Correction: Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity

Forest Soil pH and Dissolved Organic Matter Aromaticity Are Distinct Drivers for Soil Microbial Community and Carbon Metabolism Potential

The ecological niche separation of microbial interactions in forest ecosystems is critical to maintaining ecological balance and biodiversity and has yet to be comprehensively explored in microbial ecology. This study investigated the impacts of soil properties on microbial interactions and carbon metabolism potential in forest soils across 67 sites in China. Using redundancy analysis and random forest models, we identified soil pH and dissolved organic matter (DOM) aromaticity as the primary drivers of microbial interactions, representing abiotic conditions and resource niches, respectively. Our network comparison results highlighted significant differences in microbial interactions between acidic and non-acidic soils, suggesting the critical influences of abiotic conditions on microbial interactions. Conversely, abiotic resource niches played a more pivotal role in shaping the carbon metabolism of soil microbes, supporting the concept that resource niche-based processes drive microbial carbon cycling. Additionally, we demonstrated that microbial interactions contributed significantly to ecosystem function stability and served as potential ecological indicators of microbial functional resilience under environmental stress. These insights emphasize the critical need to preserve microbial interactions for effective forest ecosystem management and projection of ecological outcomes in response to future environmental changes.

Continuous cropping of Patchouli alters soil physiochemical properties and rhizosphere microecology revealed by metagenomic sequencing

Continuous cropping (CC) profoundly impacts soil ecosystems, including changes in soil factors and the structure and stability of microbial communities. These factors are interrelated and together affect soil health and plant growth. In this research, metagenomic sequencing was used to explore the effects of CC on physicochemical properties, enzyme activities, microbial community composition, and functional genes of the rhizosphere soil of patchouli. We found that this can lead to changes in various soil factors, including the continuous reduction of pH andNH 4 + -N and the unstable changes of many factors. In addition, S-PPO enzyme activity increased significantly with the cropping years, but S-NAG increased in the first 2 years and decreased in the third cropping year. Metagenomic sequencing results showed that CC significantly changed the diversity and composition of rhizosphere microbial communities. The relative abundance of Pseudomonas and Bacteroides decreased substantially from the phylum level. At the genus level, the number of microbial genera specific to the zero-year cropping (CK) and first (T1), second (T2), and third (T3) years decreased significantly, to 1798, 172, 42, and 44, respectively. The abundance of many functional genes changed, among which COG0823, a gene with the cellular process and signaling functions, significantly increased after CC. In addition,NH 4 + -N, S-CAT, S-LAP, and SOC were the main environmental factors affecting rhizosphere-dominant microbial communities at the phylum level, while pH, SOC, and AK were the key environmental factors affecting rhizosphere functional genes of Pogostemon cablin. In summary, this study showed the dynamic changes of soil factors and rhizosphere microorganisms during CC, providing a theoretical basis for understanding the formation mechanism and prevention of CC obstacles and contributing to the formulation of scientific soil management and fertilization strategies.

Effect of Nitrogen on Microbial Communities of Purple Mudstone Weathering Products in Southwest China: A Column Experiment

Nitrogen application significantly affects microorganisms in agricultural ecosystems. However, it is still unclear how nitrogen application affects soil chemical properties and microbial communities in purple mudstone weathering products. In this study, a field soil column experiment was conducted in a typical purple soil area with four nitrogen fertilizer application gradients of 0 [CK], 280 [N1], 560 [N2], and 840 [N3] N kg ha-1. Nitrogen addition decreased the bacterial chao1 value and increased the bacterial evenness index. For both α- and β-diversity, the effect of nitrogen addition on bacteria was much greater than that on fungi. Nitrogen addition significantly increased the relative abundance of Proteobacteria, Gemmatimonadetes, Bacteroidetes, and Ascomycota and decreased the relative abundance of Actinobacteria, Cyanobacteria, and Basidiomycota. Both pH and TC are the most important soil chemical properties influencing the bacterial and fungal communities. With the increases in the nitrogen application rate, the co-occurrence network complexity increased and then decreased. In summary, nitrogen fertilizer application could significantly change the soil chemical properties, microbial community diversity, composition, and co-occurrence network of purple mudstone weathering products. Among them, the N2 treatment (560 N kg∙ha-1) can more effectively stimulate the soil nutrients, enhance microbial network complexity, and promote further weathering of purple mudstone.

Metagenomics reveals the response of desert steppe microbial communities and carbon-nitrogen cycling functional genes to nitrogen deposition

Introduction

Nitrogen (N) deposition seriously affects the function of carbon (C) and N cycling in terrestrial ecosystems by altering soil microbial communities, especially in desert steppe ecosystems. However, there is a need for a comprehensive understanding of how microorganisms involved in each C and N cycle process respond to N deposition.

Methods

In this study, shotgun metagenome sequencing was used to investigate variations in soil C and N cycling-related genes in the desert steppe in northern China after 6 years of the following N deposition: N0 (control); N30 (N addition 30 kg ha-1 year-1): N50 (N addition 50 kg ha-1 year-1).

Results

N deposition significantly increased the relative abundance of Actinobacteria (P < 0.05) while significantly decreased the relative abundances of Proteobacteria and Acidobacteria (P < 0.05). This significantly impacted the microbial community composition in desert steppe soils. The annual addition or deposition of 50 kg ha-1 year-1 for up to 6 years did not affect the C cycle gene abundance but changed the C cycle-related microorganism community structure. The process of the N cycle in the desert steppe was affected by N deposition (50 kg ha-1 year-1), which increased the abundance of the pmoA-amoA gene related to nitrification and the nirB gene associated with assimilation nitrite reductase. There may be a niche overlap between microorganisms involved in the same C and N cycling processes.

Discussion

This study provides new insights into the effects of N deposition on soil microbial communities and functions in desert steppe and a better understanding of the ecological consequences of anthropogenic N addition.

Changes in Soil Bacterial Community and Function in Winter Following Long-Term Nitrogen (N) Deposition in Wetland Soil in Sanjiang Plain, China

N deposition is a key factor affecting the composition and function of soil microbial communities in wetland ecosystems. Previous studies mainly focused on the effects of N deposition in the soil during the growing season (summer and autumn). Here, we focused on the response of the soil microbial community structure and function in winter. Soil from the Sanjiang Plain wetland, China, that had been treated for the past 11 years by using artificial N deposition at three levels (no intervention in N0, N deposition with 4 g N m-2 yr-1 in N1, and with 8 g N m-2 yr-1 in N2). Soil characteristics were determined and the bacterial composition and function was characterized using high-throughput sequence technology. The N deposition significantly reduced the soil bacterial diversity detected in winter compared with the control N0, and it significantly changed the composition of the bacterial community. At the phylum level, the high N deposition (N2) increased the relative abundance of Acidobacteria and decreased that of Myxococcota and Gemmatimonadota compared with N0. In soil from N2, the relative abundance of the general Candidatus_Solibacter and Bryobacter was significantly increased compared with N0. Soil pH, soil organic carbon (SOC), and total nitrogen (TN) were the key factors affecting the soil bacterial diversity and composition in winter. Soil pH was correlated with soil carbon cycling, probably due to its significant correlation with aerobic_chemoheterotrophy. The results show that a long-term N deposition reduces soil nutrients in winter wetlands and decreases soil bacterial diversity, resulting in a negative impact on the Sanjiang plain wetland. This study contributes to a better understanding of the winter responses of soil microbial community composition and function to the N deposition in temperate wetland ecosystems.

Response of soil microbial communities and rice yield to nitrogen reduction with green manure application in karst paddy areas

Fertilizer application practices are one of the major challenges facing agroecology. The agrobenefits of combined application of green manure and chemical fertilizers, and the potential of green manure to replace chemical fertilizers are now well documented. However, little is known about the impact of fertilization practices on microbial communities and tice yield. In this study, the diversity of bacterial and fungal communities, symbiotic networks and their relationship with soil function were analyzed in five fertilization treatments (N: 100% nitrogen fertilizer alone; M: green manure alone; MN₆₀: green manure couple with 60% nitrogen fertilizer, MN₈₀: green manure couple with 80% nitrogen fertilizer; and MN₁₀₀: green manure couple with 100% nitrogen fertilizer). First, early rice yield was significantly higher by 12.6% in MN₁₀₀ treatment in 2021 compared with N. Secondly, soil bacterial diversity showed an increasing trend with increasing N fertilizer application after green manure input, however, the opposite was true for fungal diversity. Microbial interaction analysis showed that different fertilizer applications changed soil microbial network complexity and fertilizer-induced changes in soil microbial interactions were closely related to soil environmental changes. Random forest models further predicted the importance of soil environment, microorganisms and rice yield. Overall, nitrogen fertilizer green manure altered rice yield due to its effects on soil environment and microbial communities. In the case of combined green manure and N fertilizer application, bacteria and fungi showed different responses to fertilization method, and the full amount of N fertilizer in combination with green manure reduced the complexity of soil microbial network. In contrast, for more ecologically sensitive karst areas, we recommend fertilization practices with reduced N by 20-40% for rice production. Graphical Abstract.