken together, our results emphasize the critical role of the interaction between the specific agronomic practice of straw addition and eCO₂ in shaping greenhouse gas emissions in the wheat production system studied, and underline the need to test the efficacy of greenhouse gas mitigation measures under various management practices and global change scenarios.

Graphical abstract

Nitric oxide (NO) is a key substance in atmospheric chemistry, influencing the formation and destruction of tropospheric ozone and the atmosphere's oxidizing capacity. It also affects the physiological functions of organisms. NO is produced, consumed, and emitted by soils, the effects of soil NO concentrations on microbial C and N cycling and associated trace gas fluxes remain largely unclear. This study describes a new automated 12-chamber soil mesocosm system that dynamically changes incoming airflow composition. It was used to investigate how varying NO concentrations affect soil microbial C and N cycling and associated trace gas fluxes under different moisture conditions (30% and 50% WFPS). Based on detection limits for NO, NO₂, N₂O, and CH₄ fluxes of < 0.5 µg N or C m⁻² h⁻¹ and for CO₂ fluxes of < 1.2 mg C m⁻² h⁻¹, we found that soil CO₂, CH₄, NO, NO₂, and N₂O were significantly affected by different soil moisture levels. After 17 days cumulative fluxes at 50% WFPS increased by 40, 400, and 500% for CO₂, N₂O, and CH₄, respectively, when compared to 30% WFPS. However, cumulative fluxes for NO, and NO₂, decreased by 70, and 40%, respectively, at 50% WFPS when compared to 30% WFPS. Different NO concentrations tended to decrease soil C and N fluxes by about 10–20%. However, with the observed variability among individual soil mesocosms and minor fluxes change. In conclusion, the developed system effectively investigates how and to what extent soil NO concentrations affect soil processes and potential plant–microbe interactions in the rhizosphere.

Denitrification is a major source of the greenhouse gas N₂O. As a result of spatial heterogeneity of organic carbon, oxygen and nitrate, denitrification is observed even under relatively dry conditions. However, it is unclear whether denitrification potentials of microbial communities exhibit spatial patterns relative to variations in distance to soil pores facilitating oxygen exchange and nutrient transfer. Thus, we determined genetic and process-level denitrification potentials in two contrasting soils, a cropland and a grassland, with respect to the distance to air-filled pores. An X-ray computed tomography aided sampling strategy was applied for precise sampling of soil material. Process-level and genetic denitrification potentials in both soils were spatially variable, and similar with respect to distance to macropores. In the cropland soil, a minor increase of process-level potentials with distance to pores was observed and related to changes in NO₃⁻ rather than oxygen availability. Genetic denitrification potentials after the short-term incubations revealed a certain robustness of the local community. Thus, distance to macropores has a minor impact on denitrification potentials relative to the observed spatial variability. Our findings support the notion that the impact of macropore induced changes of the environmental conditions in soil does not overrule the high spatial variability due to other controlling factors, so that the rather minor proportion of spatial heterogeneity of functional genes and activity potentials related to macropore distances in soil need not be considered explicitly in modelling denitrification.