Rhizosphere bacteriome structure and functions

Nitrogenous fertilizer plays a more important role than cultivars in shaping sorghum-associated microbiomes

The plant microbiome plays a crucial role in facilitating plant growth through enhancing nutrient cycling, acquisition and transport, as well as alleviating stresses induced by nutrient limitations. Despite its significance, the relative importance of common agronomic practices, such as nitrogenous fertilizer, in shaping the plant microbiome across different cultivars remains unclear. This study investigated the dynamics of bacterial and fungal communities in leaf, root, rhizosphere, and bulk soil in response to nitrogenous fertilizer across ten sorghum varieties, using 16S rRNA and ITS gene amplicon sequencing, respectively. Our results revealed that nitrogen addition had a greater impact on sorghum-associated microbial communities compared to cultivar. Nitrogen addition significantly reduced bacterial diversity in all compartments except for the root endophytes. However, N addition significantly increased fungal diversity in both rhizosphere and bulk soils, while significantly reducing fungal diversity in the root endophytes. Furthermore, N addition significantly altered the community composition of bacteria and fungi in all four compartments, while cultivars only affected the community composition of root endosphere bacteria and fungi. Network analysis revealed that fertilization significantly reduced microbial network complexity and increased fungal-related network complexity. Collectively, this study provides empirical evidence that sorghum-associated microbiomes are predominantly shaped by nitrogenous fertilizer rather than by cultivars, suggesting that consistent application of nitrogenous fertilizer will ultimately alter plant-associated microbiomes regardless of cultivar selection.

High-throughput 16S rRNA gene-based amplicon sequencing reveals the functional divergence of halophilic bacterial communities in the Suaeda salsa root compartments on the eastern coast of China

The rhizosphere environment of plants, which harbors halophilic bacterial communities, faces significant challenges in coping with environmental stressors, particularly saline soil properties. This study utilizes a high-throughput 16S rRNA gene-based amplicon sequencing to investigate the variations in bacterial community dynamics in rhizosphere soil (RH), root surface soil (RS), root endophytic bacteria (PE) compartments of Suaeda salsa roots, and adjoining soils (CK) across six locations along the eastern coast of China: Nantong (NT), Yancheng (YC), Dalian (DL), Tianjin (TJ), Dongying (DY), and Qingdao (QD), all characterized by chloride-type saline soil. Variations in the physicochemical properties of the RH compartment were also evaluated. The results revealed significant changes in pH, electrical conductivity, total salt content, and ion concentrations in RH samples from different locations. Notably, the NT location exhibited the highest alkalinity and nitrogen availability. The pH variations were linked to HCO3- accumulation in S. salsa roots, while salinity stress influenced soil pH through H+ discharge. Despite salinity stress, enzymatic activities such as catalase and urease were higher in soils from various locations. The diversity and richness of bacterial communities were higher in specific locations, with Proteobacteria dominating PE samples from the DL location. Additionally, Vibrio and Marinobacter were prevalent in RH samples. Significant correlations were found between soil pH, salinity, nutrient content, and the abundance and diversity of bacterial taxa in RH samples. Bioinformatics analysis revealed the prevalence of halophilic bacteria, such as Bacillus, Halomonas, and Streptomyces, with diverse metabolic functions, including amino acid and carbohydrate metabolisms. Essential genes, such as auxin response factor (ARF) and GTPase-encoding genes, were abundant in RH samples, suggesting adaptive strategies for harsh environments. Likewise, proline/betaine transport protein genes were enriched, indicating potential bioremediation mechanisms against high salt stress. These findings provide insight into the metabolic adaptations facilitating resilience in saline ecosystems and contribute to understanding the complex interplay between soil conditions, bacterial communities, and plant adaptation.

Drivers of the Sisrè berry plant [Synsepalum dulcificum (Schumach & Thonn.) Daniell] rhizosphere bacterial communities in Benin

Each plant species has its own rhizobacteriome, whose activities determine both soil biological quality and plant growth. Little knowledge exists of the rhizosphere bacterial communities associated with opportunity crops with high economic potential such as Synsepalum dulcificum. Native to West Africa, this shrub is famous for its red berries representing the only natural source of miraculin, a glycoprotein, with sweetening properties, but also playing a role in the treatment of cancer and diabetes. This study aimed to characterize the structure and diversity of rhizobacterial communities associated with S. dulcificum and to identify the parameters determining this diversity. An initial sampling stage allowed the collection of rhizosphere soils from 29 S. dulcificum accessions, belonging to three distinct phenotypes, from 16 municipalities of Benin, located either on farms or in home gardens. The bacterial diversity of these rhizosphere soils was assessed by Illumina sequencing of the 16S rRNA gene after DNA extraction from these soils. Furthermore, an analysis of the physicochemical properties of these soils was carried out. All accessions combined, the most represented phylum appeared to be Actinobacteriota, with an average relative abundance of 43.5 %, followed by Proteobacteria (14.8 %), Firmicutes (14.3 %) and Chloroflexi (12.2 %), yet the relative abundance of dominant phyla varied significantly among accessions (p < 0.05). Plant phenotype, habitat, climate and soil physicochemical properties affected the bacterial communities, but our study pointed out that soil physicochemical parameters were the main driver of rhizobacterial communities' structure and diversity. Among them, the assimilable phosphorus, lead, potassium, arsenic and manganese contents, texture and cation exchange capacity of rhizosphere soils were the major determinants of the composition and diversity of rhizosphere bacterial communities. These results suggested the possibility of improving the growth conditions and productivity of S. dulcificum, by harnessing its associated bacteria of interest and better managing soil physicochemical properties.

Effect of polyethylene microplastics on antibiotic resistance genes: A comparison based on different soil types and plant types

Microplastics (MPs) and antibiotic resistance genes (ARGs) are two types of contaminants that are widely present in the soil environment. MPs can act as carriers of microbes, facilitating the colonization and spread of ARGs and thus posing potential hazards to ecosystem safety and human health. In the present study, we explored the microbial networks and ARG distribution characteristics in different soil types (heavy metal (HM)-contaminated soil and agricultural soil planted with different plants: Bidens pilosa L., Ipomoea aquatica F., and Brassica chinensis L.) after the application of MPs and evaluated environmental factors, potential microbial hosts, and ARGs. The microbial communities in the three rhizosphere soils were closely related to each other, and the modularity of the microbial networks was greater than 0.4. Moreover, the core taxa in the microbial networks, including Actinobacteriota, Proteobacteria, and Myxococcota, were important for resisting environmental stress. The ARG resistance mechanisms were dominated by antibiotic efflux in all three rhizosphere soils. Based on the annotation results, the MP treatments induced changes in the relative abundance of microbes carrying ARGs, and the G1-5 treatment significantly increased the abundance of MuxB in Verrucomicrobia, Elusimicrobia, Actinobacteria, Planctomycetes, and Acidobacteria. Path analysis showed that changes in MP particle size and dosage may indirectly affect soil enzyme activities by changing pH, which affects microbes and ARGs. We suggest that MPs may provide surfaces for ARG accumulation, leading to ARG enrichment in plants. In conclusion, our results demonstrate that MPs, as potentially persistent pollutants, can affect different types of soil environments and that the presence of ARGs may cause substantial environmental risks.

Different microbial functional traits drive bulk and rhizosphere soil phosphorus mobilization in an alpine meadow after nitrogen input

Enhanced nitrogen (N) input is expected to influence the soil phosphorus (P) cycling through biotic and abiotic factors. Among these factors, soil microorganisms play a vital role in regulating soil P availability. However, the divergent contribution of functional microorganisms to soil P availability in the rhizosphere and bulk soil under N addition remains unclear. We conducted an N addition experiment with four N input rates (0, 5, 10, and 15 g N m-2 year-1) in an alpine meadow over three years. Metagenomics was employed to investigate the functional microbial traits in the rhizosphere and bulk soil. We showed that N addition had positive effects on microbial functional traits related to P-cycling in the bulk and rhizosphere soil. Specifically, high N addition significantly increased the abundance of most microbial genes in the bulk soil but only enhanced the abundance of five genes in the rhizosphere soil. The soil compartment, rather than the N addition treatment, was the dominant factor explaining the changes in the diversity and network of functional microorganisms. Furthermore, the abundance of functional microbial genes had a profound effect on soil available P, particularly in bulk soil P availability driven by the ppa and ppx genes, as well as rhizosphere soil P availability driven by the ugpE gene. Our results highlight that N addition stimulates the microbial potential for soil P mobilization in alpine meadows. Distinct microbial genes play vital roles in soil P availability in bulk and rhizosphere soil respectively. This indicates the necessity for models to further our knowledge of P mobilization processes from the bulk soil to the rhizosphere soil, allowing for more precise predictions of the effects of N enrichment on soil P cycling.

Intercropping enhances maize growth and nutrient uptake by driving the link between rhizosphere metabolites and microbiomes

Intercropping leads to different plant roots directly influencing belowground processes and has gained interest for its promotion of increased crop yields and resource utilization. However, the precise mechanisms through which the interactions between rhizosphere metabolites and the microbiome contribute to plant production remain ambiguous, thus impeding the understanding of the yield-enhancing advantages of intercropping. This study conducted field experiments (initiated in 2013) and pot experiments, coupled with multi-omics analysis, to investigate plant-metabolite-microbiome interactions in the rhizosphere of maize. Field-based data revealed significant differences in metabolite and microbiome profiles between the rhizosphere soils of maize monoculture and intercropping. In particular, intercropping soils exhibited higher microbial diversity and metabolite chemodiversity. The chemodiversity and composition of rhizosphere metabolites were significantly related to the diversity, community composition, and network complexity of soil microbiomes, and this relationship further impacted plant nutrient uptake. Pot-based findings demonstrated that the exogenous application of a metabolic mixture comprising key components enriched by intercropping (soyasapogenol B, 6-hydroxynicotinic acid, lycorine, shikimic acid, and phosphocreatine) significantly enhanced root activity, nutrient content, and biomass of maize in natural soil, but not in sterilized soil. Overall, this study emphasized the significance of rhizosphere metabolite-microbe interactions in enhancing yields in intercropping systems. It can provide new insights into rhizosphere controls within intensive agroecosystems, aiming to enhance crop production and ecosystem services.

Structure and dynamics of microbial communities associated with the resurrection plant Boea hygrometrica in response to drought stress

MAIN CONCLUSION

The resurrection plant Boea hygrometrica selectively recruits and assembles drought-specific microbial communities across the plant-soil compartments, which may benefit plant growth and fitness under extreme drought conditions. Plant-associated microbes are essential for facilitating plant growth and fitness under drought stress. The resurrection plant Boea hygrometrica in natural habitats with seasonal rainfall can survive rapid desiccation, yet their interaction with microbiomes under drought conditions remains unexplored. This study examined the bacterial and fungal microbiome structure and drought response across plant-soil compartments of B. hygrometrica by high-throughput amplicon sequencing of 16S rRNA gene and internal transcribed spacer. Our results demonstrated that the diversity, composition, and functional profile of the microbial community varied considerably across the plant-soil compartments and were strongly affected by drought stress. Bacterial and fungal diversity was significantly reduced from soil to endosphere and belowground to aboveground compartments. The compartment-specific enrichment of the dominant bacteria phylum Cyanobacteriota and genus Methylorubrum in leaf endosphere, genera Pseudonocardia in rhizosphere soil and Actinoplanes in root endosphere, and fungal phylum Ascomycota in the aboveground compartments and genera Knufia in root endosphere and Cladosporium in leaf endosphere composed part of the core microbiota with corresponding enrichment of beneficial functions for plant growth and fitness. Moreover, the recruitment of dominant microbial genera Sphingosinicella and Plectosphaerella, Ceratobasidiaceae mycorrhizal fungi, and numerous plant growth-promoting bacteria involving nutrient supply and auxin regulation was observed in desiccated B. hygrometrica plants. Our results suggest that the stable assembled drought-specific microbial community of B. hygrometrica may contribute to plant survival under extreme environments and provide valuable microbial resources for the microbe-mediated drought tolerance enhancement in crops.

Meta-analysis reveals the effects of microbial inoculants on the biomass and diversity of soil microbial communities

Microbial inoculation involves transplanting microorganisms from their natural habitat to new plants or soils to improve plant performance, and it is being increasingly used in agriculture and ecological restoration. However, microbial inoculants can invade and alter the composition of native microbial communities; thus, a comprehensive analysis is urgently needed to understand the overall impact of microbial inoculants on the biomass, diversity, structure and network complexity of native communities. Here we provide a meta-analysis of 335 studies revealing a positive effect of microbial inoculants on soil microbial biomass. This positive effect was weakened by environmental stress and enhanced by the use of fertilizers and native inoculants. Although microbial inoculants did not alter microbial diversity, they induced major changes in the structure and bacterial composition of soil microbial communities, reducing the complexity of bacterial networks and increasing network stability. Finally, higher initial levels of soil nutrients amplified the positive impact of microbial inoculants on fungal biomass, actinobacterial biomass, microbial biomass carbon and microbial biomass nitrogen. Together, our results highlight the positive effects of microbial inoculants on soil microbial biomass, emphasizing the benefits of native inoculants and the important regulatory roles of soil nutrient levels and environmental stress.

Hindrance to sustainable development: Global inequities, non-progressive education and inadequate science-policy dialogue

Social habits and economies driven by profit are opposing efforts to reach a path of sustainable development. In addition, many communities worldwide have diverged away from nature through consumerism and technology. In the context of the escalating risks and consequences related to global challenges such as the climate crisis and ecosystem degradation, education for sustainable development and science-driven decision-making offer tremendous opportunities for improvement.

Graphitic carbon nitride alleviates cadmium toxicity to soybeans through nitrogen supply

Graphitic carbon nitride (g-C3N4) is a promising candidate for heavy metal remediation, primarily composed of carbon (C) and nitrogen (N). It has been demonstrated that g-C3N4 adjusts rhizosphere physicochemical conditions, especially N conditions, alleviating the absorption and accumulation of Cadmium (Cd) by soybeans. However, the mechanisms by which g-C3N4 induces N alterations to mitigates plant uptake of Cd remain unclear. This study investigated the impact of g-C3N4-mediated changes in N conditions on the accumulation of Cd by soybeans using pot experiments. It also explored the microbiological mechanisms underlying alterations in soybean rhizospheric N cycling induced by g-C3N4. It was found that g-C3N4 significantly increased N content in the soybean rhizosphere (p < 0.05), particularly in terms of available nitrogen (AN) of nitrate and ammonium. Plants absorbed more ammonium nitrogen (NH₄⁺-N), the content of which in the roots showed a significant negative correlation with Cd concentration in plant (p < 0.05). Additionally, g-C3N4 significantly affected rhizospheric functional genes associated with N cycling (p < 0.05) by increasing the ratio of the N-fixation functional gene nifH and decreasing the ratios of functional genes amoA and nxrA involved in nitrification. This enhances soybean's N-fixing potential and suppresses denitrification potential in the rhizosphere, preserving NH₄⁺-N. Niastella, Flavisolibacter, Opitutus and Pirellula may play a crucial role in the N fixation and preservation process. In summary, the utilization of g-C3N4 offers a novel approach to ensure safe crop production in Cd-contaminated soils. The results of this study provide valuable data and a theoretical foundation for the remediation of Cd polluted soils.

Rare taxa mediate microbial carbon and nutrient limitation in the rhizosphere and bulk soil under sugarcane-peanut intercropping systems

Introduction

Microbial carbon (C) and nutrient limitation exert key influences on soil organic carbon (SOC) and nutrient cycling through enzyme production for C and nutrient acquisition. However, the intercropping effects on microbial C and nutrient limitation and its driving factors between rhizosphere and bulk soil are unclear.

Methods

Therefore, we conducted a field experiment that covered sugarcane-peanut intercropping with sole sugarcane and peanut as controls and to explore microbial C and nutrient limitation based on the vector analysis of enzyme stoichiometry; in addition, microbial diversity was investigated in the rhizosphere and bulk soil. High throughput sequencing was used to analyze soil bacterial and fungal diversity through the 16S rRNA gene and internal transcribed spacer (ITS) gene at a phylum level.

Results

Our results showed that sugarcane-peanut intercropping alleviated microbial C limitation in all soils, whereas enhanced microbial phosphorus (P) limitation solely in bulk soil. Microbial P limitation was also stronger in the rhizosphere than in bulk soil. These results revealed that sugarcane-peanut intercropping and rhizosphere promoted soil P decomposition and facilitated soil nutrient cycles. The Pearson correlation results showed that microbial C limitation was primarily correlated with fungal diversity and fungal rare taxa (Rozellomycota, Chyltridiomycota, and Calcarisporiellomycota) in rhizosphere soil and was correlated with bacterial diversity and most rare taxa in bulk soil. Microbial P limitation was solely related to rare taxa (Patescibacteria and Glomeromycota) in rhizosphere soil and related to microbial diversity and most rare taxa in bulk soil. The variation partitioning analysis further indicated that microbial C and P limitation was explained by rare taxa (7%-35%) and the interactions of rare and abundant taxa (65%-93%).

Conclusion

This study indicated the different intercropping effects on microbial C and nutrient limitation in the rhizosphere and bulk soil and emphasized the importance of microbial diversity, particularly rare taxa.

Dissecting the role of soybean rhizosphere-enriched bacterial taxa in modulating nitrogen-cycling functions

Crop roots selectively recruit certain microbial taxa that are essential for supporting their growth. Within the recruited microbes, some taxa are consistently enriched in the rhizosphere across various locations and crop genotypes, while others are unique to specific planting sites or genotypes. Whether these differentially enriched taxa are different in community composition and how they interact with nutrient cycling need further investigation. Here, we sampled bulk soil and the rhizosphere soil of five soybean varieties grown in Shijiazhuang and Xuzhou, categorized the rhizosphere-enriched microbes into shared, site-specific, and variety-specific taxa, and analyzed their correlation with the diazotrophic communities and microbial genes involved in nitrogen (N) cycling. The shared taxa were dominated by Actinobacteria and Thaumarchaeota, the site-specific taxa were dominated by Actinobacteria in Shijiazhuang and by Nitrospirae in Xuzhou, while the variety-specific taxa were more evenly distributed in several phyla and contained many rare operational taxonomic units (OTUs). The rhizosphere-enriched taxa correlated with most diazotroph orders negatively but with eight orders including Rhizobiales positively. Each group within the shared, site-specific, and variety-specific taxa negatively correlated with bacterial amoA and narG in Shijiazhuang and positively correlated with archaeal amoA in Xuzhou. These results revealed that the shared, site-specific, and variety-specific taxa are distinct in community compositions but similar in associations with rhizosphere N-cycling functions. They exhibited potential in regulating the soybean roots' selection for high-efficiency diazotrophs and the ammonia-oxidizing and denitrification processes. This study provides new insights into soybean rhizosphere-enriched microbes and their association with N cycling. KEY POINTS: • Soybean rhizosphere affected diazotroph community and enriched nifH, amoA, and nosZ. • Shared and site- and variety-specific taxa were dominated by different phyla. • Rhizosphere-enriched taxa were similarly associated with N-cycle functions.

Developing stable, simplified, functional consortia from Brachypodium rhizosphere for microbial application in sustainable agriculture

The rhizosphere microbiome plays a crucial role in supporting plant productivity and ecosystem functioning by regulating nutrient cycling, soil integrity, and carbon storage. However, deciphering the intricate interplay between microbial relationships within the rhizosphere is challenging due to the overwhelming taxonomic and functional diversity. Here we present our systematic design framework built on microbial colocalization and microbial interaction, toward successful assembly of multiple rhizosphere-derived Reduced Complexity Consortia (RCC). We enriched co-localized microbes from Brachypodium roots grown in field soil with carbon substrates mimicking Brachypodium root exudates, generating 768 enrichments. By transferring the enrichments every 3 or 7 days for 10 generations, we developed both fast and slow-growing reduced complexity microbial communities. Most carbon substrates led to highly stable RCC just after a few transfers. 16S rRNA gene amplicon analysis revealed distinct community compositions based on inoculum and carbon source, with complex carbon enriching slow growing yet functionally important soil taxa like Acidobacteria and Verrucomicrobia. Network analysis showed that microbial consortia, whether differentiated by growth rate (fast vs. slow) or by succession (across generations), had significantly different network centralities. Besides, the keystone taxa identified within these networks belong to genera with plant growth-promoting traits, underscoring their critical function in shaping rhizospheric microbiome networks. Furthermore, tested consortia demonstrated high stability and reproducibility, assuring successful revival from glycerol stocks for long-term viability and use. Our study represents a significant step toward developing a framework for assembling rhizosphere consortia based on microbial colocalization and interaction, with future implications for sustainable agriculture and environmental management.

Deciphering Microbial Adaptation in the Rhizosphere: Insights into Niche Preference, Functional Profiles, and Cross-Kingdom Co-occurrences

Rhizosphere microbial communities are to be as critical factors for plant growth and vitality, and their adaptive differentiation strategies have received increasing amounts of attention but are poorly understood. In this study, we obtained bacterial and fungal amplicon sequences from the rhizosphere and bulk soils of various ecosystems to investigate the potential mechanisms of microbial adaptation to the rhizosphere environment. Our focus encompasses three aspects: niche preference, functional profiles, and cross-kingdom co-occurrence patterns. Our findings revealed a correlation between niche similarity and nucleotide distance, suggesting that niche adaptation explains nucleotide variation among some closely related amplicon sequence variants (ASVs). Furthermore, biological macromolecule metabolism and communication among abundant bacteria increase in the rhizosphere conditions, suggesting that bacterial function is trait-mediated in terms of fitness in new habitats. Additionally, our analysis of cross-kingdom networks revealed that fungi act as intermediaries that facilitate connections between bacteria, indicating that microbes can modify their cooperative relationships to adapt. Overall, the evidence for rhizosphere microbial community adaptation, via differences in gene and functional and co-occurrence patterns, elucidates the adaptive benefits of genetic and functional flexibility of the rhizosphere microbiota through niche shifts.

Zonation of bulk and rhizosphere soil bacterial communities and their covariation patterns along the elevation gradient in riparian zones of three Gorges reservoir, China

Zonation is a typical pattern of soil distribution and species assembly across riparian habitats. Microorganisms are essential members of riparian ecosystems and whether soil microbial communities demonstrate similar zonation patterns and how bulk and rhizosphere soil microorganisms interact along the elevation (submergence stress) gradient remain largely unknown. In this study, bulk and rhizosphere (dominant plant) soil samples were collected and investigated across riparian zones where the submergence stress intensity increased as the elevation decreased. Results showed that the richness of bacterial communities in bulk and rhizosphere soil samples was significantly different and presented a zonation pattern along with the submergence stress gradient. Bulk soil at medium elevation that underwent moderate submergence stress had the most abundant bacterial communities, while the species richness of rhizobacteria at low elevation that experienced serious submergence stress was the highest. Additionally, principal coordinate analysis (PCoA) and significance tests showed that bulk and rhizosphere soil samples were distinguished according to the structure of bacterial communities, and so were bulk or rhizosphere soil samples from different elevations. Redundancy analysis (RDA) and Mantel test suggested that bacterial communities of bulk soil mainly relied on the contents of soil organic matter, total carbon (TC), total nitrogen (TN), sodium (Na), calcium (Ca) and magnesium (Mg). Contrastingly, the contents of Na and Mg were the main factors explaining the variation in rhizobacterial community composition. Correlation and microbial source tracking analyses showed thatthe relationship of bulk and rhizosphere soil bacteria became much stronger, and the rhizosphere soil may get more bacterial communities from bulk soil with the increase in submergence severity. Our results suggest that the abiotic and biotic components of the riparian ecosystem are closely covariant along the submergence stress gradient and imply that the bacterial community may be a key node linking soil physiochemical properties and vegetation communities.

Nitrogen fertilization practices alter microbial communities driven by clonal integration in Moso bamboo

Nitrogen (N) fertilization is crucial for maintaining plant productivity. Clonal plants can share resources between connected ramets through clonal integration influencing microbial communities and regulating soil biogeochemical cycling, especially in the rhizosphere. However, the effect of various N fertilization practices on microbial communities in the rhizosphere of clonal ramets remain unknown. In this study, clonal fragments of Moso bamboo (Phyllostachys edulis), consisting of a parent ramet, an offspring ramet, and an interconnecting rhizome, were established in the field. NH4NO3 solution was applied to the parent, offspring ramets or rhizomes to investigate the effect of fertilization practices on the structure and function of rhizosphere microbial communities. The differences in N availability, microbial biomass and community composition, and abundance of nitrifying genes among rhizosphere soils of ramets gradually decreased during the rapid growth of Moso bamboo, irrespective of fertilization practice. The soil N availability variation, particularly in NO3-, caused by fertilization practices altered the rhizosphere microbial community. Soil N availability and stable microbial biomass N in parent fertilization were the highest, being 9.0 % and 18.7 %, as well as 60.8 % and 90.4 % higher than rhizome and offspring fertilizations, respectively. The microbial network nodes and links in rhizome fertilization were 1.8 and 7.5 times higher than in parent and offspring fertilization, respectively. However, the diversity of bacterial community and abundance of nitrifying and denitrifying genes were the highest in offspring fertilization among three practices, which may be associated with increased N loss. Collectively, the rhizosphere microbial community characteristics depended on fertilization practices by altering the clonal integration of N in Moso bamboo. Parent and rhizome fertilization were favorable for N retention in plant-soil system and resulted in more stable microbial functions than offspring fertilization. Our findings provide new insights into precision fertilization for the sustainable Moso bamboo forest management.

Characteristics of the phyllosphere microbial community and its relationship with major aroma precursors during the tobacco maturation process

Numerous bacteria, fungi and other microorganisms in the tobacco phyllosphere interstellar area participate in the physiological metabolism of plants by interacting with the host. However, there is currently little research on the characteristics of tobacco phyllosphere microbial communities, and the correlation between tobacco phyllosphere microbial communities and phyllosphere factor indicators is still unknown. Therefore, high-throughput sequencing technology based on the 16S rRNA/ITS1 gene was used to explore the diversity and composition characteristics of tobacco phyllosphere bacterial and fungal communities from different maturation processes, and to identify marker genera that distinguish phyllosphere microbial communities. In this study, the correlations between tobacco phyllosphere bacterial and fungal communities and the precursors of major aroma compounds were explored. The results showed that as the tobacco plants matured, the density of glandular trichomes on the tobacco leaves gradually decreased. The surface physicochemical properties of tobacco leaves also undergo significant changes. In addition, the overall bacterial alpha diversity in the tobacco phyllosphere area increased with maturation, while the overall fungal alpha diversity decreased. The beta diversity of bacteria and fungi in the tobacco phyllosphere area also showed significant differences. Specifically, with later top pruning time, the relative abundances of Acidisoma, Ralstonia, Bradyrhizobium, Alternaria and Talaromyces gradually increased, while the relative abundances of Pseudomonas, Filobassidium, and Tausonia gradually decreased. In the bacterial community, Acidisoma, Ralstonia, Bradyrhizobium, and Alternaria were significantly positively correlated with tobacco aroma precursors, with significant negative correlations with tobacco phyllosphere trichome morphology, while Pseudomonas showed the opposite pattern; In the fungal community, Filobasidium and Tausonia were significantly negatively correlated with tobacco aroma precursors, and significantly positively correlated with tobacco phyllosphere trichome morphology, while Alternaria showed the opposite pattern. In conclusion, the microbiota (bacteria and fungi) and aroma precursors of the tobacco phyllosphere change significantly as tobacco matures. The presence of Acidisoma, Ralstonia, Bradyrhizobium and Alternaria in the phyllosphere microbiota of tobacco may be related to the aroma precursors of tobacco.

Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations

BACKGROUND

Soil microbial communities are difficult to measure and critical to soil processes. The bulk soil microbiome is highly diverse and spatially heterogeneous, which can make it difficult to detect and monitor the responses of microbial communities to differences or changes in management, such as different crop rotations in agricultural research. Sampling a subset of actively growing microbes should promote monitoring how soil microbial communities respond to management by reducing the variation contributed by high microbial spatial and temporal heterogeneity and less active microbes. We tested an in-growth bag method using sterilized soil in root-excluding mesh, "sterile sentinels," for the capacity to differentiate between crop rotations. We assessed the utility of different incubation times and compared colonized sentinels to concurrently sampled bulk soils for the statistical power to differentiate microbial community composition in low and high diversity crop rotations. We paired this method with Oxford Nanopore MinION sequencing to assess sterile sentinels as a standardized, fast turn-around monitoring method.

RESULTS

Compared to bulk soil, sentinels provided greater statistical power to distinguish between crop rotations for bacterial communities and equivalent power for fungal communities. The incubation time did not affect the statistical power to detect treatment differences in community composition, although longer incubation time increased total biomass. Bulk and sentinel soil samples contained shared and unique microbial taxa that were differentially abundant between crop rotations.

CONCLUSIONS

Overall, compared to bulk soils, the sentinels captured taxa with copiotrophic or ruderal traits, and plant-associated taxa. The sentinels show promise as a sensitive, scalable method to monitor soil microbial communities and provide information complementary to traditional soil sampling.

Maize functional requirements drive the selection of rhizobacteria under long-term fertilization practices

Rhizosphere microbiomes are pivotal for crop fitness, but the principles underlying microbial assembly during root-soil interactions across soils with different nutrient statuses remain elusive. We examined the microbiomes in the rhizosphere and bulk soils of maize plants grown under six long-term (≥ 29 yr) fertilization experiments in three soil types across middle temperate to subtropical zones. The assembly of rhizosphere microbial communities was primarily driven by deterministic processes. Plant selection interacted with soil types and fertilization regimes to shape the structure and function of rhizosphere microbiomes. Predictive functional profiling showed that, to adapt to nutrient-deficient conditions, maize recruited more rhizobacteria involved in nutrient availability from bulk soil, although these functions were performed by different species. Metagenomic analyses confirmed that the number of significantly enriched Kyoto Encyclopedia of Genes and Genomes Orthology functional categories in the rhizosphere microbial community was significantly higher without fertilization than with fertilization. Notably, some key genes involved in carbon, nitrogen, and phosphorus cycling and purine metabolism were dominantly enriched in the rhizosphere soil without fertilizer input. In conclusion, our results show that maize selects microbes at the root-soil interface based on microbial functional traits beneficial to its own performance, rather than selecting particular species.

Rhizosphere metabolic cross-talk from plant-soil-microbe tapping into agricultural sustainability: Current advance and perspectives

Rhizosphere interactions from plant-soil-microbiome occur dynamically all the time in the "black microzone" underground, where we can't see intuitively. Rhizosphere metabolites including root exudates and microbial metabolites act as various chemical signalings involving in rhizosphere interactions, and play vital roles on plant growth, development, disease suppression and resistance to stress conditions as well as proper soil health. Although rhizosphere metabolites are a mixture from plant roots and soil microbes, they often are discussed alone. As a rapid appearance of various omics platforms and analytical methods, it offers possibilities and opportunities for exploring rhizosphere interactions in unprecedented breadth and depth. However, our comprehensive understanding about the fine-tuning mechanisms of rhizosphere interactions mediated by these chemical compounds still remain clear. Thus, this review summarizes recent advances systemically including the features of rhizosphere metabolites and their effects on rhizosphere ecosystem, and looks forward to the future research perspectives, which contributes to facilitating better understanding of biochemical communications belowground and helping identify novel rhizosphere metabolites. We also address challenges for promoting the understanding about the roles of rhizosphere metabolites in different environmental stresses.

Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally

Agriculture contributes to a decline in local species diversity and to above- and below-ground biotic homogenization. Here, we conduct a continental survey using 1185 soil samples and compare microbial communities from natural ecosystems (forest, grassland, and wetland) with converted agricultural land. We combine our continental survey results with a global meta-analysis of available sequencing data that cover more than 2400 samples across six continents. Our combined results demonstrate that land conversion to agricultural land results in taxonomic and functional homogenization of soil bacteria, mainly driven by the increase in the geographic ranges of taxa in croplands. We find that 20% of phylotypes are decreased and 23% are increased by land conversion, with croplands enriched in Chloroflexi, Gemmatimonadota, Planctomycetota, Myxcoccota and Latescibacterota. Although there is no significant difference in functional composition between natural ecosystems and agricultural land, functional genes involved in nitrogen fixation, phosphorus mineralization and transportation are depleted in cropland. Our results provide a global insight into the consequences of land-use change on soil microbial taxonomic and functional diversity.

A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists

Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.

Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition

Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.

Application Progress of Culturomics in the Isolated Culture of Rhizobacteria: A Review

Comprehending the structure and function of rhizobacteria components and their regulation are crucial for sustainable agricultural management. However, obtaining comprehensive species information for most bacteria in the natural environment, particularly rhizobacteria, presents a challenge using traditional culture methods. To obtain diverse and pure cultures of rhizobacteria, this study primarily reviews the evolution of rhizobacteria culturomics and associated culture methods. Furthermore, it explores new strategies for enhancing the application of culturomics, providing valuable insights into efficiently enriching and isolate target bacterial strains/groups from the environment. The findings will help improve rhizobacteria's culturability and enrich the functional bacterial library.

Classification, biosynthesis, and biological functions of triterpene esters in plants

Triterpene esters comprise a class of secondary metabolites that are synthesized by decorating triterpene skeletons with a series of oxidation, glycosylation, and acylation modifications. Many triterpene esters with important bioactivities have been isolated and identified, including those with applications in the pesticide, pharmaceutical, and cosmetic industries. They also play essential roles in plant defense against pests, diseases, physical damage (as part of the cuticle), and regulation of root microorganisms. However, there has been no recent summary of the biosynthetic pathways and biological functions of plant triterpene esters. Here, we classify triterpene esters into five categories based on their skeletons and find that C-3 oxidation may have a significant effect on triterpenoid acylation. Fatty acid and aromatic moieties are common ligands present in triterpene esters. We further analyze triterpene ester synthesis-related acyltransferases (TEsACTs) in the triterpene biosynthetic pathway. Using an evolutionary classification of BAHD acyltransferases (BAHD-ATs) and serine carboxypeptidase-like acyltransferases (SCPL-ATs) in Arabidopsis thaliana and Oryza sativa, we classify 18 TEsACTs with identified functions from 11 species. All the triterpene-skeleton-related TEsACTs belong to BAHD-AT clades IIIa and I, and the only identified TEsACT from the SCPL-AT family belongs to the CP-I subfamily. This comprehensive review of the biosynthetic pathways and bioactivities of triterpene esters provides a foundation for further study of their bioactivities and applications in industry, agricultural production, and human health.

Recruitment of beneficial cucumber rhizosphere microbes mediated by amino acid secretion induced by biocontrol Bacillus subtilis isolate 1JN2

Introduction

At present, the use of beneficial microorganisms to control cucumber Fusarium wilt is a widely used method, and the rhizosphere microecological reset is one of the mechanisms involved. However, how biocontrol strains reshape cucumber rhizosphere microecology remains to be further studied.

Methods

The composition changes of cucumber root exudates induced by biocontrol strain 1JN2, the microbial ecology of cucumber rhizosphere and the colonization ability of biocontrol strain 1JN2 in cucumber rhizosphere were analyzed through UHPLC-MS/MS analysis, Illumina high-throughput sequencing and SEM, respectively.

Results

First, cucumber plants treated with biocontrol Bacillus 1JN2 reduced the disease severity of Fusarium wilt by 60%. Significant changes in cucumber root exudates were found after 1JN2 inoculation and the contents of four amino acids including glutamine, tryptophan, glycine and glutamic acid were significantly increased. Second, It was found that the bacterial diversity in the rhizosphere of cucumber was significantly increased in both the strain treatment group and the amino acid mixture treatment group, The number of Bacillus was the largest in all dominant populations, exceeded 20% in all treatment groups. The bacteria of Hydrogenispora and Vicinamibacteria were significantly increased after treatment.

Discussion

Overall, the results demonstrated that amino acid substances in cucumber root exudates induced by biocontrol strain 1JN2 can shift the cucumber root microenvironment and prevent the occurrence of Fusarium wilt disease.

Bacillus velezensis SQR9 promotes plant growth through colonization and rhizosphere-phyllosphere bacteria interaction

The rhizosphere and phyllosphere of plants are home to a diverse range of microorganisms that play pivotal roles in ecosystem services. Consequently, plant growth-promoting bacteria (PGPB) are extensively utilized as inoculants to enhance plant growth and boost productivity. Despite this, the interactions between the rhizosphere and phyllosphere, which are influenced by PGPB inoculation, have not been thoroughly studied to date. In this study, we inoculated Bacillus velezensis SQR9, a PGPB, into the bulk soil, rhizosphere or phyllosphere, and subsequently examined the bacterial communities in the rhizosphere and phyllosphere using amplicon sequencing. Our results revealed that PGPB inoculation increased its abundance in the corresponding compartment, and all treatments demonstrated plant growth promotion effects. Further analysis of the sequencing data indicated that the presence of PGPB exerted a more significant impact on bacterial communities in both the rhizosphere and phyllosphere than in the inoculation compartment. Notably, the PGPB stimulated similar rhizosphere-beneficial microbes regardless of the inoculation site. We, therefore, conclude that PGPB can promote plant growth both directly and indirectly through the interaction between the rhizosphere and phyllosphere, leading to the enrichment of beneficial microorganisms.

Negative plant-soil feedback in Arabidopsis thaliana: Disentangling the effects of soil chemistry, microbiome, and extracellular self-DNA

Nutrient deficiency, natural enemies and litter autotoxicity have been proposed as possible mechanisms to explain species-specific negative plant-soil feedback (PSF). Another potential contributor to negative PSF is the plant released extracellular self-DNA during litter decay. In this study, we sought to comprehensively investigate these hypotheses by using Arabidopsis thaliana (L.) Heynh as a model plant in a feedback experiment. The experiment comprised a conditioning phase and a response phase in which the conditioned soils underwent four treatments: (i) addition of activated carbon, (ii) washing with tap water, (iii) sterilization by autoclaving, and (iv) control without any treatment. We evaluated soil chemical properties, microbiota by shotgun sequencing and the amount of A. thaliana extracellular DNA in the differently treated soils. Our results showed that washing and sterilization treatments mitigated the negative PSF effect. While shifts in soil chemical properties were not pronounced, significant changes in soil microbiota were observed, especially after sterilization. Notably, plant biomass was inversely associated with the content of plant self-DNA in the soil. Our results suggest that the negative PSF observed in the conditioned soil was associated to increased amounts of soilborne pathogens and plant self-DNA. However, fungal pathogens were not limited to negative conditions, butalso found in soils enhancing A.thaliana growth. In-depth multivariate analysis highlights that the hypothesis of negative PSF driven solely by pathogens lacks consistency. Instead, we propose a multifactorial explanation for the negative PSF buildup, in which the accumulation of self-DNA weakens the plant's root system, making it more susceptible to pathogens.

Combined effects of azoxystrobin and oxytetracycline on rhizosphere microbiota of Arabidopsis thaliana

The rhizosphere is one of the key determinants of plant health and productivity. Mixtures of pesticides are commonly used in intensified agriculture. However, the combined mechanisms underlying their impacts on soil microbiota remain unknown. The present study revealed that the rhizosphere microbiota was more sensitive to azoxystrobin and oxytetracycline, two commonly used pesticides, than was the microbiota present in bulk soil. Moreover, the rhizosphere microbiota enhanced network complexity and stability and increased carbohydrate metabolism and xenobiotic biodegradation as well as the expression of metabolic genes involved in defence against pesticide stress. Co-exposure to azoxystrobin and oxytetracycline had antagonistic effects on Arabidopsis thaliana growth and soil microbial variation by recruiting organic-degrading bacteria and regulating ABC transporters to reduce pesticide uptake. Our study explored the composition and function of soil microorganisms through amplicon sequencing and metagenomic approaches, providing comprehensive insights into the synergistic effect of plants and rhizosphere microbiota on pesticides and contributing to our understanding of the ecological risks associated with pesticide use.

Heritable microbiome variation is correlated with source environment in locally adapted maize varieties

Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant-microbiota interactions in the face of environmental stresses. Here we surveyed 3,168 root and rhizosphere microbiome samples from 129 accessions of locally adapted Zea, sourced from diverse habitats and grown under control and different stress conditions. We quantified stress treatment and host genotype effects on the microbiome. Plant genotype and source environment were predictive of microbiome abundance. Genome-wide association analysis identified host genetic variants linked to both rhizosphere microbiome abundance and source environment. We identified transposon insertions in a candidate gene linked to both the abundance of a keystone bacterium Massilia in our controlled experiments and total soil nitrogen in the source environment. Isolation and controlled inoculation of Massilia alone can contribute to root development, whole-plant biomass production and adaptation to low nitrogen availability. We conclude that locally adapted maize varieties exert patterns of genetic control on their root and rhizosphere microbiomes that follow variation in their home environments, consistent with a role in tolerance to prevailing stress.

Understanding Salinity-Driven Modulation of Microbial Interactions: Rhizosphere versus Edaphic Microbiome Dynamics

Soil salinization poses a global threat to terrestrial ecosystems. Soil microorganisms, crucial for maintaining ecosystem services, are sensitive to changes in soil structure and properties, particularly salinity. In this study, contrasting dynamics within the rhizosphere and bulk soil were focused on exploring the effects of heightened salinity on soil microbial communities, evaluating the influences shaping their composition in saline environments. This study observed a general decrease in bacterial alpha diversity with increasing salinity, along with shifts in community structure in terms of taxa relative abundance. The size and stability of bacterial co-occurrence networks declined under salt stress, indicating functional and resilience losses. An increased proportion of heterogeneous selection in bacterial community assembly suggested salinity's critical role in shaping bacterial communities. Stochasticity dominated fungal community assembly, suggesting their relatively lower sensitivity to soil salinity. However, bipartite network analysis revealed that fungi played a more significant role than bacteria in intensified microbial interactions in the rhizosphere under salinity stress compared to the bulk soil. Therefore, microbial cross-domain interactions might play a key role in bacterial resilience under salt stress in the rhizosphere.

Enriched rhizospheric functional microbiome may enhance adaptability of Artemisia lavandulaefolia and Betula luminifera in antimony mining areas

Dominant native plants are crucial for vegetation reconstruction and ecological restoration of mining areas, though their adaptation mechanisms in stressful environments are unclear. This study focuses on the interactions between dominant indigenous species in antimony (Sb) mining area, Artemisia lavandulaefolia and Betula luminifera, and the microbes in their rhizosphere. The rhizosphere microbial diversity and potential functions of both plants were analyzed through the utilization of 16S, ITS sequencing, and metabarcoding analysis. The results revealed that soil environmental factors, rather than plant species, had a more significant impact on the composition of the rhizosphere microbial community. Soil pH and moisture significantly affected microbial biomarkers and keystone species. Actinobacteria, Proteobacteria and Acidobacteriota, exhibited high resistance to Sb and As, and played a crucial role in the cycling of carbon, nitrogen (N), phosphorus (P), and sulfur (S). The genes participating in N, P, and S cycling exhibited metabolic coupling with those genes associated with Sb and As resistance, which might have enhanced the rhizosphere microbes' capacity to endure environmental stressors. The enrichment of these rhizosphere functional microbes is the combined result of dispersal limitations and deterministic assembly processes. Notably, the genes related to quorum sensing, the type III secretion system, and chemotaxis systems were significantly enriched in the rhizosphere of plants, especially in B. luminifera, in the mining area. The phylogenetic tree derived from the evolutionary relationships among rhizosphere microbial and chloroplast whole-genome resequencing results, infers both species especially B. luminifera, may have undergone co-evolution with rhizosphere microorganisms in mining areas. These findings offer valuable insights into the dominant native rhizosphere microorganisms that facilitate plant adaptation to environmental stress in mining areas, thereby shedding light on potential strategies for ecological restoration in such environments.

Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere

Nitrogen is the most limiting factor in crop production. Legumes establish a symbiotic relationship with rhizobia and enhance nitrogen fixation. We analyzed 1,624 rhizosphere 16S rRNA gene samples and 113 rhizosphere metagenomic samples from three typical legumes and three non-legumes. The rhizosphere microbial community of the legumes had low diversity and was enriched with nitrogen-cycling bacteria (Sphingomonadaceae, Xanthobacteraceae, Rhizobiaceae, and Bacillaceae). Furthermore, the rhizosphere microbiota of legumes exhibited a high abundance of nitrogen-fixing genes, reflecting a stronger nitrogen-fixing potential, and Streptomycetaceae and Nocardioidaceae were the predominant nitrogen-fixing bacteria. We also identified helper bacteria and confirmed through metadata analysis and a pot experiment that the synthesis of riboflavin by helper bacteria is the key factor in promoting nitrogen fixation. Our study emphasizes that the construction of synthetic communities of nitrogen-fixing bacteria and helper bacteria is crucial for the development of efficient nitrogen-fixing microbial fertilizers.

Distinct toxic effects, gene expression profiles, and phytohormone responses of Polygonatum cyrtonema exposed to two different antibiotics

The excessive usage of veterinary antibiotics has raised significant concerns regarding their environmental hazard and agricultural impact when entering surface water and soil. Animal waste serves as a primary source of organic fertilizer for intensive large-scale agricultural cultivation, including the widely utilized medicinal and edible plant, Polygonatum cyrtonem. In this study, we employed a novel plant stress tissue culture technology to investigate the toxic effects of tetracycline hydrochloride (TCH) and sulfadiazine (SDZ) on P. cyrtonema. TCH and SDZ exhibited varying degrees of influence on plant growth, photosynthesis, and the reactive oxygen species (ROS) scavenging system. Flavonoid levels increased following exposure to TCH and SDZ. The biosynthesis and signaling pathways of the growth hormones auxin and gibberellic acid were suppressed by both antibiotics, while the salicylic acid-mediated plant stress response was specifically induced in the case of SDZ. Overall, the study unveiled both common and unique responses at physiological, biochemical, and molecular levels in P. cyrtonema following exposure to two distinct types of antibiotics, providing a foundational framework for comprehensively elucidating the precise toxic effects of antibiotics and the versatile adaptive mechanisms in plants.

Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice

The soil-root interface harbors complex fungal communities that play vital roles in the fitness of host plants. However, little is known about the assembly rules and potential functions of rhizospheric and endospheric mycobiota. A greenhouse experiment was conducted to explore the fungal communities inhabiting the rhizosphere and roots of 87 rice cultivars at the tillering stage via amplicon sequencing of the fungal internal transcribed spacer 1 region. The potential relationships between these communities and host plant functional traits were also investigated using Procrustes analysis, generalized additive model fitting, and correlation analysis. The fungal microbiota exhibited greater richness, higher diversity, and lower structural variability in the rhizosphere than in the root endosphere. Compared with the root endosphere, the rhizosphere supported a larger coabundance network, with greater connectivity and stronger cohesion. Null model-based analyses revealed that dispersal limitation was primarily responsible for rhizosphere fungal community assembly, while ecological drift was the dominant process in the root endosphere. The community composition of fungi in the rhizosphere was shown to be more related to plant functional traits, such as the root/whole plant biomass, root:shoot biomass ratio, root/shoot nitrogen (N) content, and root/shoot/whole plant N accumulation, than to that in the root endosphere. Overall, at the early stage of rice growth, diverse and complex rhizospheric fungal communities are shaped by stochastic-based processes and exhibit stronger associations with plant functional traits.

IMPORTANCE

The assembly processes and functions of root-associated mycobiota are among the most fascinating yet elusive topics in microbial ecology. Our results revealed that stochastic forces (dispersal limitation or ecological drift) act on fungal community assembly in both the rice rhizosphere and root endosphere at the early stage of plant growth. In addition, high covariations between the rhizosphere fungal community compositions and plant functional trait profiles were clearly demonstrated in the present study. This work provides empirical evidence of the root-associated fungal assembly principles and ecological relationships of plant functional traits with rhizospheric and root endospheric mycobiota, thereby potentially providing novel perspectives for enhancing plant performance.

Root-associated bacteria strengthen their community stability against disturbance of antibiotics on structure and functions

Antibiotics affect bacterial community structure and functions in soil. However, the response and adaptation of root-associated bacterial communities to antibiotic stress remains poorly understood. Here, rhizobox experiments were conducted with maize (Zea mays L.) upon exposure to antibiotics ciprofloxacin or tetracycline. High-throughput sequencing analysis of bacterial community and quantitative PCR analysis of nitrogen cycling genes show that ciprofloxacin and tetracycline significantly shift bacterial community structure in bulk soil, whereas plant host may mitigate the disturbances of antibiotics on bacterial communities in root-associated niches (i.e., rhizosphere and rhizoplane) through the community stabilization. Deterministic assembly, microbial interaction, and keystone species (e.g., Rhizobium and Massilia) of root-associated bacterial communities benefit the community stability compared with those in bulk soil. Meanwhile, the rhizosphere increases antibiotic dissipation, potentially reducing the impacts of antibiotics on root-associated bacterial communities. Furthermore, rhizospheric effects deriving from root exudates alleviate the impacts of antibiotics on the nitrogen cycle (i.e., nitrification, organic nitrogen conversion and denitrification) as confirmed by functional gene quantification, which is largely attributed to the bacterial community stability in rhizosphere. The present study enhances the understanding on the response and adaptation of root-associated bacterial community to antibiotic pollution.

Meta-analysis of biodynamic (BD) preparations reveal the bacterial population involved in improving soil health, crop yield and quality

BACKGROUND

Bacterial community found in biodynamic preparations (BD500-BD507) can help improve soil health, plant development, yield, and quality. The current work describes a metagenomic investigation of these preparations to identify the bacterial communities along with the functional diversity present within them.

RESULTS

Metagenome sequencing was performed using the Illumina MiSeq platform, which employs next-generation sequencing (NGS) technology, to provide an understanding of the bacterial communities and their functional diversity in BD preparations. NGS data of BD preparations revealed that maximum operational taxonomic units (OTUs) of the phylum Proteobacteria were present in BD506 (23429) followed by BD505 (22712) and BD501 (21591), respectively. Moreover, unclassified phylum (16657) and genus (16657) were also highest in BD506. Maximum alpha diversity was reported in BD501 (1095 OTU) and minimum in BD507 (257 OTU). Further, the OTUs for five major metabolic functional groups viz carbohydrate metabolism, xenobiotic degradation, membrane transport functions, energy metabolism, and enzyme activities were abundant in BD506 and BD501.

CONCLUSION

The bacterial communities in BD506 and BD501 are found to be unique and rare; they belong to functional categories that are involved in enzyme activity, membrane transport, xenobiotic degradation, and carbohydrate metabolism. These preparations might therefore be thought to be more effective. The investigation also found a highly varied population of bacteria, which could explain why BD preparations work well in the field. In view of this, the BD preparations may be utilized for unexploited bacterial communities for sustainable agriculture production.

Holistic Approaches to Plant Stress Alleviation: A Comprehensive Review of the Role of Organic Compounds and Beneficial Bacteria in Promoting Growth and Health

Plants select microorganisms from the surrounding bulk soil, which act as a reservoir of microbial diversity and enrich a rhizosphere microbiome that helps in growth and stress alleviation. Plants use organic compounds that are released through root exudates to shape the rhizosphere microbiome. These organic compounds are of various spectrums and technically gear the interplay between plants and the microbial world. Although plants naturally produce organic compounds that influence the microbial world, numerous efforts have been made to boost the efficiency of the microbiome through the addition of organic compounds. Despite further crucial investigations, synergistic effects from organic compounds and beneficial bacteria combinations have been reported. In this review, we examine the relationship between organic compounds and beneficial bacteria in determining plant growth and biotic and abiotic stress alleviation. We investigate the molecular mechanism and biochemical responses of bacteria to organic compounds, and we discuss the plant growth modifications and stress alleviation done with the help of beneficial bacteria. We then exhibit the synergistic effects of both components to highlight future research directions to dwell on how microbial engineering and metagenomic approaches could be utilized to enhance the use of beneficial microbes and organic compounds.

Dynamic root microbiome sustains soybean productivity under unbalanced fertilization

Root-associated microbiomes contribute to plant growth and health, and are dynamically affected by plant development and changes in the soil environment. However, how different fertilizer regimes affect quantitative changes in microbial assembly to effect plant growth remains obscure. Here, we explore the temporal dynamics of the root-associated bacteria of soybean using quantitative microbiome profiling (QMP) to examine its response to unbalanced fertilizer treatments (i.e., lacking either N, P or K) and its role in sustaining plant growth after four decades of unbalanced fertilization. We show that the root-associated bacteria exhibit strong succession during plant development, and bacterial loads largely increase at later stages, particularly for Bacteroidetes. Unbalanced fertilization has a significant effect on the assembly of the soybean rhizosphere bacteria, and in the absence of N fertilizer the bacterial community diverges from that of fertilized plants, while lacking P fertilizer impedes the total load and turnover of rhizosphere bacteria. Importantly, a SynCom derived from the low-nitrogen-enriched cluster is capable of stimulating plant growth, corresponding with the stabilized soybean productivity in the absence of N fertilizer. These findings provide new insights in the quantitative dynamics of the root-associated microbiome and highlight a key ecological cluster with prospects for sustainable agricultural management.

Integrated microbiome and metabolomics analysis reveal the relationship between plant-specialized metabolites and microbial community in Phellodendron amurense

Phellodendron amurense is the essential source of bisbenzylisoquinoline alkaloids (BIAs), making it a highly valued raw material in traditional Chinese medicine. The plant's root secondary metabolism is intricately linked to the microbial communities that surround it. However, the root-associated microbiomes of P. amurense, as well as the potential correlation between its bioactive compounds and these microbiomes, remain poorly understood. Here, the metabolic profiles of root, rhizosphere, and bulk soils of P. amurense revealed the dramatic differences in the relative content of plant-specialized metabolites. A total of 31, 21, and 0 specialized metabolites in P. amurense were identified in the root, rhizosphere soil, and bulk soil, respectively, with higher content of the seven major BIAs observed in the rhizosphere compared with that in the bulk soils. The composition of the bulk and rhizosphere microbiomes was noticeably distinct from that of the endospheric microbiome. The phylum Cyanobacteria accounted for over 60% of the root endosphere communities, and the α-diversity in root was the lowest. Targeted seven BIAs, namely, berberine, palmatine, magnocurarine, phellodendrine, jatrorrhizine, tetrahydropalmatine, and magnoflorine, were significantly positively correlated with Nectriaceae and Sphingobacteriaceae. This study has illuminated the intricate interaction networks between P. amurense root-associated microorganisms and their key chemical compounds, providing the theoretical foundation for discovering biological fertilizers and laying the groundwork for cultivating high-quality medicinal plants.

Microplastics alter Cr accumulation and fruit quality in Cr(VI) contaminated soil-cucumber system during the lifecycle: Insight from rhizosphere bacteria and root metabolism

Both microplastics and Cr(VI) potentially threaten soil and crops, but little is known about their interaction in the soil-plant system. This study investigated the effect and mechanism of polyethylene (PE), polyamide (PA), and polylactic acid (PLA) microplastics on Cr bioaccumulation and toxicity in a Cr(VI) contaminated soil-cucumber system during the lifecycle. The results show that microplastics had a greater effect on Cr accumulation in cucumber roots, stems, and leaves than in fruits. PE microplastics increased, but PA and PLA microplastics decreased the Cr accumulation in cucumber. Microplastics, especially high-dose, small, and aged microplastics, exacerbated the effects of accumulated Cr in cucumber on fresh weight and fruit yield. The nutrient contents in fruits except soluble sugars were reduced by microplastics. The random forest regression model shows that the microplastic type was the most important factor causing changes in the soil-cucumber system except for Cr(VI) addition. Under Cr(VI) and microplastic co-exposure, bacteria that could simultaneously tolerate Cr(VI) stress and degrade microplastics were enriched in the rhizosphere soil. The partial least squares path model shows that microplastics reduced the beneficial effect of the bacterial community on cucumber growth. Microplastics, especially PLA microplastics, alleviated the adverse effects of Cr(VI) stress on root metabolism.

Evaluating the role of rhizosphere microbial home-field advantage in Betula luminifera adaptation to antimony mining areas

It has been established that the coevolution of plants and the rhizosphere microbiome in response to abiotic stress can result in the recruitment of specific functional microbiomes. However, the potential of inoculated rhizosphere microbiomes to enhance plant fitness and the inheritance of adaptive traits in subsequent generations remains unclear. In this study, cross-inoculation trials were conducted using seeds, rhizosphere microbiome, and in situ soil collected from areas of Betula luminifera grown in both antimony mining and control sites. Compared to the control site, plants originating from mining areas exhibited stronger adaptive traits, specifically manifested as significant increases in hundred-seed weight, specific surface area, and germination rate, as well as markedly enhanced seedling survival rate and biomass. Inoculation with mining microbiomes could enhance the fitness of plants in mining sites through a "home-field advantage" while also improving the fitness of plants originating from control sites. During the initial phase of seedling development, bacteria play a crucial role in promoting growth, primarily due to their mechanisms of metal resistance and nutrient cycling. This study provided evidence that the outcomes of long-term coevolution between plants and the rhizosphere microbiome in mining areas can be passed on to future generations. Moreover, it has been demonstrated that transgenerational inheritance and rhizosphere microbiome inoculation are important factors in improving the adaptability of plants in mining areas. The findings have important implications for vegetation restoration and ecological environment improvement in mining areas.

Response and adaptation of rhizosphere microbiome to organic pollutants with enriching pollutant-degraders and genes for bioremediation: A critical review

Phytoremediation largely involves microbial degradation of organic pollutants in rhizosphere for removing organic pollutants like polycyclic aromatic hydrocarbons, phthalates and polychlorinated biphenyls. Microbial community in rhizosphere experiences complex processes of response-adaptation-feedback up on exposure to organic pollutants. This review summarizes recent research on the response and adaptation of rhizosphere microbial community to the stress of organic pollutants, and discusses the enrichment of the pollutant-degrading microbial community and genes in the rhizosphere for promoting bioremediation. Soil pollution by organic contaminants often reduces the diversity of rhizosphere microbial community, and changes its functions. Responses vary among rhizosphere microbiomes up on different classes of organic pollutants (including co-contamination with heavy metals), plant species, root-associated niches (e.g., rhizosphere, rhizoplane and endosphere), geographical location and soil properties. Soil pollution can deplete some sensitive microbial taxa and enrich some tolerant microbial taxa in rhizosphere. Furthermore, rhizosphere enriches pollutant-degrading microbial community and functional genes including different gene clusters responsible for biodegradation of organic pollutants and their intermediates, which improve the adaptation of microbiome and enhance the remediation efficiency of the polluted soil. The knowledge gaps and future research challenges are highlighted on rhizosphere microbiome in response-adaptation-feedback processes to organic pollution and rhizoremediation. This review will hopefully update understanding on response-adaptation-feedback processes of rhizosphere microbiomes and rhizoremediation for the soil with organic pollutants.

Granular bacterial inoculant alters the rhizosphere microbiome and soil aggregate fractionation to affect phosphorus fractions and maize growth

The constraint of phosphorus (P) fixation on crop production in alkaline calcareous soils can be alleviated by applying bioinoculants. However, the impact of bacterial inoculants on this process remains inadequately understood. Here, a field study was conducted to investigate the effect of a high-concentration, cost-effective, and slow-release granular bacterial inoculant (GBI) on maize (Zea mays L.) plant growth. Additionally, we explored the effects of GBI on rhizosphere soil aggregate physicochemical properties, rhizosphere soil P fraction, and microbial communities within aggregates. The outcomes showed a considerable improvement in plant growth and P uptake upon application of the GBI. The application of GBI significantly enhanced the AP, phoD gene abundance, alkaline phosphatase activity, inorganic P fractions, and organic P fractions in large macroaggregates. Furthermore, GBI impacted soil aggregate fractionation, leading to substantial alterations in the composition of fungal and bacterial communities. Notably, key microbial taxa involved in P-cycling, such as Saccharimonadales and Mortierella, exhibited enrichment in the rhizosphere soil of plants treated with GBI. Overall, our study provides valuable insight into the impact of GBI application on microbial distributions and P fractions within aggregates of alkaline calcareous soils, crucial for fostering healthy root development and optimal crop growth potential. Subsequent research endeavors should delve into exploring the effects of diverse GBIs and specific aggregate types on P fraction and community composition across various soil profiles.

Study of the Bacterial, Fungal, and Archaeal Communities Structures near the Bulgarian Antarctic Research Base "St. Kliment Ohridski" on Livingston Island, Antarctica

As belonging to one of the most isolated continents on our planet, the microbial composition of different environments in Antarctica could hold a plethora of undiscovered species with the potential for biotechnological applications. This manuscript delineates our discoveries after an expedition to the Bulgarian Antarctic Base "St. Kliment Ohridski" situated on Livingston Island, Antarctica. Amplicon-based metagenomics targeting the 16S rRNA genes and ITS2 region were employed to assess the metagenomes of the bacterial, fungal, and archaeal communities across diverse sites within and proximal to the research station. The predominant bacterial assemblages identified included Oxyphotobacteria, Bacteroidia, Gammaprotobacteria, and Alphaprotobacteria. A substantial proportion of cyanobacteria reads were attributed to a singular uncultured taxon within the family Leptolyngbyaceae. The bacterial profile of a lagoon near the base exhibited indications of penguin activity, characterized by a higher abundance of Clostridia, similar to lithotelm samples from Hannah Pt. Although most fungal reads in the samples could not be identified at the species level, noteworthy genera, namely Betamyces and Tetracladium, were identified. Archaeal abundance was negligible, with prevalent groups including Woesearchaeales, Nitrosarchaeum, Candidatus Nitrosopumilus, and Marine Group II.

Soil fertility impact on recruitment and diversity of the soil microbiome in sub-humid tropical pastures in Northeastern Brazil

Soil fertility is key point to pastures systems and drives the microbial communities and their functionality. Therefore, an understanding of the interaction between soil fertility and microbial communities can increase our ability to manage pasturelands and maintain their soil functioning and productivity. This study probed the influence of soil fertility on microbial communities in tropical pastures in Brazil. Soil samples, gathered from the top 20 cm of twelve distinct areas with diverse fertility levels, were analyzed via 16S rRNA sequencing. The soils were subsequently classified into two categories, namely high fertility (HF) and low fertility (LF), using the K-Means clustering. The random forest analysis revealed that high fertility (HF) soils had more bacterial diversity, predominantly Proteobacteria, Nitrospira, Chloroflexi, and Bacteroidetes, while Acidobacteria increased in low fertility (LF) soils. High fertility (HF) soils exhibited more complex network interactions and an enrichment of nitrogen-cycling bacterial groups. Additionally, functional annotation based on 16S rRNA varied between clusters. Microbial groups in HF soil demonstrated enhanced functions such as nitrate reduction, aerobic ammonia oxidation, and aromatic compound degradation. In contrast, in the LF soil, the predominant processes were ureolysis, cellulolysis, methanol oxidation, and methanotrophy. Our findings expand our knowledge about how soil fertility drives bacterial communities in pastures.

Nitrogen sources enhance siderophore-mediated competition for iron between potato common scab and late blight causative agents

How do pathogens affecting the same host interact with each other? We evaluated here the types of microbe-microbe interactions taking place between Streptomyces scabiei and Phytophthora infestans, the causative agents of common scab and late blight diseases in potato crops, respectively. Under most laboratory culture conditions tested, S. scabiei impaired or completely inhibited the growth of P. infestans by producing either soluble and/or volatile compounds. Increasing peptone levels correlated with increased inhibition of P. infestans. Comparative metabolomics showed that production of S. scabiei siderophores (desferrioxamines, pyochelin, scabichelin, and turgichelin) increased with the quantity of peptone, thereby suggesting that they participate in the inhibition of the oomycete growth. Mass spectrometry imaging further uncovered that the zones of secreted siderophores and of P. infestans growth inhibition coincided. Moreover, either the repression of siderophore production or the neutralization of their iron-chelating activity led to a resumption of P. infestans growth. Replacement of peptone by natural nitrogen sources such as ammonium nitrate, sodium nitrate, ammonium sulfate, and urea also triggered siderophore production in S. scabiei. Interestingly, nitrogen source-induced siderophore production also inhibited the growth of Alternaria solani, the causative agent of the potato early blight. Overall, our work further emphasizes the importance of competition for iron between microorganisms that colonize the same niche. As common scab never alters the vegetative propagation of tubers, we propose that S. scabiei, under certain conditions, could play a protective role for its hosts against much more destructive pathogens through exploitative iron competition and volatile compound production.

Appropriately Reduced Nitrogen and Increased Phosphorus in Ratooning Rice Increased the Yield and Reduced the Greenhouse Gas Emissions in Southeast China

Reducing greenhouse gas emissions while improving productivity is the core of sustainable agriculture development. In recent years, rice ratooning has developed rapidly in China and other Asian countries, becoming an effective measure to increase rice production and reduce greenhouse gas emissions in these regions. However, the lower yield of ratooning rice caused by the application of a single nitrogen fertilizer in the ratooning season has become one of the main reasons limiting the further development of rice ratooning. The combined application of nitrogen and phosphorus plays a crucial role in increasing crop yield and reducing greenhouse gas emissions. The effects of combined nitrogen and phosphorus application on ratooning rice remain unclear. Therefore, this paper aimed to investigate the effect of combined nitrogen and phosphorus application on ratooning rice. Two hybrid rice varieties, 'Luyou 1831' and 'Yongyou 1540', were used as experimental materials. A control treatment of nitrogen-only fertilization (187.50 kg·ha-1 N) was set, and six treatments were established by reducing nitrogen fertilizer by 10% (N1) and 20% (N2), and applying three levels of phosphorus fertilizer: N1P1 (168.75 kg·ha-1 N; 13.50 kg·ha-1 P), N1P2 (168.75 kg·ha-1 N; 27.00 kg·ha-1 P), N1P3 (168.75 kg·ha-1 N; 40.50 kg·ha-1 P), N2P1 (150.00 kg·ha-1 N; 13.50 kg·ha-1 P), N2P2 (150.00 kg·ha-1 N; 27.00 kg·ha-1 P), and N2P3 (150.00 kg·ha-1 N; 40.50 kg·ha-1 P). The effects of reduced nitrogen and increased phosphorus treatments in ratooning rice on the yield, the greenhouse gas emissions, and the community structure of rhizosphere soil microbes were examined. The results showed that the yield of ratooning rice in different treatments followed the sequence N1P2 > N1P1 > N1P3 > N2P3 > N2P2 > N2P1 > N. Specifically, under the N1P2 treatment, the average two-year yields of 'Luyou 1831' and 'Yongyou 1540' reached 8520.55 kg·ha-1 and 9184.90 kg·ha-1, respectively, representing increases of 74.30% and 25.79% compared to the N treatment. Different nitrogen and phosphorus application combinations also reduced methane emissions during the ratooning season. Appropriately combined nitrogen and phosphorus application reduced the relative contribution of stochastic processes in microbial community assembly, broadened the niche breadth of microbial communities, enhanced the abundance of functional genes related to methane-oxidizing bacteria and soil ammonia-oxidizing bacteria in the rhizosphere, and decreased the abundance of functional genes related to methanogenic and denitrifying bacteria, thereby reducing greenhouse gas emissions in the ratooning season. The carbon footprint of ratooning rice for 'Luyou 1831' and 'Yongyou 1540' decreased by 25.82% and 38.99%, respectively, under the N1P2 treatment compared to the N treatment. This study offered a new fertilization pattern for the green sustainable development of rice ratooning.

Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model

Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.