Different Amounts of Nitrogen Fertilizer Applications Alter the Bacterial Diversity and Community Structure in the Rhizosphere Soil of Sugarcane

Changes and driving factors of microbial community composition and functional groups during the decomposition of Pinus massoniana deadwood

Clarifying changes in the microbial community in deadwood at different stages of decomposition is crucial for comprehending the role of deadwood in the biogeochemical processes and the sustainability of forest development. However, there have been no reports on the dynamics of microbial community during the decomposition of Pinus massoniana. We used the "space-for-time" substitution to analyze the characteristics of microbial community changes and the key influencing factors in the P. massoniana deadwood during different decomposition stages by 16S and ITS rRNA gene sequencing. The results suggest that the microbial community structure of the early decomposition (decay class I) was significantly different from the other decay classes, while the diversity and richness of the microbial community were the highest in the late decomposition (decay class V). The Linear Discriminant Analysis Effect Size analysis revealed that most bacterial and fungal taxa were significantly enriched in decay classes I and V deadwood. During the initial stages of decomposition, the relative abundance of the bacterial functional group responsible for carbohydrate metabolism was greater than the later stages. As decomposition progressed, the relative abundance of saprophytic fungi gradually decreased, and there was a shift in the comparative abundance of mixed saprophytic-symbiotic fungi from low to high before eventually decreasing. Total organic carbon, total nitrogen, carbon-to-nitrogen ratio, total potassium, total phenol, condensed tannin, lignin, and cellulose were significantly correlated with microbial community structure, with the carbon-to-nitrogen ratio having the greatest effect. Our results indicate that the physicochemical properties of deadwood, microbial community structural composition and functional group changes were related to the decay class, among which the carbon-to-nitrogen ratio may be an important factor affecting the composition and diversity of microbial communities.

Drive soil nitrogen transformation and improve crop nitrogen absorption and utilization - a review of green manure applications

Green manure application presents a valuable strategy for enhancing soil fertility and promoting ecological sustainability. By leveraging green manures for effective nitrogen management in agricultural fields can significantly reduce the dependency of primary crops on chemical nitrogen fertilizers, thereby fostering resource efficiency. This review examines the current advancements in the green manure industry, focusing on the modulation of nitrogen transformation in soil and how crops absorb and utilize nitrogen after green manure application. Initially, the influence of green manure on soil nitrogen transformation is delineated, covering processes such as soil nitrogen immobilization, and mineralization, and losses including NH3, N2O, and NO3 --N leaching. The review then delves into the effects of green manure on the composition and function of soil microbial communities, highlighting their role in nitrogen transformation. It emphasizes the available nitrogen content in the soil, this article discussing nitrogen uptake and utilization by plants, including aspects such as nitrogen translocation, distribution, the root system, and the rhizosphere environment of primary crops. This provides insights into the mechanisms that enhance nitrogen uptake and utilization when green manures are reintroduced into fields. Finally, the review anticipates future research directions in modulating soil nitrogen dynamics and crop nitrogen uptake through green manure application, aiming to advance research and the development of the green manure sector.

Biochar alleviates the crop failure of rice production induced by low-nitrogen cultivation mode by regulating the soil microbes taxa composition

To improve the nitrogen utilization efficiency and a series of environmental problems caused by excessive application of nitrogen fertilizer, actual agricultural production often reduced the usage ratio of nitrogen fertilizer. However, the reduction in nitrogen fertilizer not only affects the soil microenvironment but also leads to adverse effects on rice yield. Due to its unique properties, biochar can regulate soil nutrient distribution and significantly affect soil microbial community structure/functions. To further understand the effects of different levels of biochar on soil nutrient indicators, soil microorganisms and crop growth under the nitrogen-reduction condition, our experiment with four groups was set up as followed: 0%, 2.5% and 5% biochar application rates with 99 kg/hm2 nitrogen fertilizer and one control group (the actual fertilizer standard used in the field:110 kg/hm2) without no exogenous biochar supplement. The rice yield and soil nutrient indexes were observed, and the differences between groups were analyzed based on multiple comparisons. 16S ribosomal RNA and ITS sequencing were used to analyze the community structure of soil bacteria and fungi. Redundancy analysis was performed to obtain the correlation relationships between microbial community marker species, soil nutrient indexes, and rice yield. Path analysis was used to determine the mechanism by which soil nutrient indexes affect rice yield. The results showed that a higher application rate of biochar led to a significant increased trend in the soil pH, organic matter and total nitrogen content. In addition, a high concentration of biochar under nitrogen-reduction condition decreased the soil bacterial diversity but elevated the fungal diversity. Different concentrations of biochar resulted in these changes in the relative abundance of soil bacteria/fungi but did not alter the dominant species taxa. Taken together, appropriate usage for biochar under the nitrogen-reduction background could induce alteration in soil nutrient indicators, microbial communities and crop yields. These results provide a theoretical basis for exploring scientific, green and efficient fertilization strategies in the rice cultivation industry. Notably, the interaction relationship between rhizosphere microorganisms in rice and soil microbial taxa are not yet clear, so further research on its detailed effects on rice production is needed. In addition, the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis for the physiological functions of the soil microbes could only predict the potential metabolic pathways. Therefore, the next-generation metagenome techonology might be performed to explore detailed metabolic differences and accurate taxa alteration at the "species" level.

Interkingdom multi-omics analysis reveals the effects of nitrogen application on growth and rhizosphere microbial community of Tartary buckwheat

Tartary buckwheat (Fagopyrum tataricum Gaertn.) is an important pseudocereal crop with excellent edible, nutritional and medicinal values. However, the yield of Tartary buckwheat (TB) is very low due to old-fashioned cultivation techniques, particularly unreasonable application of nitrogen fertilizer. To improve the understanding on the theories of nitrogen use in TB, the effects of nitrogen application on growth, as well as chemical properties and microbial community of rhizosphere soil were investigated in this study. Nitrogen application could promote the plant height, stem diameter, nitrogen accumulation and yield of TB. The relative abundance and diversity of bacteria and fungi in the rhizosphere soil of TB were improved by nitrogen fertilizer. Nitrogen application increased the abundance of beneficial bacteria such as Lysobacter and Sphingomonas in rhizosphere soil, and decreased the abundance of pathogenic fungi such as Fusarium and Plectosphaerella. The results indicated that nitrogen application changed the distribution of microbial communities in TB rhizosphere soil. Furthermore, the specific enriched or depleted microorganisms in the rhizosphere soil of four TB varieties were analyzed at OTU level. 87 specific nitrogen-responsive genes with sequence variation were identified in four varieties by integrating genomic re-sequencing and transcriptome analysis, and these genes may involve in the recruitment of specific rhizosphere microorganisms in different TB varieties. This study provided new insights into the effects of nitrogen application on TB growth and rhizosphere microbial community, and improved the understanding on the mechanisms of TB root-microbe interactions.

Effects of peach branch organic fertilizer on the soil microbial community in peach orachards

Peach branches is a by-product of peach industry. Making peach branch waste into peach branch organic fertilizer (PBOF) is a promising strategy of ecological utilization. In this study, the effects of PBOF on the yield and quality of peach fruit, chemical properties of bulk soil, and soil bacterial communities were investigated in a peach orchard. The results showed that the yield and sugar/acid ratio of two high-level PBOF treatments (SDH.4 and SKR.4) was higher than no fertilization treatment (CK), but there was no significant difference compared to the commercial organic fertilizer treatment (SYT.4). Moreover, the three fertilizer treatments increased soil nutrients such as soil organic matter (SOM) and available potassium (AK), compared to CK. Furthermore, PBOF increased the relative abundance of beneficial bacteria, and enhanced the soil bacterial co-occurrence pattern and the potential function of bacterial communities to degrade exogenous compounds. In addition, thanks to the local policy of encouraging the use of PBOF, the use cost of PBOF is lower than commercial organic fertilizer, which is conducive to the development of ecological agriculture.

Research progress and hotspot analysis of rhizosphere microorganisms based on bibliometrics from 2012 to 2021

Rhizosphere microorganisms are important organisms for plant growth promotion and bio-control. To understand the research hot topics and frontier trends of rhizosphere microorganisms comprehensively and systematically, we collected 6,056 publications on rhizosphere microorganisms from Web of Science and performed a bibliometric analysis by CiteSpace 6.1.3 and R 5.3.1. The results showed that the total number of references issued in this field has been on the rise in the past decades. China, India, and Pakistan are the top three countries in terms of the number of articles issued, while Germany, the United States, and Spain were the countries with the highest number of co-published papers with other countries. The core research content in this field were the bio-control, bacterial community, ACC deaminase, phytoremediation, induced systematic resistance, and plant growth promotion. Seeding growth, Bacillus velezensis, plant-growth, and biological-control were currently and may be the highlights in the field of rhizosphere microorganisms research for a long time in the future. The above study results quantitatively, objectively, and scientifically described the research status and research focus of rhizosphere microorganisms from 2012 to 2021 from the perspective of referred papers, with a view to promoting in-depth research in this field and providing reference information for scholars in related fields to refine research trends and scientific issues.

Effects of Bacillus subtilis A-5 and its fermented γ-polyglutamic acid on the rhizosphere bacterial community of Chinese cabbage

Chemical fertilizer reduction combined with novel and green agricultural inputs has become an important practice to improve microecological health in agricultural production. Given the close linkages between rhizosphere processes and plant nutrition and productivity, understanding how fertilization impacts this critical zone is highly important for optimizing plant–soil interactions and crop fitness for agricultural sustainability. Here, by using a pot experimental system, we demonstrated that nitrogen fertilizer reduction and microbial agent application promoted plant fitness and altered the microbial community structure in the rhizosphere soil with the following treatments: no fertilization, CK; conventional chemical fertilizer, CF; 30% reduced nitrogen fertilizer, N; 30% reduced nitrogen fertilizer with pure γ-PGA, PGA; 30% reduced nitrogen fertilizer with Bacillus subtilis A-5, A5; 30% reduced nitrogen fertilizer with γ-PGA fermentation broth, FJY. The PGA, A5, and FJY treatments all significantly promoted crop growth, and the FJY treatment showed the strongest positive effect on Chinese cabbage yield (26,385.09 kg/hm²) (P < 0.05). Microbial agents affected the α diversity of the rhizosphere bacterial community; the addition of B. subtilis A-5 (A5 and FJY treatments) significantly affected rhizospheric bacterial community structure. Urease activity and soil pH were the key factors affecting bacterial community structure and composition. The FJY treatment seemed to influence the relative abundances of important bacterial taxa related to metabolite degradation, predation, and nitrogen cycling. This discovery provides insight into the mechanism underlying the effects of microbial agent inputs on rhizosphere microbial community assembly and highlights a promising direction for the manipulation of the rhizosphere microbiome to yield beneficial outcomes.

Unraveling Nitrogen Fixing Potential of Endophytic Diazotrophs of Different Saccharum Species for Sustainable Sugarcane Growth

Sugarcane (Saccharum officinarum L.) is one of the world’s highly significant commercial crops. The amounts of synthetic nitrogen (N₂) fertilizer required to grow the sugarcane plant at its initial growth stages are higher, which increases the production costs and adverse environmental consequences globally. To combat this issue, sustainable environmental and economic concerns among researchers are necessary. The endophytic diazotrophs can offer significant amounts of nitrogen to crops through the biological nitrogen fixation mediated nif gene. The nifH gene is the most extensively utilized molecular marker in nature for studying N₂ fixing microbiomes. The present research intended to determine the existence of novel endophytic diazotrophs through culturable and unculturable bacterial communities (EDBCs). The EDBCs of different tissues (root, stem, and leaf) of five sugarcane cultivars (Saccharum officinarum L. cv. Badila, S. barberi Jesw.cv Pansahi, S. robustum, S. spontaneum, and S. sinense Roxb.cv Uba) were isolated and molecularly characterized to evaluate N₂ fixation ability. The diversity of EDBCs was observed based on nifH gene Illumina MiSeq sequencing and a culturable approach. In this study, 319766 operational taxonomic units (OTUs) were identified from 15 samples. The minimum number of OTUs was recorded in leaf tissues of S. robustum and maximum reads in root tissues of S. spontaneum. These data were assessed to ascertain the structure, diversity, abundance, and relationship between the microbial community. A total of 40 bacterial families with 58 genera were detected in different sugarcane species. Bacterial communities exhibited substantially different alpha and beta diversity. In total, 16 out of 20 genera showed potent N₂-fixation in sugarcane and other crops. According to principal component analysis (PCA) and hierarchical clustering (Bray–Curtis dis) evaluation of OTUs, bacterial microbiomes associated with root tissues differed significantly from stem and leaf tissues of sugarcane. Significant differences often were observed in EDBCs among the sugarcane tissues. We tracked and validated the plethora of individual phylum strains and assessed their nitrogenase activity with a culture-dependent technique. The current work illustrated the significant and novel results of many uncharted endophytic microbial communities in different tissues of sugarcane species, which provides an experimental system to evaluate the biological nitrogen fixation (BNF) mechanism in sugarcane. The novel endophytic microbial communities with N₂-fixation ability play a remarkable and promising role in sustainable agriculture production.

Untangling the Rhizosphere Bacterial Community Composition and Response of Soil Physiochemical Properties to Different Nitrogen Applications in Sugarcane Field

Minimizing the use of chemical fertilizers and investigating an appropriate ecofriendly level of nitrogen fertilizer is the key to sustainable agriculture. Sugarcane is the main cash crop of China, especially in the Guangxi region. Information regarding the effect of different nitrogen levels on sugarcane rhizosphere microbiota is still limited. In this study, we evaluated the effect of four different levels of nitrogen fertilizers on rhizosphere bacterial composition using high throughput sequencing, along with soil physiochemical properties, sugarcane agronomic and yield performance. The four treatment combinations were CK (no fertilizers), L (Low, 100 kg ha^–1), M (Medium, 150 kg ha^–1), and H (High, 200 kg ha^–1). The results showed that M nitrogen application significantly altered the rhizosphere bacterial community, soil properties, and sugarcane yield. The richness and evenness of the bacterial community were higher in M treatment than CK. In M treatment important bacterial phyla Acidobacteria and Proteobacteria increased by 47 and 71%, respectively; and at genus level, Acidothermus and Bradyrhizobium increased by 77.2 and 30.3%, respectively, compared to CK. Principal component analysis (PCA) and cluster analysis further confirmed the level of differences among the treatments. The PCA analysis explained 80% of the total variation among the treatments. Spearmen correlation heatmap showed that environmental factors such as pH, AP (available phosphorous), AK (available potassium), and SCAT (soil catalase) were the key factors impacting sugarcane rhizosphere microbiome composition. The H and L nitrogen application alter the bacterial community and sugarcane performance but the M nitrogen application appears to be ecofriendly, productive, and an appropriate nitrogen application rate that could be further used in the Guangxi region.

Soil pH: a key edaphic factor regulating distribution and functions of bacterial community along vertical soil profiles in red soil of pomelo orchard

Background

Soil microbes exist throughout the soil profile and those inhabiting topsoil (0–20 cm) are believed to play a key role in nutrients cycling. However, the majority of the soil microbiology studies have exclusively focused on the distribution of soil microbial communities in the topsoil, and it remains poorly understood through the subsurface soil profile (i.e., 20–40 and 40–60 cm). Here, we examined how the bacterial community composition and functional diversity changes under intensive fertilization across vertical soil profiles [(0–20 cm (RS1), 20–40 cm (RS2), and 40–60 cm (RS3)] in the red soil of pomelo orchard, Pinghe County, Fujian, China.

Results

Bacterial community composition was determined by 16S rRNA gene sequencing and interlinked with edaphic factors, including soil pH, available phosphorous (AP), available nitrogen (AN), and available potassium (AK) to investigate the key edaphic factors that shape the soil bacterial community along with different soil profiles. The most dominant bacterial taxa were Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Crenarchaeota, and Bacteriodetes. Bacterial richness and diversity was highest in RS1 and declined with increasing soil depth. The distinct distribution patterns of the bacterial community were found across the different soil profiles. Besides, soil pH exhibited a strong influence (pH ˃AP ˃AN) on the bacterial communities under all soil depths. The relative abundance of Proteobacteria, Actinobacteria, Crenarchaeota, and Firmicutes was negatively correlated with soil pH, while Acidobacteria, Chloroflexi, Bacteriodetes, Planctomycetes, and Gemmatimonadetes were positively correlated with soil pH. Co-occurrence network analysis revealed that network topological features were weakened with increasing soil depth, indicating a more stable bacterial community in the RS1. Bacterial functions were estimated using FAPROTAX and the relative abundance of functional bacterial community related to metabolic processes, including C-cycle, N-cycle, and energy production was significantly higher in RS1 compared to RS2 and RS3, and soil pH had a significant effect on these functional microbes.

Conclusions

This study provided the valuable findings regarding the structure and functions of bacterial communities in red soil of pomelo orchards, and highlighted the importance of soil depth and pH in shaping the soil bacterial population, their spatial distribution and ecological functioning. These results suggest the alleviation of soil acidification by adopting integrated management practices to preserve the soil microbial communities for better ecological functioning.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02452-x.