Rhizosphere Bacterial Communities Research Articles

Breed Selection of Poplars Imposes Greater Selection Pressure on the Rhizosphere Bacterial Community

Breed selection alters the coevolution of plant–microbiome associations that have developed over long periods of natural evolution. We investigated the effects of breed selection on the rhizosphere microbiomes and metabolites of hybrid parents (I101 and 84K) and their offspring (Q1–Q5) using metagenomics and untargeted metabolomics. Rhizosphere archaeal, bacterial and fungal community β-diversity significantly differed among hybrid parents and offspring, but only the dominant bacterial phyla and bacterial community α-diversity revealed significant differences. Approximately 5.49%, 14.90% and 7.86% of the archaeal, bacterial and fungal species significantly differed among the poplar hybrid parents and offspring. Rhizosphere microbial functional genes and metabolites were both clustered into the following three groups: I101 and 84K; Q2 and Q4; and Q1, Q3 and Q5. Compared with the hybrid parents, 15 phytochemical compounds were enriched in the hybrid offspring and explained 7.15%, 18.24% and 6.68% of the total variation in the archaeal, bacterial and fungal community compositions, respectively. Rhizosphere metabolites significantly affected the bacterial community, rather than the archaeal and fungal communities. Our observations suggested that poplar breed selection imposed greater selection pressure on the rhizosphere bacterial community, which was mainly driven by metabolites.

Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities.

Associations with soil microorganisms are crucial for plants' overall health and functioning. While much work has been done to understand drivers of rhizosphere microbiome structure and function, the relative importance of geography, climate, soil properties, and plant genetics remains unclear, as results have been mixed and comprehensive studies across many sites and genotypes are limited. Rhizosphere microbiomes are crucial for crop resistance to pathogens, stress tolerance, nutrient availability, and ultimately yield. Here, we quantify the relative roles of plant genotype, environment, and their interaction in shaping soil rhizosphere communities, using 16S and ITS gene sequencing of rhizosphere soils from 10 genotypes of cultivated sunflower (Helianthus annuus) at 15 sites across the Great Plains of the United States. While site generally outweighed genotype overall in terms of effects on archaeal, bacterial, and fungal richness, community composition, and taxa relative abundances, there was also a significant interaction such that genotype exerted a significant influence on archaeal, bacterial, and fungal microbiomes in certain sites. Site effects were attributed to a combination of spatial distance and differences in climate and soil properties. Microbial taxa that were previously associated with resistance to the fungal necrotrophic pathogen Sclerotinia were present in most sites but differed significantly in relative abundance across sites. Our results have implications for plant breeding and agronomic microbiome manipulations for agricultural improvement across different geographic regions.IMPORTANCEDespite the importance of plant breeding in agriculture, we still have a limited understanding of how plant genetic variation shapes soil microbiome composition across broad geographic regions. Using 15 sites across the Great Plains of North America, we show that cultivated sunflower rhizosphere archaeal, bacterial, and fungal communities are driven primarily by site soil and climatic differences, but genotype can interact with site to influence the composition, especially in warmer and drier sites with lower overall microbial richness. We also show that all taxa that were previously found to be associated with resistance to the fungal pathogen Sclerotinia sclerotiorum were widespread but significantly affected by site, while a subset was also significantly affected by genotype. Our results contribute to a broader understanding of rhizosphere archaeal, bacterial, and fungal community assembly and provide foundational knowledge for plant breeding efforts and potential future microbiome manipulations in agriculture.

Understanding rhizospheric microbial dynamics in gladiolus corms through quorum sensing and quorum quenching for disease control and growth promotion

Gladiolus, a widely cultivated cut flower known for its aesthetically pleasing multicoloured spikes, has earned significant commercial popularity. A comprehensive understanding of the rhizosphere bacterial community associated with gladiolus is imperative for revealing its potential benefits. Molecular characterization is considered an effective method to gain insights into the structural and functional aspects of microbial populations. The soil characteristics and bacterial communities in the rhizosphere are typically influenced by quorum sensing (QS) and quorum quenching (QQ) mechanisms. This study aims to explore the niceties and diversity of rhizospheric bacterial populations linked with gladiolus corms, with a specific focus on understanding the dynamics of QS and QQ mechanisms in their complex interactions. The isolation of bacterial strains was achieved through the serial dilution method on nutrient agar (NA) media. The identification of the isolates was accomplished by amplifying 16 S rRNA gene sequences via polymerase chain reaction (PCR) via the use of universal primers. Sequence analysis was conducted via BLAST on the National Center for Biotechnology Information (NCBI) database. The characteristics of the isolated bacteria were elucidated via biosensors. This study identified three QS strains and five QQ strains. A consortium of quenchers was formulated utilizing five strains that demonstrated efficacy in mitigating the impact of disease on gladiolus and fostering growth. Among the three treatments—Scale, Descale, and Descale and Cut Half (DSC)—the DSC treatment emerged as the most effective. This treatment exhibited a broader range of variation in biological parameters over time, aligning with prevailing trends in the local market.

The structure and function of rhizosphere bacterial communities: impact of chemical vs. bio-organic fertilizers on root disease, quality, and yield of Codonopsis pilosula

IntroductionLong-term use of chemical fertilizers (CFs) can cause soil compaction and acidification. In recent years, bio-organic fertilizers (BOFs) have begun to replace CFs in some vegetables and cash crops, but the application of CFs or BOFs has resulted in crop quality and disease occurrence.MethodsThis study aimed to analyze the microbial mechanism of differences between CFs and BOFs in root disease, quality, and yield of tuber Chinese herbal medicine. We studied the effects of CFs, organic fertilizers, commercial BOFs, biocontrol bacteria BOFs, and biocontrol fungi BOFs on rhizosphere microbial community structure and function, root rot, quality, and yield of Codonopsis pilosula at different periods after application and analyzed the correlation.Results and discussionCompared to CFs, the emergence rate and yield in BOF treatments were increased by 21.12 and 33.65%, respectively, and the ash content, water content, and disease index in the BOF treatments were decreased by 17.87, 8.19, and 76.60%, respectively. The structural equation model showed that CFs promoted the quality and yield of C. pilosula by influencing soil environmental factors, while BOFs directly drove soil bacterial community to reduce disease index and improve the quality and yield of C. pilosula. There was a stronger interaction and stability of soil microbial networks after BOF treatments. Microlunatus, Rubrobacter, Luteitalea, Nakamurella, and Pedomicrobium were identified as effector bacteria, which were related to disease prevention and yield and quality increase of C. pilosula. Microbial functional analysis indicated that the signal transduction and amino acid metabolism of soil bacteria might play a major role in improving the quality and yield of C. pilosula in the early and middle growth stages. In conclusion, compared to CFs, BOFs obtained a lower disease index of root rot and a higher quality and yield of C. pilosula by changing the structure and function of the rhizosphere bacterial community.

Enhancing the Growth of Chili Plants and Soil Health: Synergistic Effects of Coconut Shell Biochar and Bacillus Sp. Strain Ya-1 on Rhizosphere Microecology and Plant Metabolism

To mitigate soil degradation and decrease dependency on chemical inputs in agriculture, this study examined the joint effects of coconut shell biochar and Bacillus strain Ya-1 on soil fertility, rhizosphere bacterial communities, and the growth of chili (Capsicum annuum L.). A controlled pot experiment with four treatments was conducted: control (CK), biochar only (C), Bacillus strain Ya-1 only (B), and a combination of both (BC). The BC treatment significantly enhanced the soil carbon and available phosphorus contents by approximately 20% and the soil nitrogen content and pH by 18% and 0.3 units, respectively, compared to the control. It also increased microbial biomass carbon and nitrogen by 25% and 30%, respectively, indicating improved soil microbial diversity as shown by the highest Pielou evenness index and Shannon index values. The combined application of biochar and the Ya-1 strain resulted in a 15% increase in chili plant height and a 40% improvement in root dehydrogenase activity, suggesting enhanced nutrient uptake and metabolism. Metabolic profiling showed shifts in stress response and nutrient assimilation under different treatments. Collectively, these results indicate the potential of biochar and microbial inoculants to significantly promote soil and plant health, providing a sustainable strategy to improve agricultural productivity and reduce reliance on chemical inputs.

Key Chemical Soil Parameters for the Assembly of Rhizosphere Bacteria Associated with Avocado Cv Hass Grafted on Landrace Rootstocks

Avocado cultivation holds significant economic importance in many countries, ranking Colombia as the fifth largest global producer. Particularly, the Hass cultivar plays a pivotal role in Colombia’s avocado industry, especially in the Department of Antioquia, the primary export region. This cultivar is grown under diverse soil and climate conditions and exhibits considerable genetic polymorphism due to the hybridization of varieties of agronomic significance, leading to a diverse array of landrace rootstocks. However, the role of soil conditions and rootstock genotype in structuring rhizosphere bacterial communities is still lacking. In addressing this knowledge gap, we investigated the influence of two soil conditions on the structure of rhizosphere bacterial communities associated with two landrace genotypes of Persea americana cv. Hass, utilizing 16S rRNA sequencing. Notably, no significant differences related to genotypes were observed. This study reports that the rhizosphere bacterial microbiome remains consistent across avocado landrace rootstocks, while variations in key parameters such as phosphorus, pH, Mg, and Ca drive distinct rhizosphere effects. Our results reveal that despite the soils having similar management, increases in these crucial parameters can lead to bacterial communities with lower alpha diversity and a more complex co-occurrence network. In addition, we found substantial variations in beta diversity, bacterial composition, and metagenome predictions between the two farms, underscoring the role of soil variables in shaping the bacterial microbiome. These findings provide valuable insights into the factors influencing the bacterial communities that may play a role in the health and productivity of crops with agro-industrial potential, such as Hass avocado.

Diversity and interactions of rhizobacteria determine multinutrient traits in tomato host plants under nitrogen and water disturbances

Abstract Coevolution within the plant holobiont extends the capacity of host plants for nutrient acquisition and stress resistance. However, the role of the rhizospheric microbiota in maintaining multinutrient utilization (i.e., multinutrient traits) in the host remains to be elucidated. Multinutrient cycling index (MNC), analogous to the widely used multifunctionality index, provides a straightforward and interpretable measure of the multinutrient traits in host plants. Using tomato as a model plant, we characterized MNC (based on multiple aboveground nutrient contents) in host plants under different nitrogen and water supply regimes and explored the associations between rhizospheric bacterial community assemblages and host-plant multinutrient profiles. Rhizosphere bacterial community diversity, quantitative abundance, predicted function, and key topological features of the co-occurrence network were more sensitive to water supply than to nitrogen supply. A core bacteriome comprising 61 genera, such as Candidatus Koribacter and Streptomyces, persisted across different habitats and served as a key predictor of host-plant nutrient uptake. The MNC index increased with greater diversity and higher core taxon abundance in the rhizobacterial community, while decreasing with higher average degree and graph density of rhizobacterial co-occurrence network. Multinutrient absorption by host plants was primarily regulated by community diversity and rhizobacterial network complexity under the interaction of nitrogen and water. The high biodiversity and complex species interactions of the rhizospheric bacteriome play crucial roles in host-plant performance. This study supports the development of rhizosphere microbiome engineering, facilitating effective manipulation of the microbiome for enhanced plant benefits, which supports sustainable agricultural practices and plant health.

Mangrove afforestation as an ecological control of invasive Spartina alterniflora affects rhizosphere soil physicochemical properties and bacterial community in a subtropical tidal estuarine wetland

Background The planting of mangroves is extensively used to control the invasive plant Spartina alterniflora in coastal wetlands. Different plant species release diverse sets of small organic compounds that affect rhizosphere conditions and support high levels of microbial activity. The root-associated microbial community is crucial for plant health and soil nutrient cycling, and for maintaining the stability of the wetland ecosystem. Methods High-throughput sequencing was used to assess the structure and function of the soil bacterial communities in mudflat soil and in the rhizosphere soils of S. alterniflora, mangroves, and native plants in the Oujiang estuarine wetland, China. A distance-based redundancy analysis (based on Bray–Curtis metrics) was used to identify key soil factors driving bacterial community structure. Results S. alterniflora invasion and subsequent mangrove afforestation led to the formation of distinct bacterial communities. The main soil factors driving the structure of bacterial communities were electrical conductivity (EC), available potassium (AK), available phosphorus (AP), and organic matter (OM). S. alterniflora obviously increased EC, OM, available nitrogen (AN), and NO3−-N contents, and consequently attracted copiotrophic Bacteroidates to conduct invasion in the coastal areas. Mangroves, especially Kandelia obovata, were suitable pioneer species for restoration and recruited beneficial Desulfobacterota and Bacilli to the rhizosphere. These conditions ultimately increased the contents of AP, available sulfur (AS), and AN in soil. The native plant species Carex scabrifolia and Suaeda glauca affected coastal saline soil primarily by decreasing the EC, rather than by increasing nutrient contents. The predicted functions of bacterial communities in rhizosphere soils were related to active catabolism, whereas those of the bacterial community in mudflat soil were related to synthesis and resistance to environmental factors. Conclusions Ecological restoration using K. obovata has effectively improved a degraded coastal wetland mainly through increasing phosphorus availability and promoting the succession of the microbial community.

Immunomodulating melatonin-decorated silica nanoparticles suppress bacterial wilt (Ralstonia solanacearum) in tomato (Solanum lycopersicum L.) through fine-tuning of oxidative signaling and rhizosphere bacterial community

BackgroundTomato (Solanum lycopersicum L.) production is severely threatened by bacterial wilt, caused by the phytopathogenic bacterium Ralstonia solanacearum. Recently, nano-enabled strategies have shown tremendous potential in crop disease management.ObjectivesThis study investigates the efficacy of biogenic nanoformulations (BNFs), comprising biogenic silica nanoparticles (SiNPs) and melatonin (MT), in controlling bacterial wilt in tomato.MethodsSiNPs were synthesized using Zizania latifolia leaves extract. Further, MT containing BNFs were synthesized through the one-pot approach. Nanomaterials were characterized using standard characterization techniques. Greenhouse disease assays were conducted to assess the impact of SiNPs and BNFs on tomato plant immunity and resistance to bacterial wilt.ResultsThe SiNPs and BNFs exhibited a spherical morphology, with particle sizes ranging from 13.02 nm to 22.33 nm for the SiNPs and 17.63 nm to 21.79 nm for the BNFs, indicating a relatively uniform size distribution and consistent shape across both materials. Greenhouse experiments revealed that soil application of BNFs outperformed SiNPs, significantly enhancing plant immunity and reducing bacterial wilt incidence by 78.29% in tomato plants by maintaining oxidative stress homeostasis via increasing the activities of antioxidant enzymes such as superoxide dismutase (31.81%), peroxidase (32.9%), catalase (32.65%), and ascorbate peroxidase (47.37%) compared to untreated infected plants. Additionally, BNFs induced disease resistance by enhancing the production of salicylic acid and activating defense-related genes (e.g., SlPAL1, SlICS1, SlNPR1, SlEDS, SlPD4, and SlSARD1) involved in phytohormones signaling in infected tomato plants. High-throughput 16 S rRNA sequencing revealed that BNFs promoted growth of beneficial rhizosphere bacteria (Gemmatimonadaceae, Ramlibacter, Microscillaceae, Anaerolineaceae, Chloroplast and Phormidium) in both healthy and diseased plants, while suppressing R. solanacearum abundance in infected plants.ConclusionOverall, these findings suggest that BNFs offer a more promising and sustainable approach for managing bacterial wilt disease in tomato plants.Graphical

Synergy between Arbuscular Mycorrhizal Fungi and Rhizosphere Bacterial Communities Increases the Utilization of Insoluble Phosphorus and Potassium in the Soil by Maize.

Arbuscular mycorrhizal (AM) fungi can enhance plant uptake of phosphorus (P) and potassium (K), but it is not yet clear whether rhizosphere bacteria can enhance the ability of AM fungi to acquire insoluble P and K from the soil. Here, pot experiments confirmed that AM fungus-promoted insoluble P and K uptake by plants requires rhizosphere bacteria. The changes of rhizosphere bacterial communities associated with AM fungi were explored by 16S rRNA amplicon sequencing and metagenomic sequencing. Five core bacteria genera identified were involved in P and K cycles. Synthetic community (SynCom) inoculation revealed that SynCom increased soil available P and K and its coinoculation with AM fungi increased P and K concentration in the plants. This study revealed that AM fungi interact with rhizosphere bacteria and promote insoluble P and K acquisition, which provided a foundation for the application of AM fungal-bacterial biofertilizers and was beneficial for the sustainable development of agriculture.

Intercropping of tobacco and maize at seedling stage promotes crop growth through manipulating rhizosphere microenvironment.

Changes in the rhizosphere microbiome and metabolites resulting from crop intercropping can significantly enhance crop growth. While there has been an increasing number of studies on various crop combinations, research on the intercropping of tobacco and maize at seedling stage remains limited. This study is the first to explore rhizosphere effects of intercropping between tobacco and maize seedling stages, we analyzed the nitrogen, phosphorus and potassium nutrients in the soil, and revealed the important effects on soil microbial community composition and metabolite profiles, thereby regulating crop growth and improving soil balance. Compared with mono-cropping, intercropping increased the biomass of the two crops and promoted the nutrient absorption of nitrogen, phosphorus and potassium. Under intercropping conditions, the activities of sucrase, catalase and nitrate reductase in tobacco rhizosphere soil and the content of available potassium, the activities of nitrate reductase and acid phosphatase in maize rhizosphere soil were significantly increasing. Rhizosphere soil bacterial and fungal communities such as Sphingomonas, Massilia, Humicola and Penicillium respond differently to crop planting patterns, and soil dominant microbial communities are regulated by environmental factors such as pH, Organic Matter, Available Potassium, Nitrate Reductase, and Urease Enzyme. Network analysis showed that soil microbial communities were more complex after intercropping, and the reciprocal relationship between bacteria and fungi was enhanced. The difference of metabolites in soil between intercropping and monocropping system was mainly concentrated in galactose metabolism, starch and sucrose metabolism pathway, and the content of carbohydrate metabolites was significantly higher than that of monocropping soil. Key metabolites such as D-Sucrose, D-Fructose-6-Phosphate, D-Glucose-1-Phosphatel significantly influence the composition of dominant microbial communities such as Sphingomonas and Penicillium. This study explained the effects of intercropping between flue-cured tobacco and maize on the content of soil metabolites and soil microbial composition in rhizosphere soil, and deepened the understanding that intercropping system can improve the growth of flue-cured crops seedlings through rhizosphere effects.

Circadian rhythms of microbial communities and their role in regulating nitrogen and phosphorus cycling in the rhizosphere of tea plants

Abstract The circadian clock mediates metabolic functions of plants and rhythmically shapes structure and function of microbial communities in the rhizosphere. However, it is unclear how the circadian rhythm of plant hosts regulates changes in rhizosphere bacterial and fungal communities and nutrient cycles. In the present study, we measured diel changes in the rhizosphere of bacterial and fungal communities, and in nitrogen (N) and phosphorus (P) cycling in 20-year-old tea plantations. The fungal communities were more stable in their responses to circadian changes than bacterial communities in the rhizosphere of the variants LJ43 and ZC108. Nevertheless, fungal genera with circadian rhythms were more numerous and had a higher abundance at midnight. Organic P and N mineralization in the rhizosphere was more intensive in LJ43 under day-night alterations, while inorganic N and P cycling were more easily affected by circadian rhythms in ZC108. The rhizosphere denitrification encoded by the genes AOA and AOB was intensive in the morning, irrespective of tea species. Genes related to rhizosphere N fixation (nifH) and denitrification (nosZ and nirK) expressed at greater levels in ZC108, and they reached a peak at midnight. Moreover, the diel rhythm of rhizosphere microbial communities in ZC108 largely regulated dial changes in N and P cycling. These results suggested that the bacterial and fungal communities in the rhizosphere respond differently to circadian rhythms, and they vary between tea species. The timing of bacterial and fungal cycling largely regulates rhizosphere N and P cycling and their ecological functions.

Effects of Paecilomyces lilacinus and Bacillus pumilus on stem nematode and rhizosphere bacterial communities of sweet potato

Stem nematode (Ditylenchus destructor Thorne) is considered one of the most economically devastating species affecting sweet potato production. Biocontrol offers a sustainable strategy for nematode control. This study conducted a pot experiment to evaluate the biocontrol efficacy of Paecilomyces lilacinus CS-Z and Bacillus pumilus Y-26 against the stem nematode, as well as to examine their influence on the bacterial communities in the sweet potato rhizosphere. The findings indicated that B.pumilus Y-26 and P.lilacinus CS-Z exhibited respective suppression rates of 82.9% and 85.1% against the stem nematode, while also stimulating sweet potato plant growth. Both high-throughput sequencing and Biolog analysis revealed distinct impacts of the treatments on the bacterial communities. At the phylum level, B.pumilus Y-26 enhanced the abundance of Actinobacteria but reduced the abundance of Cyanobacteria, with P.lilacinus CS-Z exhibiting similar effects. Additionally, the treatment with B.pumilus Y-26 resulted in increased abundances of Crossiella, Gaiella, Bacillus, and Streptomyces at the genus level, while the treatment with P.lilacinus CS-Z showed increased abundances of Crossiella and Streptomyces. In contrast, the abundance of Pseudarthrobacter was reduced in the treatment with B.pumilus Y-26. Conversely, the application of the nematicide fosthiazate exhibited minor influence on the bacterial community. The findings indicated that the application of P.lilacinus CS-Z and B.pumilus Y-26 led to an increase in the relative abundances of beneficial microorganisms, including Gaiella, Bacillus, and Streptomyces, in the rhizosphere soil. In conclusion, P.lilacinus CS-Z and B.pumilus Y-26 demonstrated their potential as environmentally friendly biocontrol agents for managing stem nematode disease of sweet potato.

Dynamic alterations and ecological implications of rice rhizosphere bacterial communities induced by an insect-transmitted reovirus across space and time

BackgroundCereal diseases caused by insect-transmitted viruses are challenging to forecast and control because of their intermittent outbreak patterns, which are usually attributed to increased population densities of vector insects due to cereal crop rotations and indiscriminate use of pesticides, and lack of resistance in commercial varieties. Root microbiomes are known to significantly affect plant health, but there are significant knowledge gaps concerning epidemics of cereal virus diseases at the microbiome-wide scale under a variety of environmental and biological factors.ResultsHere, we characterize the diversity and composition of rice (Oryza sativa) root-associated bacterial communities after infection by an insect-transmitted reovirus, rice black-streaked dwarf virus (RBSDV, genus Fijivirus, family Spinareoviridae), by sequencing the bacterial 16S rRNA gene amplified fragments from 1240 samples collected at a consecutive 3-year field experiment. The disease incidences gradually decreased from 2017 to 2019 in both Langfang (LF) and Kaifeng (KF). BRSDV infection significantly impacted the bacterial community in the rice rhizosphere, but this effect was highly susceptible to both the rice-intrinsic and external conditions. A greater correlation between the bacterial community in the rice rhizosphere and those in the root endosphere was found after virus infection, implying a potential relationship between the rice-intrinsic conditions and the rhizosphere bacterial community. The discrepant metabolites in rhizosphere soil were strongly and significantly correlated with the variation of rhizosphere bacterial communities. Glycerophosphates, amino acids, steroid esters, and triterpenoids were the metabolites most closely associated with the bacterial communities, and they mainly linked to the taxa of Proteobacteria, especially Rhodocyclaceae, Burkholderiaceae, and Xanthomonadales. In addition, the greenhouse pot experiments demonstrated that bulk soil microbiota significantly influenced the rhizosphere and endosphere communities and also regulated the RBSDV-mediated variation of rhizosphere bacterial communities.ConclusionsOverall, this study reveals unprecedented spatiotemporal dynamics in rhizosphere bacterial communities triggered by RBSDV infection with potential implications for disease intermittent outbreaks. The finding has promising implications for future studies exploring virus-mediated plant-microbiome interactions.2AL1xEb7k2nunVBmbuNCsVVideo

Different responses of soil bacterial community to plant-plant interactions under organic-inorganic fertilizers affect seedling establishment during subalpine forest succession.

Rhizosphere bacterial community as a valuable indicator of soil quality and function, has been widespread studied. However, little knowledge is about the response of bacterial communities to plant-plant interaction and different fertilizers during secondary forest succession. We conducted a field pot experiment applying organic and inorganic fertilizers to monocultures and mixed cultures of dominant plant species from mid- to late-successional stages (Salix oritrepha, Betula albosinensis, and Picea asperata), and investigated the responses of plant growth and rhizosphere bacterial communities. Results indicated that growth rate of plant height varied among plant species, but no significant differences were observed in soil bacterial diversity and composition among plant species or inter-specific interactions under control. Compared to control, inorganic fertilizer resulted in increases in plant growth and the relative abundance of Proteobacteria, Patescibacteria, Bacteroidetes and Gemmatimonadetes, while simultaneously leading to decrease in the relative abundance of Acidobacteria, Actinobacteria, Chloroflexi, Rokubacteria and Planctomycetes. When grown with other species, the bacterial communities in the mixture resembled those of S. oritrepha in singular monoculture under inorganic fertilizer treatment, but plant growth was not affected by interspecific interaction. Unlike inorganic fertilizer, organic fertilizer significantly affected bacterial communities and increased bacterial diversity, but did not alter the effects of plant-plant interactions on bacterial communities. It was also observed that organic fertilizer facilitated later successional species' growth (P. asperata and B. albosinensis) by the mid-successional species (S. oritrepha), ultimately facilitating secondary forest succession. In addition, plants at different successional stages harbor specific bacterial communities to affect their growth, and the bacterial communities contributed more than soil properties to the variations in the plant growth of S. oritrepha and P. asperata though the bacterial communities were regulated by soil factors. This finding highlights the significance of the rhizosphere bacteria on plant growth and plant community succession. It also emphasize the importance of considering both plant-plant interactions and diverse fertilizer types in forest restoration efforts and provide valuable insights into optimizing agronomic practices for secondary forest succession.

Synergistic co-evolution of rhizosphere bacteria in response to acidification amelioration strategies: impacts on the alleviation of tobacco wilt and underlying mechanisms.

Soil acidification represents a severe threat to tobacco cultivation regions in South China, exacerbating bacterial wilt caused by Ralstonia solanacearum. The comprehension of the underlying mechanisms that facilitate the restoration of rhizosphere microbial communities in "healthy soils" is imperative for ecologically managing tobacco bacterial wilt. This study focuses on acidified tobacco soils that have been subjected to continuous cultivation for 20 years. The experimental treatments included lime (L), biochar (B), and a combination of lime and biochar (L+B), in addition to a control group (CK). Utilizing rhizosphere biology and niche theory, we assessed disease suppression effects, changes in soil properties, and the co-evolution of the rhizosphere bacterial community. Each treatment significantly reduced tobacco bacterial wilt by 16.67% to 20.14% compared to the control group (CK) (p < 0.05) and increased yield by 7.86% to 27.46% (p < 0.05). The biochar treatment (B) proved to be the most effective, followed by the lime-biochar combination (L+B). The key factors controlling wilt were identified through random forest regression analysis as an increase in soil pH and exchangeable bases, along with a decrease in exchangeable acidity. However, lime treatment alone led to an increase in soil bulk density and a decrease in available nutrients, whereas both biochar and lime-biochar treatments significantly improved these parameters (p < 0.05). No significant correlation was found between the abundance of Ralstonia and wilt incidence. Nonetheless, all treatments significantly expanded the ecological niche breadth and average variation degree (AVD), enhanced positive interactions and cohesion within the community, and intensified negative interactions involving Ralstonia. This study suggests that optimizing community niches and enhancing pathogen antagonism are key mechanisms for mitigating tobacco wilt in acidified soils. It recommends using lime-biochar mixtures as soil amendments due to their potential ecological and economic benefits. This study offers valuable insights for disease control strategies and presents a novel perspective for research on Solanaceous crops.

Rhizosphere bacterial community influence on &lt;i&gt;Deschampsia antarctica&lt;/i&gt; È Desv. adaptability in context of temperature near plants in local spatial scales of Galindez Island, Argentine Islands (the maritime Antarctic)

The effect of rhizosphere bacterial community index (Irbi) influence on the nine populations of Antarctic hair grass (Deschampsia antarctica) adaptability was studied in the Galindez Island (summer season 2017/18). Moreover, the corresponding influence indices Irbi (i=1÷9) and Irbpi (p=1÷5 for the most common bacteria) were evaluated as well. The objective was to compare the Irbi and Irbpi series with the united temperature influence index on plant populations (It1i(z)) series and the united quality latent index of adaptability Iq1i. The study used data on the rhizosphere metagenome composition based on 16S RNA analysis. Methods determining the plant number in populations, and measuring the morphometric indices of D. antarctica populations were used. Reserve and protective seed proteins spectra were studied by polyacrylamide gel electrophoresis. Method of extreme grouping the spatial variables of these indices was applied for nine populations to obtain a Iq1I and It1i and Irbi, Irbpi. Sets of united indices were compared by regression technique. A comparative statistical analysis of the It1i and Irbi, Irbpi sets in this season was carried out. This possible influence appeared to be individual for each D. antarctica studied population. In each population, part of the plants reacted positively to the bacteria influence, while the other part either did not react or reacted negatively. Dependence of the plant adaptation indices on rhizospheric bacterial communities z(x) is shown in our data. This means that the rhizosphere bacterial community and temperature-dependent rhizosphere bacteria (x) can play an active role in plant adaptation of D. antarctica populations (z) to individual temperature conditions in the microscale of Galindez Island from a biological point of view.

Agricultural management reshaped the diversity patterns and community assembly of rhizosphere bacterial communities in a desert farming system

Desert farming represents human intervention in previously untouched desert landscapes, transforming natural desert areas into managed agricultural farmland. Despite the growing prevalence of desert farming, the effects of agricultural management on soil and microbial dynamics in desert environments are not well understood. This study analyzed rhizosphere bacterial community from crops (corn and wheat) in desert farms and desert plants (Artemisia desertorum) in natural desert environments to explore how bacterial communities respond to agricultural management in desert farming systems. Our results showed that the composition and diversity of rhizosphere bacterial communities were influenced more by the sampling region than by plant type. Bacterial species richness, phylogenetic diversity, and functional traits were significantly affected by moisture and temperature, whereas pH and nitrogen-related factors (total nitrogen, NO3-N, and NH4-N) were stronger correlates of functional differences in the microbial community. We found that the co-occurrence network of bacterial communities exhibited tighter and more positive interactions in natural desert, but was more stable in desert farm. Deterministic processes predominantly governed bacterial community assembly in both desert farms and natural desert, but the importance of stochastic processes increased in desert farms due to reduced environmental stress from agricultural management. These findings provide valuable insights into the impacts of agricultural management on rhizosphere bacterial communities, highlighting the roles of temperature, moisture, and nutrient supply in predicting microbial diversity, function, species interactions, and community assembly. Given the crucial functional roles of rhizosphere microbes, our conclusions can inform desert farm management practices to better manipulate microbial communities for optimized crop production.

Transformed biosolids promote ryegrass growth and microbial carbon cycling at the ‘cost’ of soil carbon

Soil carbon supports desirable ecosystem functions for global agricultural productivity and climate resilience objectives. Wastewater biosolids can be transformed into soil amendments that return carbon and nutrients to agricultural systems in stoichiometric ratios that support carbon stabilisation. However, practicable delivery that enhances stable soil carbon and plant yield remains challenging. Soil carbon stability and nutrient availability are mediated partly by microbial community composition and function, which are poorly understood in soils amended with transformed biosolids. We conducted a 56-day study in a temperature-controlled glasshouse, growing perennial ryegrass (Lolium perenne) in pasture soil amended with straw, straw supplemented with nutrients, or transformed biosolids (composted biosolids, dried biosolids or biosolids biochar), all with equal added carbon (3500 kg ha−1). Control soils, with and without supplementary nutrients, were also included. Plant dry mass, soil chemical characteristics, and soil carbon fractions were measured at harvest. 16S rRNA sequencing was used to infer the composition and putative function of rhizosphere bacterial communities. Shoot dry mass increased for composted biosolids (236%) and dried biosolids (559%), but total carbon in rhizosphere soil decreased for composted biosolids (16.3%), dried biosolids (13.3%) and biosolids biochar (12.7%) when compared to unamended soils. Fine-fraction carbon in rhizosphere soil decreased for straw with supplementary nutrients (6.8%), dried biosolids (6.3%) and biosolids biochar (4.6%). Rhizosphere bacterial communities clustered by treatment, with populations correlated with fine-fraction carbon distinct from those populations correlated with shoot and root dry mass. Path analysis linked fine-fraction carbon loss with increased putative carbon cycling genes, driven by available nutrients and plant growth. Transformed biosolids can trigger a microbial response that reallocates nutrients from organic matter to plants, disrupting soil carbon-nutrient stoichiometry and facilitating carbon loss. Understanding the carbon cost of this ecosystem service is fundamental when translating benefits of transformed biosolids to end users.

Effects of volatile fatty acids on soil properties, microbial communities, and volatile metabolites in wheat rhizosphere of loess

The Loess Plateau faces critical challenges due to soil degradation. In this context, using volatile fatty acids (VFAs) from biowaste as readily available soil conditioners offer promising sustainable solutions to restore soil quality and enhance agricultural productivity. The study examined how applying different VFAs as soil amendments in arid and high-salt loess soil affected wheat plant growth, soil properties, soil microbial community diversity, volatile metabolites in soil and root exudate. The non-targeted analysis was used to identify and classify 49 soil volatile organic compounds (VOCs) and 63 root exudate VOCs to seek further specific functional volatile metabolites and explore the interaction mechanisms among plants, microorganisms, and soil. The results showed that acetic acid increased soil EC by 21.0% and decreased soil organic matter by 14.4%. Propionic acid reduced soil organic matter by 14.7%. Valeric acid increased the average root diameter by 15.1%. Further analysis revealed that rhizosphere bacterial communities, but not fungal communities, showed greater sensitivity to VFAs application. Bacterial α diversity was significantly reduced in the acetic acid treatment. The main contribution of VOCs in soil with acetic acid and propionic acid applications was alcohol, and its relative percentage was 50.06% and 43.54%, respectively, which has a significantly negative correlation with the α diversity of soil bacteria. On the contrary, the content of acylamides in soil with butyric acid and valeric acid applications was higher and significantly positively correlated with the average root diameter. It was concluded that soil microbial communities respond rapidly to acetic acid, propionic acid, butyric, and valeric acid applications by adjusting the concentration of alcohols and acylamides as secondary metabolites, respectively. This study revealed the close relationship between VFAs application type and soil properties, soil microbial community diversity, soil VOCs, and root exudates VOCs. VFAs derived from biowaste will contribute to restoring loess soil quality and achieving sustainable agriculture.