Rhizosphere Bacterial Diversity Research Articles

Impact of Pristine and Aged Tire Wear Particles on Ipomoea aquatica and Rhizospheric Microbial Communities: Insights from a Long-Term Exposure Study.

Tire wear particles (TWPs), generated from tire abrasion, contribute significantly to environmental contamination. The toxicity of TWPs to organisms has raised significant concerns, yet their effects on terrestrial plants remain unclear. Here, we investigated the long-term impact of pristine and naturally aged TWPs on water spinach (Ipomoea aquatica) and its rhizospheric soil. The results indicated that natural aging reduced the toxicity of TWPs, as evidenced by decreased levels of polycyclic aromatic hydrocarbons (PAHs) in soil and TWPs themselves. Consequently, aged TWPs were found to enhance the plant growth and chlorophyll content, whereas pristine TWPs increased the plant stress. Furthermore, aged TWPs improved soil organic matter (SOM) and total organic carbon (TOC), thereby boosting the microbial enzymes involved in nitrogen cycling. Metabolomic analysis revealed that aged TWPs upregulated key pathways related to carbon and nitrogen metabolism, enhancing plant growth and stress responses. Additionally, rhizosphere bacterial diversity was higher under aged TWPs, favoring nutrient-cycling taxa such as Acidobacteriota and Nitrospirota. Pristine TWPs may lead to overproliferation of certain dominant species, thereby reducing microbial diversity in soil, which could ultimately compromise the soil health. These findings contribute to a deeper understanding of the mechanisms underlying TWP toxicity in plants and highlight the necessity for further research on the impact of aged TWPs across various plant species over different exposure durations for comprehensive risk assessment.

Soil metabolic processes influenced by rice roots co-regulates the environmental evolution of antibiotic resistome

Plant root activities lead to significant differences in metabolites between the rhizosphere and non-rhizosphere soil, profoundly affecting microbial distribution. However, how this process drives the migration and propagation of manure-derived antibiotic resistance genes (ARGs) in farmland ecosystems remains unclear. Herein, we used a rice pot microcosm experiment to explore the characteristics of antibiotic resistome and bacterial communities in rhizosphere and non-rhizosphere soils and the driving effects of rhizosphere metabolites on ARG propagation. The results showed significant differences in some ARGs and bacterial diversity in rhizosphere and non-rhizosphere soils with varied differential ARGs between different growth stages of rice (P < 0.05). The biosynthesis of secondary metabolites and glutathione metabolism were found to be the main pathways affecting ARG differences in rhizosphere and non-rhizosphere soils under manure application. Structural equation modeling (SEM) analysis further indicated that ARG distribution differences between rhizosphere and non-rhizosphere soils were mainly regulated by differential metabolites, which influenced the ARG distribution by altering the succession of soil microbial communities. These results demonstrate the role of differential metabolites resulting from rice root activities in co-regulating ARG distribution, providing new insights into the regulatory mechanisms of soil ARG dynamics in paddy fields.

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.

Sex-Dependent Rhizosphere Microbial Dynamics and Function in Idesia polycarpa through Floral and Fruit Development

Male Idesia polycarpa, which display distinct morphological and physiological traits, exhibit greater adaptability to stressful environments than females. However, the connection between this adaptability and rhizosphere processes remains unclear. Here, we investigate the differences in root bacterial community structures between male and female plants at different developmental stages, identifying bacterial strains associated with plant sex through functional predictions. This study aims to inform the optimal allocation of male and female plants during cultivation and provide a theoretical basis for sex identification and breeding. Samples from seven-year-old male and female plants were collected during the flowering (May) and fruit ripening (October) stages. Rhizosphere nutrient content and bacterial diversity were analyzed using Illumina high-throughput sequencing technology. The results demonstrate that total nitrogen (TN), total carbon (TC), and available potassium (AK) varied between sexes at different times. No significant differences between male and female plants were observed in the Shannon, Simpson, and Chao1 indexes during the flowering period. However, the Chao1 and Shannon indexes were significantly higher at fruit maturity in male rather than female plants. The predominant phyla of rhizosphere bacteria were Pseudomonadota, Acidobacteriota, and Actinomycetes. Interestingly, from flowering to fruit ripening, the dominant phyla in both male and female plants shifted from Actinomycetes to Pseudomonadota. A significant correlation was observed between pH and AK and rhizosphere bacteria (p &lt; 0.05), with metabolism being the main functional difference. This study provides preliminary insights into the functional predictions and analyses of bacteria associated with Idesia polycarpa. The above findings lay the groundwork for further investigation into the sex-specific differences in microbial flora across different developmental stages, elucidating the mechanisms underlying flora changes and offering theoretical support for the high-quality management of Idesia polycarpa.

Bacillus licheniformisYB06: A Rhizosphere-Genome-Wide Analysis and Plant Growth-Promoting Analysis of a Plant Growth-Promoting Rhizobacterium Isolated from Codonopsis pilosula.

Codonopsis pilosula, commonly known as Dangshen, is a valuable medicinal plant, but its slow growth and susceptibility to environmental stress pose challenges for its cultivation. In pursuit of sustainable agricultural practices to enhance the yield and quality of Dangshen, the present study isolated a bacterial strain exhibiting plant growth-promoting potential from the rhizosphere of C. pilosula. This strain was subsequently identified as Bacillus licheniformisYB06. Assessment of its plant growth-promoting attributes revealed the potential of B. licheniformis YB06 as a biofertilizer. Whole-genome sequencing of B. licheniformis YB06 revealed a genome size of 4,226,888 bp with a GC content of 46.22%, harboring 4325 predicted protein-coding sequences. Genomic analysis of B. licheniformis YB06 revealed a diverse array of genes linked to induced systemic resistance (ISR) and plant growth-promoting (PGP) traits, encompassing phytohormone production, nitrogen assimilation and reduction, siderophore biosynthesis, phosphate solubilization, biofilm formation, synthesis of PGP-related amino acids, and flagellar motility. Seed germination assays demonstrated the positive effects of B. licheniformis YB06 on the germination and growth of C. pilosula seedlings. Furthermore, we explored various fertilization regimes, particularly the B. licheniformis YB06-based biofertilizer, were investigated for their impact on the structure and diversity of the C. pilosula rhizosphere soil bacterial community. Our findings revealed that fertilization significantly impacted soil bacterial composition and diversity, with the combined application of B. licheniformis YB06-based biofertilizer and organic fertilizer exhibiting a particularly pronounced enhancement of rhizosphere bacterial community structure and diversity. This study represents the first report on the beneficial effects of B. licheniformis YB06 on both the growth of C. pilosula and the composition of its rhizosphere soil microbial community. These findings provide a theoretical foundation and practical guidance for the development of novel bio-organic compound fertilizers, thereby contributing to the sustainable cultivation of C. pilosula.

Maize/soybean intercropping with nitrogen supply levels increases maize yield and nitrogen uptake by influencing the rhizosphere bacterial diversity of soil.

Intercropping practices play a crucial role in enhancing and maintaining the biodiversity and resiliency of agroecosystems, as well as promoting stable and high crop yields. Yet the relationships between soil nitrogen, microbes, and yield in maize cultivated under maize/soybean intercropping systems remain unclear. To fill that knowledge gap, here we collected maize rhizosphere soil at the staminate stage after 6 consecutive years of maize/soybean intercropping, to investigate how intercropping and nitrogen application rates affected nitrogen utilization by crops and soil microbial community composition and function. We also examined correlations of those responses with yields, to clarify the main ways that yield is enhanced via intercropping and by nitrogenous fertilizer gradient changes generated by different nitrogen application rates. The amount of applied fertilizer was 240 kg N ha-1 was best for obtaining a high maize yield and also led to the greatest nitrogen-use efficiency and bacterial diversity. Under the same N application rate, intercropping increased the maize yield by 31.17% and soil nitrogen (total, ammonium and nitrate nitrogen) by 14.53%, on average, in comparison to monocropping. The enrichment of Gemmatimonas and Bradyrhizobium significantly increased the soil nitrogen content, and a greater relative abundance of Sphingomonas and Gemmatimonas increased the maize yield, whereas enrichment of Candidatus_Udaeobacter and Bradyrhizobium decreased it. The benefits of intercropping mainly arise from augmenting the abundance of beneficial microorganisms and enhancing the efficiency of N use by crop plants. This study's findings are of key importance to bolster the stability of agro-ecosystems, to guide the scientific rational use of nitrogen fertilizers, and to provide a sound theoretical basis for achieving the optimalmanagement of intensive crop-planting patterns and green sustainable development.

Combined effects of cadmium and simulated acid rain on soil microbial communities in the early cultivation of Populus beijingensis seedlings

The combined cadmium (Cd) and acid rain pollution poses a significant threat to the global ecological environment. Previous studies on the combined adverse effects have predominantly focused on the aboveground plant physiological responses, with limited reports on the microbial response in the rhizosphere soil. This study employed Populus beijingensis seedlings and potting experiments to simulate the impacts of combined mild acid rain (pH=4.5, MA) or highly strong acid rain (pH=3.0, HA), and soil Cd pollution on the composition and diversity of microbial communities, as well as the physiochemical properties in the rhizosphere soil. The results showed that Cd decreased the content of inorganic nitrogen, resulting in an overall decrease of 49.10 % and 46.67 % in ammonium nitrogen and nitrate nitrogen, respectively. Conversely, acid rain was found to elevate the content of total potassium and soil organic carbon by 4.68 %-6.18 % and 8.64–19.16 %, respectively. Additionally, simulated acid rain was observed to decrease the pH level by 0.29–0.35, while Cd increased the pH level by 0.11. Moreover, Cd alone reduced the rhizosphere bacterial diversity, however, when combined with acid rain, regardless of its intensity, Cd was observed to increase the diversity. Fungal diversity was not influenced by the acid rain, but Cd increased fungal diversity to some extend under HA as observed in bacterial diversity. In addition, composition of the rhizosphere bacterial community was primarily influenced by the inorganic nitrogen components, while the fungal community was driven mainly by soil pH. Furthermore, “Metabolism” was emerged as the most significant bacterial function, which was markedly affected by the combined pollution, while Cd pollution led to a shift from symbiotroph to other trophic types for fungi. These findings suggest that simulated acid rain has a mitigating effect on the diversity of rhizosphere bacteria affected by Cd pollution, and also alters the trophic type of these microorganisms. This can be attributed to the acid rain-induced direct acidic environment, as well as the indirect changes in the availability or sources of carbon, nitrogen, or potassium.

The Impact of Organic Fertilizers on Growth, Yield, and Rhizospheric Bacterial Diversity in Black Turmeric (Curcuma caesia)

The Impact of Organic Fertilizers on Growth, Yield, and Rhizospheric Bacterial Diversity in Black Turmeric (Curcuma caesia)

Microbial diversity loss and wheat genotype-triggered rhizosphere bacterial and protistan diversity constrain soil multifunctionality: Evidence from greenhouse experiment

Microbial diversity loss and wheat genotype-triggered rhizosphere bacterial and protistan diversity constrain soil multifunctionality: Evidence from greenhouse experiment

Plant colonizers of a mercury contaminated site: trace metals and associated rhizosphere bacteria

Background and aimsMercury (Hg) contamination poses severe human and environmental health risks. We aimed to evaluate the colonization of Hg-contaminated sites by native plants and the prokaryotic composition of rhizosphere soil communities of the dominant plant species.MethodsA field study was conducted at a Hg-contaminated site in Romania. Metal concentrations in soil and plant samples were analyzed using portable X-ray fluorescence spectrometry. The prokaryotic composition of rhizosphere soil communities was determined through 16S rRNA amplicon sequencing and community functionality was predicted through PICRUSt2.ResultsSite-specific trace metal distribution across the site drove plant species distribution in the highly contaminated soil, with Lotus tenuis and Diplotaxis muralis associated with higher Hg concentrations. In addition, for the bacterial communities in the rhizosphere soil of D. muralis, there was no observable decrease in alpha diversity with increasing soil Hg levels. Notably, Actinomycetota had an average of 24% relative abundance in the rhizosphere communities that also tested positive for the presence of merA, whereas in the absence of merA the phylum’s relative abundance was approximately 2%. merA positive rhizosphere communities also displayed an inferred increase in ABC transporters.ConclusionsThe results suggest a dependence of species-wise plant survival on local trace metal levels in soil, as well as an intricate interplay of the latter with rhizosphere bacterial diversity. Knowledge of these interdependencies could have implications for phytoremediation stakeholders, as it may allow for the selection of plant species and appropriate soil microbial inoculates with elevated Hg tolerance.

Effects of intercropping teak with Alpinia katsumadai Hayata and Amomum longiligulare T.L. Wu on rhizosphere soil nutrients and bacterial community diversity, structure, and network.

Teak is a precious hardwood species in tropical and subtropical regions with a long growth cycle and slow economic returns. Intercropping medicinal plants is an effective method for obtaining early returns during the growth period of teak. However, currently, we lack sufficient knowledge about the impact of intercropping on the soil microenvironment, especially on rhizosphere soil bacterial communities. We selected two medicinal plants Alpinia katsumadai Hayata and Amomum longiligulare T.L. Wu, for an intercropping experiment with teak, and the non-intercropping teak forest area was used for comparison. By collecting soil rhizosphere samples and conducting 16S rDNA sequencing and property analysis, we aimed to investigate the influence of teak intercropping on soil microbial communities. The results showed that intercropping significantly improved soil nutrients contents, such as soil organic matter, soil total potassium and soil available nitrogen, and significantly altered bacterial community structure. Co-occurrence network analysis revealed that intercropping tightened the connections of the soil bacterial network and increased its complexity (by increasing the number of nodes and the proportion of positive edges). Teak intercropping with Amomum longiligulare T.L. Wu resulted in tighter network connections than teak intercropping with A. katsumadai Hayata. Changes in the soil bacterial community structure may related to environmental factors such as total potassium content and pH. These results demonstrated that the introduction of medicinal plants exerts a significant impact on the soil bacterial community of teak, fostering the enrichment of specific bacterial taxa (such as Firmicutes and Methylomirabilota), and makes the rhizosphere bacterial network denser and more complex. This study provides valuable insights for the management of teak plantations.

Stochastic Processes Shape Bacterial Community Diversity Patterns along Plant Niche Gradients

The ecological niche gradient is an important determinant of microbial community structure. In this paper, we studied variation in rhizosphere bacterial diversity and community composition along an ecological niche gradient. We used the high-throughput sequencing of 16S rRNA genes to study changes in the rhizosphere soil microbial communities of six grass and four shrub species during the secondary succession of abandoned farmland on the Loess Plateau of China. A structural equation model (SEM) was employed to disentangle the relative contribution of ecological niche and soil properties to bacterial diversity and community composition. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla of rhizosphere bacteria in all samples. During the dynamics of the plant niche from low to high, bacterial community composition transitioned from Actinobacteria + Acidobacteria to Proteobacteria + Bacteroidetes higher abundance. Moreover, the bacterial diversity and species richness changed with an increasing niche gradient, showing a clear differentiation in the rhizosphere bacterial community of grassland and shrubland. Further, diversity and species richness decreased from the middle niche of B. ischaemum to the poles, indicating that the succession process had not yet reached the climax community stage. Community assembly analysis suggested that the stochastic process gradually strengthened along the increasing ecological niche gradient, especially the drift effect. Furthermore, SEM analysis showed that the ecological niche had significant negative effects on soil properties and bacterial richness, while the effects on bacterial diversity and the stochastic processes of community assembly were weakened and insignificant. Altogether, our findings suggest that the complex interaction of the ecological niche with bacterial diversity and composition was determined by soil properties. Further, bacterial diversity was not necessarily higher with increasing ecological niche gradients.

Rhizosphere microbial community changes due to weed-weed competition

Many species of weeds are present in agricultural areas, but weeds with greater competitive ability normally become dominant in the field. Rhizosphere soil microbiota can influence weed-weed interactions. However, the role of rhizosphere soil microorganisms in weed-weed interactions remains largely unexplored. In this study, we investigated the ecological relationships and microbial taxa present in the rhizosphere of weeds in monoculture and coexistence systems. The weed species Ageratum conyzoides, Ipomoea ramosissima, and Bidens pilosa were grown in monoculture and coexistence pairs under greenhouse conditions for 80 days. The ecological relationships between weeds were analyzed by calculating the Relative Interaction Index (RII) based on the total dry mass of the plants. The rhizosphere microbiome was analyzed after extracting the metagenomic DNA from rhizosphere microbial populations, followed by PCR amplification and sequencing of the 16S rDNA gene and ITS region, using the Illumina MiSeq platform. Competitive interactions were observed for all combinations of weed species. Ageratum conyzoides showed the greatest decrease in dry matter production due to competition. Weed-weed competition changed rhizosphere microbial community composition and bacterial diversity. The abundance of different bacterial genera in rhizosphere soil varied according to the treatments. When comparing the competition between A. conyzoides and B. pilosa and their respective monocultures, the abundances of Opitutus, Diplorickettisiales uncultured and Bdellovibrio increased in B. pilosa monoculture. When comparing the competition between A. conyzoides and I. ramosissima and their respective monocultures, the abundance of Pseudonocardia increased while the abundance of Fimbriiglobus decreased in A. conyzoides monoculture. Already the abundances of Actinospica, Chitinophaga, Gemmatirosa, 1921-2 and Hymenobacter decreased I. ramosissima monoculture. When comparing the competition between B. pilosa and I. ramosissima, and their respective monocultures, the abundances of Flexibacter and Candidatus Xiphinematobacter decreased I. ramosissima monoculture. The abundances of Clostridium and Rhodobacter increased in competition while the abundance of Pajaroellobacter increased in B. pilosa monoculture. The fungal genera that had their abundances significantly altered were Scytalidium, whose abundance decreased in competition of A. conyzoides and B. pilosa when compared to the respective monocultures, while the abundance of Robillarda increased in B. pilosa monoculture. Already the abundance of Myriodontium increased in B. pilosa monoculture when compared with I. ramosissima monoculture and competition between both plants. Weeds can recruit specific taxa depending on the competition situation in which they are involved. Such changes in the rhizobiome are possibly related to the lower competitive ability and dry matter production of A. conyzoides. B. pilosa have a greater capacity to determine the structure of the rhizobiome when in competition with A. conyzoides. I. ramosissima seem to be less affected by rhizobiome taxon-specific changes.

Biochar relieves the toxic effects of microplastics on the root-rhizosphere soil system by altering root expression profiles and microbial diversity and functions

The accumulation of microplastics in agricultural soil brings unexpected adverse effects on crop growth and soil quality, which is threatening the sustainability of agriculture. Biochar is an emerging soil amendment material of interest as it can remediate soil pollutants. However, the mechanisms underlying biochar alleviated the toxic effects of microplastics in crops and soil were largely unknown. Using a common economic crop, peanut as targeted species, the present study evaluated the plant physiologica and molecular response and rhizosphere microbiome when facing microplastic contamination and biochar amendment. Transcriptome and microbiome analyses were conducted on peanut root and rhizosphere soil treated with CK (no microplastic and no biochar addition), MP (1.5% polystyrene microplastic addition) and MB (1.5% polystyrene microplastic+2% peanut shell biochar addition). The results indicated that microplastics had inhibitory effects on plant root development and rhizosphere bacterial diversity and function. However, biochar application could significantly promote the expressions of key genes associated with antioxidant activities, lignin synthesis, nitrogen transport and energy metabolism to alleviate the reactive oxygen species stress, root structure damage, nutrient transport limitation, and energy metabolism inhibition induced by microplastic contamination on the root. In addition, the peanut rhizosphere microbiome results showed that biochar application could restore the diversity and richness of microbial communities inhibited by microplastic contamination and promote nutrient availability of rhizosphere soil by regulating the abundance of nitrogen cycling-related and organic matter decomposition-related microbial communities. Consequently, the application of biochar could enhance root development by promoting oxidative stress resistance, nitrogen transport and energy metabolism and benefit the rhizosphere microecological environment for root development, thereby improved the plant-soil system health of microplastic-contaminated agroecosystem.

Wild plant species with broader precipitation niches exhibit stronger host selection in rhizosphere microbiome assembly.

Plants actively recruit microbes from the soil, forming species-specific root microbiomes. However, their relationship with plant adaptations to temperature and precipitation remains unclear. Here we examined the host-selected and conserved microbiomes of 13 native plant species in the Xilingol steppe, Inner Mongolia, a semi-arid region in China. By calculating the global precipitation and temperature niches of these plants, considering plant phylogenetic distances, and analyzing functional traits, we found that these factors significantly influenced the rhizosphere microbiome assembly. We further quantified the strength of host selection and observed that plants with wider precipitation niches exhibited greater host selection strength in their rhizosphere microbiome assembly and higher rhizosphere bacterial diversity. In general, the rhizosphere microbiome showed a stronger link to plant precipitation niches than temperature niches. Haliangium exhibited consistent responsiveness to host characteristics. Our findings offer novel insights into host selection effects and the ecological determinants of wild plant rhizosphere microbiome assembly, with implications for steering root microbiomes of wild plants and understanding plant-microbiome evolution.

Biochar-based organic fertilizers: Influence on yield and concentration of antioxidants in the stigma of saffron and rhizosphere bacterial diversity of slightly saline and non-saline soils

Being the most expensive spice, saffron has great economic importance. This crop grows well in cold arid deserts. Salinity is one of the important limiting factors for the cultivation of this crop. However, the use of composted manured and co-composted biochar and fertilizers can play a role in attenuating the salinity stress on this crop. In this two-year field study, manures from three sources: sheep and goat (SG), cow and buffalo (FYM), and poultry (PM) farms, and their co-compost with slow-pyrolyzed wood-derived biochar (B) were used for saffron cultivation in slightly saline (electrical conductivity 1.95 dS m−1) and non-saline soils. Yield and concentration of antioxidants of stigma and bacterial diversity in the rhizosphere of this crop, under salinity and non-salinity conditions, were evaluated. Results revealed that in non-saline soil of first-year crops, all fertilizers decreased the yield of stigma than control by 15–49 % (P ≤ 0.05) but increased the concentration of carotenoids and total polyphenolics (P ≤ 0.05). In saline soil, no difference in yield was observed between treatments for the first-year crop; however, for the second-year crop, as compared to control, PM and FYM significantly increased yield by 41 % and 44 % respectively, whereas FYM also increased the concentration of total polyphenolics (P ≤ 0.05). The FYM fertilizer was found suitable for the yield and quality of saffron stigma for second-year crops in both soils (non-saline and saline). The observed OTUs, Chao1, Fischer, and ACE indexes based on 16 s rRNA metagenomic analysis revealed 2–4 times greater bacterial diversity in the rhizosphere soil of PM-B and SG-B treatments than in the control. Furthermore, 347 bacterial species were found in PM-B- or SG-B-amended soils absent in control treatments.

Responses of the maize rhizosphere soil environment to drought-flood abrupt alternation stress.

Changes in the soil environment in the root zone will affect the growth, development and resistance of plants. The mechanism underlying the effect of drought and flood stress on rhizosphere bacterial diversity, soil metabolites and soil enzyme activity is not clear and needs further study. To analyze the dynamic changes in bacteria, metabolites and enzyme activities in the rhizosphere soil of maize under different drought-flood abrupt alternation (DFAA) stresses, the barrel test method was used to set up the 'sporadic light rain' to flooding (referring to trace rainfall to heavy rain) (DFAA1) group, 'continuous drought' to flooding (DFAA2) group and normal irrigation (CK) group from the jointing to the tassel flowering stage of maize. The results showed that Actinobacteria was the most dominant phylum in the two DFAA groups during the drought period and the rewatering period, and Proteobacteria was the most dominant phylum during the flooding period and the harvest period. The alpha diversity index of rhizosphere bacteria in the DFAA2 group during the flooding period was significantly lower than that in other stages, and the relative abundance of Chloroflexi was higher. The correlation analysis between the differential genera and soil metabolites of the two DFAA groups showed that the relative abundance of Paenibacillus in the DFAA1 group was higher during the drought period, and it was significantly positively correlated with the bioactive lipid metabolites. The differential SJA-15 bacterium was enriched in the DFAA2 group during the flooding period and were strongly correlated with biogenic amine metabolites. The relative abundances of Arthrobacter, Alphaproteobacteria and Brevibacillus in the DFAA2 group were higher compared with DFAA1 group from rewatering to harvest and were significantly positively correlated with hydrocarbon compounds and steroid hormone metabolites. The acid phosphatase activity of the DFAA1 group was significantly higher than that of the DFAA2 group during the flooding period. The study suggests that there is a yield compensation phenomenon in the conversion of 'continuous drought' to flooding compared with 'sporadic light rain', which is related to the improvement in the flooding tolerance of maize by the dominant bacteria Chloroflexi, bacterium SJA-15 and biogenic amine metabolites. These rhizosphere bacteria and soil metabolites may have the potential function of helping plants adapt to the DFAA environment. The study revealed the response of the maize rhizosphere soil environment to DFAA stress and provided new ideas for exploring the potential mechanism of crop yield compensation under DFAA.

Changes in Soil Chemical Properties and Rhizosphere Bacterial Community Induced by Soil Amendments Associated with Reduction in Cadmium Accumulation by Rice

Soil amendments have been extensively employed for the purpose of remediating soils contaminated with cadmium (Cd). However, the potential impacts of soil amendments on soil chemical properties, soil Cd bioavailability, total Cd accumulation by rice, and rhizosphere bacterial community in Cd-contaminated paddy fields located in a tropical region is still at its infancy. In this study, a commercial MgO-CaO-SiO2 conditioner (A), biochar (B), and a combination of the commercial MgO-CaO-SiO2 conditioner and biochar with a ratio of 1:1 (C) were applied at two different doses [2250 kg ha−1 (A150, B150, C150), 4500 kg ha−1 (A300, B300, C300)] to investigate their impacts on soil Cd stabilization and total Cd uptake of rice straw and grain in a Cd-contaminated remediation field experiment. Rhizosphere bacterial community diversity and composition were also assessed using high-throughput sequencing based on 16S rRNA genes. Compared with non-amendment treatment (CK), soil pH, cation exchange capacity (CEC), organic matter (OM), total nitrogen (TN), available nitrogen (AN), and nitrate (NO3−) concentrations were significantly elevated, whereas ammonium (NH4+) and soil available Cd concentrations were reduced by soil amendment treatments. Meanwhile, soil amendments significantly decreased concentrations of total Cd in both rice straw and grain, with the lowest Cd concentration in the C300 treatment. Soil pH and CEC were significantly and negatively associated with soil Cd availability and rice straw and grain Cd concentrations, while NH4+ concentration was positively correlated with soil available Cd concentration, and OM, TN, and NO3− concentrations were positively linked with rice grain Cd concentration. Soil amendments significantly increased bacterial Chao 1 and Shannon indexes and altered bacterial community composition in rhizosphere soil, due to changes in the composition of the community primarily influenced by variations in soil pH, CEC, and soil available Cd, NH4+, available phosphorous (AP) and available Potassium (AK) concentrations. Furthermore, the abundant bacterial species (Pseudomonas) and rare bacterial species (Bacillus, Candidatus_Solibacter and Streptomyces) have been up-regulated by different soil amendments, which might be in favour of soil Cd immobilization. A structural equation model also showed that soil amendments could improve bacterial diversity and change soil pH and CEC, which were conducive to hindering the removal and conversion of Cd. Overall, these results indicate that biochar-(MgO-CaO-SiO2) mixed amendments at high dosage exerted better performance compared with single application soil amendment A and B. The changes in soil chemical properties, available Cd content, and rhizosphere bacterial community assembly induced by soil amendments are closely correlated with the decrease in rice’s ability to accumulate Cd.

A microecological research reveals seasonal variation in rhizosphere-endophytic bacteria and growth and development of Codonopsis pilosula root

Codonopsis pilosula is a medicinal and edible plant. Its chemical composition and pharmacological effects have been extensively studied. However, temporal, especially seasonal variabilities of bacterial composition driving nutrient cycling are poorly understood in rhizosphere and endosphere of C. pilosula. This study aimed to investigate the relationships and distinctions among soil physicochemical characteristics, microbial diversity, and functions of C. pilosula under different seasonal conditions in Longxi, China, and how these factors influenced C. pilosula growth. Physicochemical characteristics, enzymatic activities, growth state and metabolite analysis of C. pilosula in the soil were conducted using multispectral techniques. High-throughput sequencing methods were employed to analyze the alpha- and beta-diversity of rhizospheric and endophytic bacterial communities. Seasonal changes (P < 0.05) significantly influenced physiological indicators, bacterial diversity, community structure, and ecological niche breadth of C. pilosula, which were affected by environmental variables and soil enzymes. The neutral community model indicated that stochasticity played a substantial role in bacterial community development in rhizosphere soil. Furthermore, the microbial diversity was influenced by the soil's electrical conductivity, urease, and catalase activities, as well as phosphorus and potassium concentrations. Seasonal fluctuations significantly impacted the growth, development, metabolite content, and stress resistance indicators, such as antioxidant enzymes, in C. pilosula. By analyzing the temporal characteristics between plant and soil indicators, this study provides insights into regulating environmental factors during C. pilosula growth to enhance its yield and quality.Main conclusion Both rhizosphere soil physicochemical factors and bacterial diversity indices showed strong correlations. Phylogenetic and taxonomic differences existed between rhizosphere and bulk soil bacterial communities of Codonopsis pilosula in different seasons.

Variety-Driven Effect of Rhizosphere Microbial-Specific Recruitment on Drought Tolerance of Medicago ruthenica (L.).

As one of the environmental factors that seriously affect plant growth and crop production, drought requires an efficient but environmentally neutral approach to mitigate its harm to plants. Soil microbiomes can interact with plants and soil to improve the adverse effects of drought. Medicago ruthenica (L.) is an excellent legume forage with strong drought tolerance, but the key role of microbes in fighting drought stress remains unclear. What kind of flora plays a key role? Is the recruitment of such flora related to its genotype? Therefore, we selected three varieties of M. ruthenica (L.) for drought treatment, analyzed their growth and development as well as their physiological and biochemical characteristics, and performed 16S rRNA high-throughput sequencing analysis on their rhizosphere soils to clarify the variety-mediated response of rhizosphere bacteria to drought stress. It was found that among the three varieties of M. ruthenica (L.), Mengnong No.2, Mengnong No.1 and Zhilixing were subjected to drought stress and showed a reduction in plant height increment of 24.86%, 34.37%, and 31.97% and in fresh weight of 39.19%, 50.22%, and 41.12%, respectively, whereas dry weight was reduced by 23.26%, 26.10%, and 24.49%, respectively. At the same time, we found that the rhizosphere microbial community of Mengnong No. 2 was also less affected by drought, and it was able to maintain the diversity of rhizosphere soil microflora stable after drought stress, while Mennong No. 1 and Zhilixing were affected by drought stress, resulting in a decrease in rhizosphere soil bacterial community diversity indices to 92.92% and 82.27%, respectively. Moreover, the rhizosphere of Mengnon No. 2 was enriched with more nitrogen-fixing bacteria Rhizobium than the other two varieties of M. ruthenica (L.), which made it still have a good ability to accumulate aboveground biomass after drought stress. In conclusion, this study proves that the enrichment process of bacteria is closely related to plant genotype, and different varieties enrich different types of bacteria in the rhizosphere to help them adapt to drought stress, and the respective effects are quite different. Our results provide new evidence for the study of bacteria to improve the tolerance of plants to drought stress and lay a foundation for the screening and study mechanism of drought-tolerant bacteria in the future.