Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2024.04.26.591135

Unveiling the dominant role of soil pH in shaping nitrogen cycling microbial gene abundances: Insights from 65-years of chemical fertilizer selection in acidic grassland meadow

Mitsuta, A.·Lourenco, K. S.·Ros, M.·Uchida, Y.·Kuramae, E. E.
View original source ↗Export metadata ↓

Abstract

Understanding the microbial processes driving the nitrogen (N) cycle is crucial for enhancing plant productivity and mitigating environmental pollution. The long-term application of synthetic fertilizers induces significant alterations in the microbial community functions. Microbes inhabiting acidic soils may exhibit distinct responses to chemical fertilizer application compared to soils with neutral pH. However, the chronic or occasional changes resulting from repeated nutrient flushes due to fertilizer application remain insufficiently elucidated, especially in acidic grasslands. Therefore, our study was on an acidic semi-natural grassland, where the soil was subjected to chemical fertilizer P (superphosphate), K (potassium sulfate), PK, N (ammonium nitrate), NPK, PK+N (PK applied in spring and N applied once in summer) over a span of 65 years. Gene abundances associated with the N-cycle (amoA, nifH, nirK, nirS, and nosZ) were quantified at seven different time points throughout the year considering the temporal effect caused by fertilizer application. Our findings reveal that in the long term, soil pH emerged as the predominant factor influencing the gene abundance related to N-fixation and denitrification outweighing the impact of nutrient availability. Notably, the application of N fertilizer had a positive effect on the abundance of nitrifiers, while the abundance of denitrifiers decreased due to soil acidification induced by fertilizer application. In summary, our study highlights that the microbial community involved in N cycling is more sensitive to the difference in soil pH shaped by long-term fertilizer application rather than to the direct impact of fertilizer application. HighlightO_LISeasonal sampling confirmed the long-term effect of fertilizer on microbial N-cycling genes C_LIO_LIFertilizer types shaped soil pH, consequently impacted on diazotrophs and denitrifies abundances C_LIO_LIAbundance of denitrifying microbe did not explain the increase of N2O emission by N fertilizer C_LIO_LIN2O emission was positively correlated with AOA abundance C_LI

Source connections

Explore related subjects

microbiologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Mitsuta, A., Lourenco, K. S., Ros, M., Uchida, Y., Kuramae, E. E.. 2024-04-26. Unveiling the dominant role of soil pH in shaping nitrogen cycling microbial gene abundances: Insights from 65-years of chemical fertilizer selection in acidic grassland meadow. https://doi.org/10.1101/2024.04.26.591135

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

A population-scale landscape of the subgingival microbiome reveals divergent routes to periodontal dysbiosis

Periodontitis is an archetypical mucosal inflammatory disease in which microbiome dysbiosis at the tooth-epithelial interface interacts with host genetic and behavioral risk factors to drive immune-mediated tissue destruction. Although subgingival microbiome compositional shifts are thought to parallel disease severity, microbiome variation at the population-level and its relationship to periodontal clinical phenotypes and disease-modifying factors remain poorly defined. Here, we use unsupervised manifold learning to map the compositional landscape of the subgingival microbiome in 1,355 adults spanning periodontal health to severe periodontitis. We identified eight latent microbiome states organized along a branching continuum from eubiosis to dysbiosis. An intermediate microbial configuration marked ecological destabilization and bifurcation into two distinct periodontitis-associated dysbiotic trajectories, distinguished by links to gingival inflammation and smoking. Although the microbiome trajectories broadly tracked periodontal destruction, a minority of individuals showed discordant microbiome-clinical phenotypes, with some individuals with periodontitis retaining otherwise eubiotic microbiomes enriched for low-abundance pathobionts, while some cases of health or mild disease had highly dysbiotic communities, suggesting distinct host susceptibility. Together, these findings define a population-scale ecological landscape of the subgingival microbiome, reveal divergent trajectories to periodontal dysbiosis, and highlight heterogeneity in the relationship between microbial community structure and clinical disease expression.

microbiology↗
bioRxiv2026

The iron-binding siderophore enterobactin is required for the response of multi-drug resistant Klebsiella pneumoniae to zinc limitation

To persist during infection Klebsiella pneumoniae must overcome nutrient iron and zinc limitation imposed by the host immune system through a process called nutritional immunity. Secreted small molecule siderophores are a major virulence determinant of Klebsiella pneumoniae pathogenesis and are presumed to overcome nutritional immunity by binding iron for bacterial acquisition. In this work, we set out to identify how a multi-drug resistant K. pneumoniae grows in zinc limited environments. Using unbiased transcriptomics, proteomics, and an arrayed transposon screen, we identified that synthesis and uptake of the siderophore enterobactin is required to allow for growth in low zinc conditions. Iron-specific chelators did not replicate this phenotype and addition of supplemental iron through heme in growth media could not complement severe growth defects of enterobactin mutant K. pneumoniae experiencing zinc limitation. Finally, zinc starvation induced enterobactin production independent of the canonical zinc uptake regulator (Zur) transcription factor suggesting an unidentified regulatory mechanism by which Gram-negative pathogens may respond to zinc stress. Together, these studies expand the role of enterobactin beyond iron regulation and highlight a previously unreported link between iron and zinc homeostasis in Klebsiella pneumoniae.

microbiology↗
bioRxiv2026

A microbiota-derived protease links phage susceptibility to host epithelial responses

Bacteriophages are major ecological drivers of gut microbial ecology, yet whether bacterial mechanisms that determine phage susceptibility have consequences for the mammalian host remains poorly understood. Here, we identify dipeptidyl peptidase 11 (Dpp11a), the predominant active serine protease of the prevalent gut commensal Phocaeicola vulgatus, as an unexpected bacterial defence factor. Dpp11a protects against environmental proteases and confers resistance to bacteriophage infection. Metatranscriptomic analyses further reveal increased expression of both dpp11a and P. vulgatus-associated phage transcripts in ulcerative colitis stool samples, indicating that both components of this interaction are transcriptionally active in disease-associated human microbiomes. Using the microfluidic gut-on-a-chip co-culture model HuMiX, we show that the absence of Dpp11 is accompanied by altered epithelial tight-junction remodelling during phage-bacterial infection. Together, our findings reveal that the consequences of bacterial phage defence can extend beyond phage-bacterium interactions to the mammalian epithelium.

microbiology↗