Low Nitrogen Fertilization Alter Rhizosphere Microorganism Community and Improve Sweetpotato Yield in a Nitrogen-Deficient Rocky Soil

Soil diazotrophs sustain nitrogen fixation under high nitrogen enrichment via adjustment of community composition

Biological nitrogen (N) fixation, an important pathway of N, inputs from the atmosphere to Earth's ecosystems, is well demonstrated to decline under N input. However, it remains unclear why N fixers sustain N fixation in many forests under high atmospheric N deposition. To address this knowledge gap, we analyzed the response of the diazotroph community to low N loads (short-term and low N addition; 3-year N addition at the rates of 25-50 kg N ha-1 year-1) vs high loads (chronic and high N addition; 9-year N addition at the rate of 150 kg N ha-1 year-1) in forest soils using high-throughput sequencing. Rates of N fixation decreased under low and high N loads (by 13%-27% and 10%-12%, respectively). Richness and alpha diversity (ACE and Chao1) of the soil diazotroph community decreased under low but not high N loads. Approximately 67.1%-74.4% of the nifH gene sequences at the OTU level overlapped between the control and low N loads, but only 52.0%-53.6% of those overlapped between the control and high N loads, indicating a larger shift of diazotroph community composition under high N loads. Low N loads increased soil NH4+ concentrations, which decreased diazotroph community richness, diversity, and N fixation rates, whereas the increased soil NH4+ concentrations under high N loads did not have negative impacts on the structure and function of the diazotroph community. These findings indicate that diazotrophs sustain N fixation under high N deposition via adjustment of their community composition in forest soils.

IMPORTANCE

This study examined the changes in soil diazotroph community under different loads of simulated N deposition and analyzed its relationship with N fixation rates in in five forests using high-throughput sequencing. The magnitudes of N fixation rates reduced by low N loads were higher than those by high N loads. Low N loads decreased richness and diversity of diazotroph community, whereas diazotroph community structure remained stable under high N loads. Compared with low N loads, high N loads resulted in a less similarity and overlap of nifH gene sequences among the treatments and a larger adjustment of diazotroph community. Low N loads increased soil NH4+ concentrations, which decreased diazotroph community richness, diversity, and N fixation rates, whereas the increased soil NH4+ under high N loads did not have negative impacts on diazotroph community structure and N fixation. Based on these findings, it is urgently needed to incorporate the loads of N deposition and the composition of diazotroph community into terrestrial N-cycling models for accurate understanding of N inputs in forest ecosystems.

How lignin biosynthesis responds to nitrogen in plants: a scoping review

Nitrogen (N) plays a critical role in the functioning of key amino acids and synthetic enzymes responsible for the various stages of lignin biosynthesis. However, the precise mechanisms through which N influences lignin biosynthesis have not been fully elucidated. This scoping review explores how lignin biosynthesis responds to N in plants. A systematic search of the literature in several databases was conducted using relevant keywords. Only 44 of the 1842 selected studies contained a range of plant species, experimental conditions, and research approaches. Lignin content, structure, and biosynthetic pathways in response to N are discussed, and possible response mechanisms of lignin under low N are proposed. Among the selected studies, 64.52% of the studies reter to lignin content found a negative correlation between N availability and lignin content. Usually, high N decreases the lignin content, delays cell lignification, increases p-hydroxyphenyl propane (H) monomer content, and regulates lignin synthesis through the expression of key genes (PAL, 4CL, CCR, CAD, COMT, LAC, and POD) encoding miRNAs and transcription factors (e.g., MYB, bHLH). N deficiency enhances lignin synthesis through the accumulation of phenylpropanoids, phenolics, and soluble carbohydrates, and indirect changes in phytohormones, secondary metabolites, etc. This review provides new insights and important references for future studies on the regulation of lignin biosynthesis.

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.

Nitrogen fertilization modulates rice seed endophytic microbiomes and grain quality

The intensive use of chemical fertilizer, particularly nitrogen (N) has resulted in not only markedly increased crop yields but also detrimental effects on ecosystems. Plant microbiomes represent an eco-friendly alternative for plant nutrition and productivity, and the effect of N fertilization on plant and soil microbes has been well studied. However, if and how N fertilization modulates seed endophytic microbiomes and grain quality remains largely unknown. Here, we investigated the effect of different N fertilization rates on rice seed endophytic bacterial and fungal communities as well as on grain quality. Higher bacterial and fungal community diversity and richness, but lower grain protein and amino acid contents were found in seeds of rice treated moderate N fertilization than those treated insufficient or excessive N input. There were also more complex co-occurrence networks, and an enrichment of putative beneficial bacterial taxa in seeds under moderate N application, while there was an opposite trend under the excessive N treatment. In addition, the grain amylose and amylopectin contents were positively correlated with the relative abundance of bacterial and fungal dominant genera, while the grain amino acid contents were negatively correlated with the bacterial dominant genera but positively associated with fungal dominant genera. Together, we demonstrate that moderate N fertilization can enhance bacterial and fungal community colonization in seeds and improve grain eating and cooking qualities. This study extends our knowledge regarding the significant role of rational fertilization on seed-microbe interactions in sustainable agriculture.

Response of rhizosphere microbial community of Chinese chives under different fertilization treatments

Soil microorganisms play an irreplaceable role in agricultural production, however, an understanding of response of soil microorganisms to slow-release and common fertilizer applications is limited. In this study, different amounts of slow- release fertilizer were used to overwintering Chinese chives growing area in a plastic greenhouse to investigate the effects of on rhizosphere soil physicochemical properties and soil microbial communities (bacteria and fungi) of Chinese chives. The result displayed that application of slow-release fertilizer significantly improved soil nutrients, soil enzyme activity, and soil microbial community structure and diversity compared to conventional fertilizer application. Compared with T1 treatment, the content of total nitrogen (TN) and available phosphorus (AP), and the SU-E activity in the soil of T2 (NPK: 62.8 kg · 667 m-2) increased by 42.58%, 16.67%, and 9.70%, respectively, showing the best effects. In addition, soil bacterial diversity index and soil microbial community structure were improved as indicated by increased relative abundance of each species, such as Byssovorax, Sandaracinus, and Cellvibrio. Oppositely, the both soil fungal diversity and the number of species decreased after fertilizationthe relative abundance of Ascomycota increased in each fertilization treatment detected by ITS sequencing. Further, the relative abundance of pathogenic fungi such as Pezizomycetes, Cantharellales, and Pleosporales decreased in the T2 treatment. Principal Coordinates Analysis (PCoA) showed that both the amount of fertilizer applied and the type of fertilizer applied affected the soil microbial community structure. RDA evidenced that soil bacteria, Proteobacteria and Gemmatimonadetes, were closely correlated with soil AN, SOM, and AK. Acidobacteria were closely correlated with soil pH, TN, and AP. Ascomycota was closely correlated with soil pH and TN. In conclusion, the application of slow-release fertilizers and reduced fertilizer applicationcould improve soil physical and chemical properties as well as soil microbial community structure and diversity, contributing to sustainable soil development. The recommended fertilization rate for overwintering Chinese chives is NPK: 62.8 kg · 667 m-2.

Influence of planting yellowhorn (Xanthoceras sorbifolium Bunge) on the bacterial and fungal diversity of fly ash

Phytoremediation is a low-cost solution to fly ash pollution and the rhizosphere interactions between plant roots and the fly ash microbiome were important for the phytoremediation. To analyze the dynamic changes of the rhizosphere microbiome during yellowhorn cultivation in fly ash, the bacterial 16S rRNA gene V3-V4 region and the fungal ITS region of the rhizosphere microbiome were sequenced using Illumina MiSeq technology. The changes in fly ash physicochemical properties and the heavy metal content of different yellowhorn tissues were also analyzed. The results showed that both the bacterial and fungal communities were noticeably different after yellowhorn cultivation compared with the control sample. Proteobacteria and Acidobacteria levels increased (p < 0.05) and Firmicutes and Actinobacteria decreased (p < 0.05) in the bacterial community after yellowhorn cultivation. In the fungal community, Ascomycota and Mortierellomycota decreased (p < 0.05), while Chytridiomycota increased (p < 0.05). The levels of four heavy metals (Cr, Cd, Hg, Pb and As) decreased in the fly ash after yellowhorn cultivation. These metals were absorbed by the yellowhorn plants and accumulated in the fibrous root, taproot, stem and leaf tissues of these plants. Accordingly, the abundance of bacteria that could solubilize heavy metals increased (p < 0.05). In summary, the cultivation of yellowhorn affected the composition of the rhizosphere microbial communities in fly ash, which is of great significance for the biological remediation of fly ash.

Effects of tillage and biochar on soil physiochemical and microbial properties and its linkage with crop yield

Vertisols are clayey soils with a high potential for improving production. Therefore, understanding the impact of tillage and fertilization on soil physicochemical properties and microbial community is essential for improving the vertisols with a high montmorillonite and smectite clay content. A 3-year field experiment was conducted to compare the effects of different tillage and fertilization practices at three depths of the vertisol under the wheat–maize cropping system in the North China Plain. The experimental treatments included rotary tillage without fertilization (R-CK), rotary tillage with chemical nitrogen (N), phosphorus (P), and potassium (K) fertilization (R-NPK), R-NPK plus biochar (R-NPKB), deep tillage without fertilization (D-CK), deep tillage with chemical N, P, and K fertilization (D-NPK), and D-NPK plus biochar (D-NPKB). The results showed that D-NPKB significantly improved winter wheat and summer maize yields by 14.4 and 3.8%, respectively, compared with R-NPK. The nitrate (NO₃^––N) content of the deeper soil layer in D-NPKB was significantly higher than that in D-NPK. Meanwhile, biochar application increased the pH in the three layers. Compared with R-NPK, D-NPKB significantly increased the average content of available phosphorus (AP), soil organic carbon (SOC), and total nitrogen (TN) by 73.7, 18.5, and 19.0%, respectively. Meanwhile, Gaiellale, Sphingomonadaceae, and Nocardioidaceae were the predominant bacteria at the family level across all treatments, with a total relative proportion ranging from 14.1 to 23.6%. In addition, the abundance of Bacillaceae in deep tillage was 9.4% higher in the 20–30-cm soil layer than that in rotary tillage. Furthermore, the correlation analysis revealed a significant positive correlation between crop yield and chemical factors such as NO₃^––N and the abundances of Gaiellalea, Sphingomonadaceae, and Nocardioidaceae. The findings collectively indicated that deep tillage combined with biochar application could increase the soil nutrients and modify the bacterial structure in the deeper soil layer and therefore will be beneficial for improving the productivity of the vertisols.

Spatial Distribution of the Pepper Blight (Phytophthora capsici) Suppressive Microbiome in the Rhizosphere

The properties of plant rhizosphere are dynamic and heterogeneous, serving as different habitat filters for or against certain microorganisms. Herein, we studied the spatial distribution of bacterial communities in the rhizosphere of pepper plants treated with a disease-suppressive or non-suppressive soil. The bacterial richness was significantly (p < 0.05) higher in plants treated with the disease-suppressive soil than in those treated with the non-suppressive soil. Bacterial richness and evenness greatly differed between root parts, with decrease from the upper taproot to the upper fibrous root, the lower taproot, and the lower fibrous root. As expected, the bacterial community in the rhizosphere differed between suppressive and non-suppressive soil. However, the spatial variation (36%) of the bacterial community in the rhizosphere was much greater than that explained by soils (10%). Taxa such as subgroups of Acidobacteria, Nitrosospira, and Nitrospira were known to be selectively enriched in the upper taproot. In vitro Bacillus antagonists against Phytophthora capsici were also preferentially colonized in the taproot, while the genera such as Clostridium, Rhizobium, Azotobacter, Hydrogenophaga, and Magnetospirillum were enriched in the lower taproot or fibrous root. In conclusion, the spatial distribution of bacterial taxa and antagonists in the rhizosphere of pepper sheds light on our understanding of microbial ecology in the rhizosphere.

Multi-Omics Reveal the Efficient Phosphate-Solubilizing Mechanism of Bacteria on Rocky Soil

Phosphate-solubilizing bacteria (PSB) can alleviate available phosphorus (AP)-deficiency without causing environmental pollution like chemical phosphate fertilizers. However, the research and application of PSB on the barren rocky soil is very rare. We screened six PSB from sweetpotato rhizosphere rocky soil. Among them, Ochrobactrum haematophilum FP12 showed the highest P-solubilizing ability of 1,085.00 mg/L at 7 days, which was higher than that of the most reported PSB. The assembled genome of PSB FP12 was 4.92 Mb with P-solubilizing and plant growth-promoting genes. In an AP-deficient environment, according to transcriptome and metabolomics analysis, PSB FP12 upregulated genes involved in gluconic acid synthesis and the tricarboxylic acid cycle, and increased the concentration of gluconic acid and malic acid, which would result in the enhanced P-solubilizing ability. Moreover, a series of experiments in the laboratory and field confirmed the efficient role of the screened PSB on significantly increasing AP in the barren rocky soil and promoting sweetpotato yield. So, in this study, we screened highly efficient PSB, especially suitable for the barren rocky soil, and explored the P-solubilizing mechanism. The research will reduce the demand for chemical phosphate fertilizers and promote the environment-friendly agricultural development.

Aerenchyma formation in the root of leaf-vegetable sweet potato: Programmed cell death initiated by ethylene-mediated H2 O2 accumulation

Sweet potato, commonly planted in Southeast Asia and South America with abundant rainfall, often suffers from waterlogging. The aerenchyma formation in roots is an effective way for plants to facilitate gas exchange. In the present study, tolerant and sensitive varieties, respectively, designated NC1 and C211, were evaluated under water oxygen content at 2.0 mg·L^-1 (hypoxia treatment) and 8.0 mg·L^-1 (control). The results showed that NC1 variety has a relatively higher root growth rate under low oxygen condition. In NC1 plants, aerenchyma was observed in the mid-section of the main adventitious root and spread to the proximal and distal ends, forming a complete channel in the cortex. However, in C211 plants, the aerenchyma occurred relatively later and could not turn into a whole channel. Ethylene synthesis-related (ACS1, ACS4, ACS5, etc.) and signal transduction-related (ETR1, ERS1, EIN2, etc.) genes were upregulated in the NC1 plants and led to changes in the reactive oxygen species-related genes (RBOHA, SOD, CAT, etc.) and enzyme activities. It was found that programmed cell death was induced by H₂ O₂ accumulation. A regulatory model of lysigenous aerenchyma formation in the root of sweet potato was constructed. Our study enriches the understanding of the mechanisms of the aerenchyma formation in plants.

Recent Developments in the Study of Plant Microbiomes

To date, an understanding of how plant growth-promoting bacteria facilitate plant growth has been primarily based on studies of individual bacteria interacting with plants under different conditions. More recently, it has become clear that specific soil microorganisms interact with one another in consortia with the collective being responsible for the positive effects on plant growth. Different plants attract different cross-sections of the bacteria and fungi in the soil, initially based on the composition of the unique root exudates from each plant. Thus, plants mostly attract those microorganisms that are beneficial to plants and exclude those that are potentially pathogenic. Beneficial bacterial consortia not only help to promote plant growth, these consortia also protect plants from a wide range of direct and indirect environmental stresses. Moreover, it is currently possible to engineer plant seeds to contain desired bacterial strains and thereby benefit the next generation of plants. In this way, it may no longer be necessary to deliver beneficial microbiota to each individual growing plant. As we develop a better understanding of beneficial bacterial microbiomes, it may become possible to develop synthetic microbiomes where compatible bacteria work together to facilitate plant growth under a wide range of natural conditions.

Effect of Inorganic N Top Dressing and Trichoderma harzianum Seed-Inoculation on Crop Yield and the Shaping of Root Microbial Communities of Wheat Plants Cultivated Under High Basal N Fertilization

Wheat crop production needs nitrogen (N) for ensuring yield and quality. High doses of inorganic N fertilizer are applied to soil before sowing (basal dressing), with additional doses supplied along the cultivation (top dressing). Here, a long-term wheat field trial (12 plots), including four conditions (control, N top dressing, Trichoderma harzianum T34 seed-inoculation, and top dressing plus T34) in triplicate, was performed to assess, under high basal N fertilization, the influence of these treatments on crop yield and root microbial community shaping. Crop yield was not affected by top dressing and T. harzianum T34, but top dressing significantly increased grain protein and gluten contents. Twenty-seven-week old wheat plants were collected at 12 days after top dressing application and sampled as bulk soil, rhizosphere and root endosphere compartments in order to analyze their bacterial and fungal assemblies by 16S rDNA and ITS2 high-throughput sequencing, respectively. Significant differences for bacterial and fungal richness and diversity were detected among the three compartments with a microbial decline from bulk soil to root endosphere. The most abundant wheat root phyla were Proteobacteria and Actinobacteria for bacteria, and Ascomycota and Basidiomycota for fungi. An enrichment of genera commonly associated with soils subjected to chemical N fertilization was observed: Kaistobacter, Mortierella, and Solicoccozyma in bulk soil, Olpidium in rhizosphere, and Janthinobacterium and Pedobacter in root endosphere. Taxa whose abundance significantly differed among conditions within each compartment were identified. Results show that: (i) single or strain T34-combined application of N top dressing affected to a greater extent the bulk soil bacterial levels than the use of T34 alone; (ii) when N top dressing and T34 were applied in combination, the N fertilizer played a more decisive role in the bacterial microbiome than T34; (iii) many genera of plant beneficial bacteria, negatively affected by N top dressing, were increased by the application of T34 alone; (iv) bulk soil and rhizosphere fungal microbiomes were affected by any of the three treatments assayed; and (v) all treatments reduced Claroideoglomus in bulk soil but the single application of T34 raised the rhizosphere levels of this mycorrhizal fungus.