Rhizosphere microbial stability and phosphorus availability drive garlic growth differences

doi:10.21203/rs.3.rs-7336697/v1

Background

The rhizosphere microbiome and soil nutrients are critical for crop growth, but their roles in regulating garlic productivity remain unclear. This study aimed to identify key factors driving growth differences in adjacent garlic fields with uniform management.

Methods

Rhizosphere soils from two adjacent plots (H: vigorous growth; L: stunted growth) were analyzed for physicochemical properties and microbial communities via 16S rRNA and ITS sequencing, combined with network analysis and redundancy analysis (RDA).

Results

Results showed significantly higher available phosphorus (AP) in H than L. Bacterial communities in H exhibited greater stability and core diversity, with distinct compositional clustering between sites (PERMANOVA, P < 0.001). RDA indicated AP strongly correlated with bacterial community structure (R²=0.7638, P=0.009), and H was enriched with phosphorus-transforming taxa (e.g., Arthrobacter, Thauera). Hierarchical partitioning highlighted bacterial communities as the primary driver of growth differences, followed by AP.

Conclusions

These findings reveal that AP availability and rhizosphere bacterial stability, mediated by phosphorus-transforming microbes, collectively shape garlic growth, providing insights for optimizing garlic cultivation through microbial management.

Rhizosphere microbial community

Garlic

Available phosphorus

Diversity

Phosphorus transformation

Growth differences

The rhizosphere, the interface between plant roots and soil, hosts a complex ecosystem involving plants, microorganisms, soil, and other biotic and abiotic components. Within this zone, microbial populations exhibit high activity and participate in intricate biological and ecological processes. These interactions profoundly influence soil health, plant performance, and productivity (Kou et al. 2024). The rhizosphere microbiota regulates soil organic matter stability (Nelson et al. 2022), nutrient dynamics (van der Heijden et al. 2007), and rhizosphere functionality (Mendes et al. 2011). The stability of the rhizosphere microecosystem is critical for maintaining soil health and crop productivity.

Rhizosphere microbial community composition is shaped by environmental factors such as soil moisture, pH, organic matter content, and nutrient availability (e.g., nitrogen and phosphorus (P)) (Zheng et al. 2019; Sun et al. 2022). As natural media for plant growth, soil conditions directly impact plant development (Dai et al. 2020). Soil microorganisms improve soil structure, increase fertility, and modulate pH (Nannipieri et al. 2017). For example, Kallenbach et al. reported that microbial residues contribute to the chemical diversity of soil organic matter (SOM) (Kallenbach et al. 2016). He et al. demonstrated that Bacillus species and Pseudomonas putida promote tomato growth through P solubilization, nitrogen fixation, and indole-3-acetic acid (IAA) production (He et al. 2019b). Microorganisms also increase nutrient bioavailability via metabolic activities that increase the SOM content (Coonan et al. 2020) while simultaneously inhibiting plant pathogens (García-Bayona and Comstock 2018; Anum et al. 2024; Xia et al. 2024a). Xia et al. identified Bacillus, which antagonizes Fusarium graminearum to mitigate stalk rot, as a core taxon in disease-resistant maize varieties (Xia et al. 2024b). Collectively, these findings highlight the pivotal role of soil microbes in plant growth and health.

Garlic (Allium sativum L.) is a major economic crop in China, with Jinxiang County in Shandong Province renowned the “Garlic Capital” and “World Garlic Center” owing to its long-standing cultivation practices. However, garlic yields are vulnerable to management practices, particularly when unscientific cultivation reduces soil microbial diversity (Maron et al. 2018; Singh and Gupta 2018). This decline may result in pathogen accumulation and inefficient nutrient conversion, thereby impairing garlic growth. To address this issue, we collected rhizospheric soil from two adjacent garlic fields exhibiting significant growth disparities and compared the growth performance of garlic. Investigations revealed that both fields had been cultivated with garlic for more than a decade under uniform fertilization and irrigation management, yet growth differences persisted. By analyzing the soil nutrient content and microbial community structure, we aimed to clarify the roles of physicochemical properties and the microbiota in garlic growth. This study focused on identifying the critical roles of soil nutrients and microbial communities in garlic growth, providing theoretical support and technological innovations for precision fertilization and soil management. Our findings aim to mitigate production risks caused by soil degradation and promote sustainable soil health.

Research location and sample collection

This study was conducted in farmlands of Jinxian County, Jining city, Shandong Province, China (33°02′N, 116°23′E). The region has a warm temperate monsoon climate, with an annual average temperature of 15.5°C and annual precipitation of 668.6 mm in 2023. The main soil type is natural brown soil (C. Li et al. 2021). On November 24, 2023, the research team conducted an onsite field investigation of two adjacent garlic fields. These fields shared identical cultivars (Taikong 1) and sowing dates and were free from external nutritional factor disturbances; however, they presented marked differences in growth performance. To facilitate clear distinction, plants with plant heights ranging from 30–50 cm (representing the better-developed plot) were defined as Group H, with the corresponding plot labeled as Plot H. Conversely, plants with heights below 30 cm (from the less vigorous plot) were designated as Group L, and the plot was labeled as Plot L. To ensure the representativeness and reliability of the data, 8 replicate samples were uniformly collected from each plot via the random sampling method. During sampling, intact garlic root systems were carefully excavated, and rhizosphere soil was collected by gently brushing the root surface, yielding 16 rhizosphere soil samples in total. Each sample was divided into two portions: one for physicochemical analysis and the other stored at -80°C for subsequent DNA extraction.

Determination of Soil Physical and Chemical Properties

The total nitrogen (TN) and total phosphorus (TP) contents were determined via an AutoAnalyser3 soil element flow analyzer (Bran + Luebbe, Hamburg, Germany). The soil pH and electrical conductivity (EC) were measured with a Leici pH meter (Shanghai, China) at a water-to-soil ratio of 5:1 (v/w). Nitrate nitrogen (NO₃⁻-N) and ammonium nitrogen (NH₄⁺-N) were analyzed via hydrazine sulfate reduction and indophenol blue colorimetry, respectively. The soil organic carbon (SOC) content was determined via the potassium dichromate volumetric method (Wang et al. 2023). Available phosphorus (AP) was quantified via the molybdate‒ascorbic acid method with a UV‒Vis spectrophotometer (Eppendorf, Germany). The carbon-to-nitrogen (C/N) ratio was calculated as the ratio of SOC to TN (He et al. 2019a).

DNA extraction and sequence analysis

The soil DNA was extracted via the FastDNA Spin Kit for Soil (Omega, USA), and the DNA quality was evaluated via 1.2% agarose gel electrophoresis. PCR amplification of the bacterial V5–V7 hypervariable region of the 16S rRNA gene was performed via primers 799F (5′-AACMGGATTAGATACCCKG-3′) and 1193R (5′-ACGTCATCCCCACCTTCC-3′) (Klindworth et al. 2013), whereas the fungal ITS1–ITS2 region was amplified via primers ITS1F (5′-CTTGGTCATTTAGAGGAAGTAA-3′) and ITS2R (5′-GCTGCGTTCTTCATCGATGC-3′) (Schoch et al. 2012). Paired-end sequencing was conducted on an Illumina NovaSeq 6000 platform at Guangdong Magigene Biotechnology Co., Ltd. (Guangzhou, China). Raw FASTQ files were processed according to the QIIME2 standard protocols (https://docs.qiime2.org/2019.4/tutorials/) (Straub et al. 2020). After quality filtering, denoising, merging, chimera removal, and alignment via the DADA2 plugin, nonsingleton amplicon sequence variants (ASVs) were retained for downstream analysis. Taxonomic annotation of ASVs was performed via the SILVA v138.1 and UNITE v8.2 databases (Quast et al. 2013; Nilsson et al. 2019), followed by removal of contaminant sequences (e.g., mitochondria and chloroplasts). To account for differences in sequencing depth, rarefaction was performed to the minimum depth across all samples (47,456 reads for bacteria and 84,758 reads for fungi). These ASV tables were used for downstream analyses. A total of 1,062,692 high-quality bacterial sequences were generated and assigned to 6,039 ASVs, whereas fungal samples yielded 2,267,159 sequences assigned to 1,546 ASVs. The sequence data were deposited in the NCBI Sequence Read Archive (SRA) under accession number PRJNA1174389.

Data analysis

All the statistical analyses and data visualizations were performed in R (v4.3.2, https://www.r-project.org/). The core microbial taxa were defined as ASVs with relative abundances > 0.1%. Alpha diversity indices were calculated via the picante package. Principal coordinate analysis (PCoA) based on Bray–Curtis dissimilarities was conducted via the vegan package to evaluate community structure differences between sites, with significance determined via permutation tests (P < 0.05). Redundancy analysis (RDA) and hierarchical partitioning were performed with the rdacca.hp package to identify the contributions of soil physicochemical properties to microbial diversity and community composition, with significance determined at Padj ≤ 0.05. Microbial co-occurrence networks were constructed using ASVs with average relative abundances > 0.1%. Pairwise Spearman rank correlations were calculated via the ggClusterNet package, and significant interactions were filtered using a uniform threshold (|R| >0.7, P < 0.05). Network edges were weighted by correlation strength, and layouts were generated via the Fruchterman–Reingold algorithm in Gephi v.0.9.2 (Li et al. 2023). Community stability was evaluated via the average variability degree (AVD) index (Xun et al. 2021). Graphical representations (e.g., boxplots, chord diagrams) were generated with the ggplot2 package. Statistical comparisons between groups were performed via the Wilcoxon rank-sum test in IBM SPSS Statistics (IBM Corp., Armonk, NY, USA) (Xia et al. 2024c).

Significant differences in garlic growth performance between adjacent fields

Analysis of garlic plant height revealed that the mean plant height at site H was 1.44-fold greater than that at site L (Wilcoxon rank-sum test, P < 0.001) (Fig. 1B–C). To investigate the underlying factors contributing to this discrepancy, we characterized the physicochemical properties and microbial community compositions of rhizosphere soils from both sites.

The AP content was significantly greater at site H than at site L

To determine whether rhizosphere soil physicochemical properties differed between sites H and L, we measured key parameters in garlic rhizosphere soil samples. Among the analyzed properties, the available phosphorus (AP) content at site H was significantly greater than that at site L (Wilcoxon rank-sum test, P < 0.05), whereas no significant differences were detected in pH, EC, TN, TP, NH₄⁺-N, NO₃⁻-N, SOC, or the C/N ratio (all *P > 0.05) (Fig. 2). These results highlight AP content as a key factor contributing to the observed differences in garlic growth between the two sites.

Significant differences in rhizosphere microbial community diversity

To evaluate bacterial and fungal diversity between sites H and L, α diversity indices were calculated for bacteria, core bacterial taxa (defined as ASVs with a mean relative abundance > 0.1% across samples), fungi, and core fungi. The Shannon index of the core bacteria at site H was significantly greater than that at site L (Wilcoxon rank-sum test, P < 0.05) (Fig. 3C). No significant differences were detected in bacterial, fungal, or core fungal α diversity (all P > 0.05) (Fig. 3A, B, D).

PCoA based on Bray–Curtis dissimilarities revealed distinct clustering patterns for bacterial and core bacterial communities between sites (PERMANOVA, P < 0.001) (Fig. 3E). In contrast, the fungal and core fungal communities presented no significant structural differences (PERMANOVA, P > 0.05) (Fig. 3F). Additionally, the exogenous nutrient levels were consistent between the two fields. These results suggest that bacterial community diversity and composition are critical factors contributing to the observed garlic growth disparities between sites H and L.

Higher stability of bacterial communities at location H

To evaluate rhizosphere microbial network complexity and stability, ecological networks were constructed for bacteria and fungi at sites H and L. Network analysis revealed that bacterial and fungal networks at site H presented greater complexity and connectivity than did those at site L, characterized by more nodes, a higher average degree, a larger network diameter, greater centralization, and greater closeness centralization (Fig. 4A–B; Table 1). Specifically, the bacterial network at site L presented an increased average path length, indicating decreased responsiveness to external perturbations (Table 1), whereas the fungal network at site L presented a decreased average path length, reflecting faster adaptive capacity (Table 1). Site L also harbored more keystone nodes, suggesting that garlic actively recruits critical microbes under stress. Community stability, measured by the AVD index, was significantly greater at site H for both bacteria and fungi (Fig. 4D). These results underscore bacterial community stability as a key determinant of garlic growth disparities between sites.

Table 1

Network properties of bacteria and fungi
	Bacteria_H	Bacteria_L	Fungi_H	Fungi_L
Nodes	218	219	88	88
Edges	2224	2048	370	367
Connectance	0.094026128	0.085794479	0.096656217	0.095872518
Average Degree	20.40366972	18.70319635	8.409090909	8.340909091
Average Path Length	1.879037574	1.985647338	2.298343637	2.251869175
Diameter	4.023809524	3.85206652	6.111667761	5.307278838
Centralization Degree	0.104130554	0.083930292	0.13322884	0.122518286
Centralization Closeness	0.141528417	0.113956041	0.195748564	0.163661951
The Number of Keystone Nodes	36	41	7	11

The AP content is significantly correlated with rhizosphere bacterial community composition

RDA was used to explore the influence of abiotic factors, specifically soil physicochemical properties, on bacterial and fungal communities. The first two axes of the RDA explained 30.63% of the total variation in the bacterial communities. Among these factors, AP had the most significant impact on the bacterial community structure (R² = 0.7638, P = 0.009) (Fig. 5A, Table 2). The RDA results revealed that differences in AP content affected the distribution of bacterial communities, whereas the distribution of fungal communities was not influenced by these abiotic factors (Fig. 5A, B, Table 2). These findings suggest that AP and bacterial communities are crucial factors contributing to the significant differences in garlic growth between sites H and L.

Table 2

Results of RDA permutation test for bacteria, fungi communities and soil physical and chemical properties
Name	Bacteria			Fungi
Name	R²	Padj	Individual (%)	R²	Padj	Individual (%)
PH	0.179336	0.5076	1.04	0.010451	0.901	0
EC	0.002077	0.992	0	0.04049	0.858857	0
NH₄⁺-N	0.057199	0.892286	0	0.343983	0.711	3.36
NO₃⁻-N	0.321534	0.306	1.95	0.106433	0.858857	1.09
AP	0.763771	0.009	3.8	0.069747	0.858857	0
TN	0.139292	0.582	0	0.100856	0.858857	0
TP	0.180848	0.5076	0	0.101308	0.858857	0
C/N	0.20139	0.5076	0.15	0.140689	0.858857	1.08
SOC	0.007786	0.992	0	0.012459	0.901	0.16

Location H is enriched with numerous microorganisms associated with P transformation

To quantify the contributions of soil physicochemical properties and microbial communities to garlic plant height at sites H and L, we performed hierarchical partitioning analysis. The results revealed that the bacterial community had the greatest contribution to garlic plant height, followed by AP (Fig. 6E). To further clarify the role of bacterial communities in determining garlic plant height, we analyzed the species composition of rhizosphere microbial communities at both sites. On the basis of the ASV classification results, Sphingomonas was the most abundant genus among the rhizosphere bacteria at both sites. However, the second most abundant genera differed: Flavobacterium at site H and Bacillus at site L. The most abundant fungus at site H was Mortierella, whereas at site L, it was Fusarium (Fig. 4A, B), a common soil-borne plant pathogen. To identify the bacterial and fungal genera that differed between the microbial communities at sites H and L, we conducted linear discriminant analysis effect size (LEfSe) analysis. Significant differences were found in the enriched fungi and bacteria between the two sites (Fig. 6A, B). At site H, 36 bacterial taxa met the score criteria, whereas 22 bacterial taxa met the score criteria at site L (Fig. 6C). We also found that the main enriched genera at site H, Arthrobacter and Thauera, are typically involved in the transformation of minerals such as P and sulfur, which promotes plant nutrient absorption and inhibits plant pathogens (Fig. 6C). Among the fungal taxa, 5 groups at site L and only 1 group at site H met the linear discriminant analysis (LDA) score criteria (Fig. 6D). Additionally, the enriched Penicillium at site L can cause stem-base rot and fruit rot in vegetables and fruits (Fig. 6D). Overall, these results suggest that the differences in garlic growth at sites H and L are influenced mainly by differences in the composition of rhizosphere microorganisms.

In the two fields where we investigated garlic growth performance, the fertilization rates were standardized. Thus, after excluding interference from exogenous nutrient intrusion, significant differences in available phosphorus (AP) remained between the two fields. The role of P in plants is extremely extensive, as it is involved in critical physiological processes such as energy transfer, cell division, and nucleic acid synthesis (Wang et al. 2020). P is also a structural component of plant cell membranes and plays a vital role in photosynthesis. P deficiency can significantly impair plant growth and development, ultimately reducing crop yield. In our study, the AP content at location H was significantly greater than that at location L (Fig. 2), corroborating previous findings that P deficiency disrupts plant growth and development, thereby impacting crop productivity. Plant rhizosphere microorganisms play a pivotal role in plant stress resistance, serving as major drivers of plant defense responses (Zhalnina et al. 2018). Stress tolerance is mediated by the collective activities of microbial communities, and more diverse communities are particularly effective at increasing plant stress resistance (Sun et al. 2021). This finding is consistent with our findings that the core bacterial community diversity was greater at site H than at site L (Fig. 3C). Additionally, the bacterial and fungal networks at location H presented greater complexity and connectivity (Fig. 4A, B, Table 1), which is consistent with previous reports that high-diversity microbial communities provide more ecological niches and functional redundancy, thereby strengthening plant stress tolerance.

The terrestrial microbiome is recognized as a ubiquitous and essential component of ecosystems, playing critical roles in maintaining organic carbon cycling, enhancing nutrient use efficiency, and supporting productivity (Xun et al. 2021). Fundamentally, the sustainability of terrestrial ecosystem functions and services depends on microbiome stability (Griffiths and Philippot 2012), which is typically measured by the degree of variation or turnover in microbial communities. In this study, the bacterial community stability at location H was significantly greater than that at location L (Fig. 4D). The enhanced stability at location H likely indicates greater durability and reliability of ecosystem services, contributing to overall terrestrial ecosystem health. The results of hierarchical partitioning further highlighted the critical role of bacterial communities in garlic growth (Fig. 6E). Bacterial communities are highly sensitive to soil environmental changes, possibly because of their reliance on small-molecule organic matter and short-distance nutrient exchange in the soil (Yalong Xu et al. 2024). In contrast, fungi acquire nutrients through robust mycelial growth, enabling them to form extensive network structures and maintain relatively stable community compositions (He et al. 2024).

For plants, soil P is often unavailable for direct uptake and requires conversion to AP before absorption. Soil microorganisms play a critical role in this "transformation" process (Shidong He et al. 2024). Phosphate-solubilizing bacteria (PSB), which solubilize inorganic P or mineralize organic P to facilitate plant growth (Bargaz et al. 2021; Timofeeva et al. 2022), were significantly correlated with the AP content at both locations (Fig. 5A, Table 2). Notably, Arthrobacter and Thauera were significantly enriched at location H. Previous studies have demonstrated that these genera possess phosphate-solubilizing capabilities and facilitate P transformation, effectively converting soil P into AP (Vanissa et al. 2020; Jiang et al. 2022; Ren et al. 2023). This likely explains the significant AP content difference between locations and subsequent variations in garlic growth.

In many agricultural ecosystems, soil-borne diseases pose severe threats to crop health (Raaijmakers et al. 2008). Analysis of the top ten bacterial and fungal genera revealed greater Fusarium abundance at site L (Fig. 6B). Fusarium species are common pathogens that cause garlic root rot (Garbeva et al. 2004), infect various plants and induce diseases such as root rot, stem rot, basal stem rot, blossom blight, and ear blight. These diseases are notoriously difficult to control in agricultural production (Li et al. 2020). LEfSe analysis further revealed significant enrichment of Scedosporium at site L (Fig. 6D), a genus associated with important crop diseases that can cause substantial yield losses if unmanaged (Brauer et al. 2019). Taken together, these results underscore the close association between soil microbial communities and plant growth. Further research and targeted management strategies could leverage microbial potential to advance sustainable agriculture.

This study aimed to investigate the role of garlic rhizosphere microorganisms in plant growth by comparing two adjacent plots with contrasting growth performance. Taken together, these results underscore the close association between soil microbial communities and plant growth in bacterial communities and the AP content across locations. These findings highlight the critical roles of bacterial communities and AP content as key determinants of garlic growth disparities. RDA further revealed strong correlations between bacterial community compositions and soil AP levels, suggesting that bacterial communities indirectly influence garlic growth through regulating P bioavailability. Differential abundance analysis revealed substantial enrichment of Arthrobacter and Thauera at Location H, which are known to directly mediate P transformation processes, providing mechanistic insights into soil nutrient cycling. Additionally, the presence of fungal pathogens in the rhizosphere microbiome was identified as a potential factor contributing to the observed growth disparities. Collectively, these results advance our understanding of the rhizosphere microbial mechanisms underlying garlic growth and provide a theoretical basis for developing microbe-driven management strategies for garlic cultivation.

AP

Available phosphorus

TN

Total nitrogen

TP

Total phosphorus

EC

Electrical conductivity

NO₃⁻-N

Nitrate nitrogen

NH₄⁺-N

Ammonium nitrogen

SOC

Soil organic carbon

C/N

Carbon-to-nitrogen ratio

IAA

Indole-3-acetic acid

SOM

Soil organic matter

ASVs

Amplicon sequence variants

SRA

Sequence Read Archive

PCoA

Principal coordinate analysis

RDA

Redundancy analysis

AVD

Average variability degree

LEfSe

Linear discriminant analysis effect size

LDA

Linear discriminant analysis

PSB

Phosphate-solubilizing bacteria

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing Interests

The authors declare that they have no conflicts of interest.

Funding

This work was supported by the Key Research and Development Project in Shandong Province of China (2024TZXD062, 2023CXPT045, 2023TZXD004), the National Natural Science Foundation of China (42407427, 42377309, 42077027), the ‘First Class Discipline’ Construction Project of Shandong Agricultural University (SKL81103, SKL81110).

Author Contributions

RX W and SD H planned and designed the study and completed the major data analysis. TT W and LG L assisted with sample collection. DL F, LL L, WC S and Z G were involved in writing the article. X L guided SD H and RX W in drafting the manuscript.

Acknowledgments

This work was supported by the Key Research and Development Project in Shandong Province of China (2024TZXD062, 2023CXPT045, 2023TZXD004), the National Natural Science Foundation of China (42407427, 42377309, 42077027), and the ‘First Class Discipline’ Construction Project of Shandong Agricultural University (SKL81103, SKL81110).

Availability of data and materials

The sequence data have been deposited in the NCBI SRA database under accession number PRJNA1174389.

Anum H, Tong Y, Cheng R (2024) Different Preharvest Diseases in Garlic and Their Eco-Friendly Management Strategies. https://doi.org/10.3390/plants13020267. Plants
Bargaz A, Elhaissoufi W, Khourchi S et al (2021) Benefits of phosphate solubilizing bacteria on belowground crop performance for improved crop acquisition of phosphorus. Microbiol Res. https://doi.org/10.1016/j.micres.2021.126842
Brauer VS, Rezende CP, Pessoni AM et al (2019) Antifungal Agents in Agriculture: Friends and Foes of Public Health. Biomolecules. https://doi.org/10.3390/biom9100521
Li C, Zhang C, Wang J et al (2021) Effects of ENSO on Climate and Garlic Yield in Main Garlic Production Areas of China. In: 2021 IEEE International Conference on Smart Internet of Things (SmartIoT). pp 283–288
Coonan EC, Kirkby CA, Kirkegaard JA et al (2020) Microorganisms and nutrient stoichiometry as mediators of soil organic matter dynamics. Nutr Cycl Agroecosystems. https://doi.org/10.1007/s10705-020-10076-8
Dai Y, Zheng H, Jiang Z, Xing B (2020) Combined effects of biochar properties and soil conditions on plant growth: A meta-analysis. Sci Total Environ. https://doi.org/10.1016/j.scitotenv.2020.136635
Garbeva P, van Veen JA, van Elsas JD (2004) Microbial diversity in soil: selection microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol. https://doi.org/10.1146/annurev.phyto.42.012604.135455
García-Bayona L, Comstock LE (2018) Bacterial antagonism in host-associated microbial communities. Science. https://doi.org/10.1126/science.aat2456
Griffiths BS, Philippot L (2012) Insights into the resistance and resilience of the soil microbial community. FEMS Microbiol Rev. https://doi.org/10.1111/j.1574-6976.2012.00343.x
He H, Xia G, Yang W et al (2019a) Response of soil C:N:P stoichiometry, organic carbon stock, and release to wetland grasslandification in Mu Us Desert. https://doi.org/10.1007/s11368-019-02351-1. J Soils Sediments
He S, Lv M, Wang R et al (2024) Long-term garlic–maize rotation maintains the stable garlic rhizosphere microecology. Environ Microbiome 19:90. https://doi.org/10.1186/s40793-024-00636-8
He Y, Pantigoso HA, Wu Z, Vivanco JM (2019b) Co-inoculation of Bacillus sp. and Pseudomonas putida at different development stages acts as a biostimulant to promote growth, yield and nutrient uptake of tomato. J Appl Microbiol 127:196–207. https://doi.org/10.1111/jam.14273
Jiang Y, Song Y, Jiang C et al (2022) Identification and Characterization of Arthrobacter nicotinovorans JI39, a Novel Plant Growth-Promoting Rhizobacteria Strain From Panax ginseng. Front Plant Sci. https://doi.org/10.3389/fpls.2022.873621
Kallenbach CM, Frey SD, Grandy AS (2016) Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls. Nat Commun 7:13630. https://doi.org/10.1038/ncomms13630
Klindworth A, Pruesse E, Schweer T et al (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. https://doi.org/10.1093/nar/gks808
Kou C, Song F, Li D et al (2024) A necessary considering factor for crop resistance: Precise regulation and effective utilization of beneficial microorganisms. New Crops 1:100023. https://doi.org/10.1016/j.ncrops.2024.100023
Li C, Jin L, Zhang C et al (2023) Destabilized microbial networks with distinct performances of abundant and rare biospheres in maintaining networks under increasing salinity stress. iMeta 2:e79. https://doi.org/10.1002/imt2.79
Li J, Fokkens L, Rep M (2020) A single gene in Fusarium oxysporum limits host range. Mol Plant Pathol. https://doi.org/10.1111/mpp.13011
Maron P-A, Sarr A, Kaisermann A et al (2018) High Microbial Diversity Promotes Soil Ecosystem Functioning. Appl Environ Microbiol. https://doi.org/10.1128/aem.02738-17
Mendes R, Kruijt M, de Bruijn I et al (2011) Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria. https://doi.org/10.1126/science.1203980. Science
Nannipieri P, Ascher J, Ceccherini MT et al (2017) Microbial diversity and soil functions. Eur J Soil Sci. https://doi.org/10.1111/ejss.4_12398
Nelson AR, Narrowe AB, Rhoades CC et al (2022) Wildfire-dependent changes in soil microbiome diversity and function. Nat Microbiol. https://doi.org/10.1038/s41564-022-01203-y
Nilsson RH, Larsson K-H, Taylor AFS et al (2019) The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. https://doi.org/10.1093/nar/gky1022
Quast C, Pruesse E, Yilmaz P et al (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. https://doi.org/10.1093/nar/gks1219
Raaijmakers JM, Paulitz TC, Steinberg C et al (2008) The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Plant Soil. https://doi.org/10.1007/s11104-008-9568-6
Ren T, Jin X, Deng S et al (2023) Oxygen sensing regulation mechanism of Thauera bacteria in simultaneous nitrogen and phosphorus removal process. J Clean Prod. https://doi.org/10.1016/j.jclepro.2023.140332
Schoch CL, Seifert KA, Huhndorf S et al (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A. https://doi.org/10.1073/pnas.1117018109
He S, Li L, Lv M et al (2024) PGPR: Key to Enhancing Crop Productivity and Achieving Sustainable Agriculture. Curr Microbiol. https://doi.org/10.1007/s00284-024-03893-5
Singh JS, Gupta VK (2018) Soil microbial biomass: A key soil driver in management of ecosystem functioning. Sci Total Environ. https://doi.org/10.1016/j.scitotenv.2018.03.373
Straub D, Blackwell N, Langarica-Fuentes A et al (2020) Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline. Front Microbiol. https://doi.org/10.3389/fmicb.2020.550420
Sun M, Li M, Zhou Y et al (2022) Nitrogen deposition enhances the deterministic process of the prokaryotic community and increases the complexity of the microbial co-network in coastal wetlands. Sci Total Environ. https://doi.org/10.1016/j.scitotenv.2022.158939
Sun X, Xu Z, Xie J et al (2021) Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions. ISME J. https://doi.org/10.1038/s41396-021-01125-3
Timofeeva A, Galyamova M, Sedykh S (2022) Prospects for Using Phosphate-Solubilizing Microorganisms as Natural Fertilizers in Agriculture. https://doi.org/10.3390/plants11162119. Plants
van der Heijden MGA, Bardgett RD, van Straalen NM (2007) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett. https://doi.org/10.1111/j.1461-0248.2007.01139.x
Vanissa TTG, Berger B, Patz S et al (2020) The Response of Maize to Inoculation with Arthrobacter sp. and Bacillus sp. in Phosphorus-Deficient, Salinity-Affected Soil. https://doi.org/10.3390/microorganisms8071005. Microorganisms
Wang S, Song M, Wang C et al (2023) Mechanisms underlying soil microbial regulation of available phosphorus in a temperate forest exposed to long-term nitrogen addition. Sci Total Environ. https://doi.org/10.1016/j.scitotenv.2023.166403
Wang Y, Chen Y-F, Wu W-H (2020) Potassium and phosphorus transport and signaling in plants. J Integr Plant Biol. https://doi.org/10.1111/jipb.13053
Xia X, Wei Q, Wu H et al (2024a) Bacillus species are core microbiota of resistant maize cultivars that induce host metabolic defense against corn stalk rot. https://doi.org/10.1186/s40168-024-01887-w. Microbiome
Xia X, Wei Q, Wu H et al (2024b) Bacillus species are core microbiota of resistant maize cultivars that induce host metabolic defense against corn stalk rot. Microbiome 12:156. https://doi.org/10.1186/s40168-024-01887-w
Xia X, Wei Q, Wu H et al (2024c) Bacillus species are core microbiota of resistant maize cultivars that induce host metabolic defense against corn stalk rot. https://doi.org/10.1186/s40168-024-01887-w. Microbiome
Xun W, Liu Y, Li W et al (2021) Specialized metabolic functions of keystone taxa sustain soil microbiome stability. https://doi.org/10.1186/s40168-020-00985-9. Microbiome
Xu Y, Li J, Qiao C et al (2024) Rhizosphere bacterial community is mainly determined by soil environmental factors, but the active bacterial diversity is mainly shaped by plant selection. BMC Microbiol. https://doi.org/10.1186/s12866-024-03611-y
Zhalnina K, Louie KB, Hao Z et al (2018) Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol. https://doi.org/10.1038/s41564-018-0129-3
Zheng Q, Hu Y, Zhang S et al (2019) Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity. Soil Biol Biochem. https://doi.org/10.1016/j.soilbio.2019.107521

Rhizosphere microbial stability and phosphorus availability drive garlic growth differences

Status:

Version 1

Abstract

Figures

Background

Materials and methods