Rhizosphere Bacterial Diversity Research Articles

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

Abstract Background and aims Mercury (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. Methods A 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. Results Site-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. Conclusions The 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.

Impacts of Oak Mulch Amendments on Rhizosphere Microbiome of Citrus Trees Grown in Florida Flatwood Soils.

Rhizosphere interactions are an understudied component of citrus production. This is even more important in Florida flatwood soils, which pose significant challenges in achieving sustainable and effective fruit production due to low natural fertility and organic matter. Citrus growers apply soil amendments, including oak mulch, to ameliorate their soil conditions. Thus, the aim of this research was to evaluate the effects of oak mulch on citrus nutrient uptake, soil characteristics, and rhizosphere composition. The plant material consisted of 'Valencia' sweet orange (Citrus × sinensis) trees grafted on 'US-812' (C. reticulata × C. trifoliata) rootstock. The experiment consisted of two treatments, which included trees treated with oak mulch (300 kg of mulch per plot) and a control. The soil and leaf nutrient contents, soil pH, cation exchange capacity, moisture, temperature, and rhizosphere bacterial compositions were examined over the course of one year (spring and fall 2021). During the spring samplings, the citrus trees treated with oak mulch resulted in significantly greater soil Zn and Mn contents, greater soil moisture, and greater rhizosphere bacterial diversity compared to the control, while during the fall samplings, only a greater soil moisture content was observed in the treated trees. The soil Zn and Mn content detected during the spring samplings correlated with the significant increases in the diversity of the rhizosphere bacterial community composition. Similarly, the reduced rates of leaching and evaporation (at the soil surface) of oak mulch applied to Florida sandy soils likely played a large role in the significant increase in moisture and nutrient retention.

Differences in Rhizosphere Microbial Community Structure and Composition in Resistance and Susceptible Wheat to Fusarium Head Blight

Fusarium head blight (FHB) is a serious disease of wheat that threatens wheat production worldwide. In this study, high-throughput sequencing technology was used to analyze the rhizosphere soil microbial metagenomes of 4 wheat cultivars with different levels of resistance to FHB. The results showed that there were differences in the diversity, structure, and composition of rhizosphere microorganisms between resistant and sensitive varieties. The rhizosphere soil bacterial diversity of the resistant wheat varieties Su Mai 3 and Yang Mai 16 was higher than that of the susceptible wheat varieties Zheng Mai 9023 and Zhou Mai 20. The diversity of rhizosphere fungi in resistant varieties was lower than that in susceptible varieties, but the abundance was higher than that in susceptible varieties. Variety was found to alter the community structure of wheat rhizosphere microorganisms. Resistant varieties SM3 and YM16 and moderately susceptible variety ZM9023 had similar microbial community structure, while highly susceptible variety ZM20 was significantly different from other varieties. The study is aimed at analyzing the effects of wheat varieties of different resistance to FHB on the composition and abundance of rhizosphere soil microbial community to screen out bacteria or fungi that can be used to control FHB, providing the theoretical basis for FHB biological control.

Genotypic variation in grain cadmium concentration in wheat: Insights into soil pollution, agronomic characteristics, and rhizosphere microbial communities

Soil cadmium (Cd) pollution poses a serious threat to both the productivity and quality of wheat. This study aimed to investigate the genotypic variation in grain Cd concentration in wheat through field and pot experiments. Among 273 wheat genotypes, a significant genotypic difference was found in grain Cd concentration, ranging from 0.01 to 0.14 mg kg−1. Two contrasting genotypes, X321 (a low grain Cd accumulator) and X128 (a high grain Cd accumulator), were selected for pot experiments. X321 exhibited a 17.9% greater reduction in yield and a 10.2% lower shoot-to-grain Cd translocation rate than X128 under Cd treatment. Grain Cd content showed a positive correlation with soil available Cd content and a negative correlation with Cu content. Soil catalase activity significantly decreased in X128 under Cd stress, whereas no difference was found in X321. The grains of X321 exhibited a more compact spatial distribution of starch grains and protein matrix than those of X128. Moreover, the size of A-type starch in X128 was larger than in X321. Meanwhile, X128 contained much B-type starch, with some surface pits observed on A-type granules under Cd stress. Cd treatment increased the abundance of rhizosphere microorganism communities, with Ellin6067 and Ramlibacter being enriched in X128 under Cd treatment, which might facilitate Cd uptake. The accumulation of Cd in grains demonstrated a strong positive correlation with the rhizosphere bacterial diversity (correlation coefficient = 0.78). These findings provide new insights into the basis of grain Cd accumulation in wheat and have potential implications for developing new verities with low Cd accumulation to ensure food safety and minimize human exposure.

Effects of polystyrene microplastics on the agronomic traits and rhizosphere soil microbial community of highland barley

This study investigated the influence of polystyrene microplastics (MPs) with two different particle sizes (<1 mm, 1–5 mm) and three concentrations (1 g/m2, 10 g/m2, 50 g/m2), as well as added degrading bacteria, on the agronomic traits of highland barley and the bacterial communities in the rhizosphere soil. Results revealed that the small particle size treatment had a significant effect on reducing the 1000-grain weight of highland barley, while the large particle size treatment had an effect on reducing the spike length, width, and awn length (P < 0.05). Additionally, the MP treatment was found to significantly reduce the rhizosphere soil bacterial diversity and richness, including the Shannon, Chao1, observed species, and dominance indices (P < 0.05). Interestingly, the inoculation treatment also reduced microbial diversity, though the microbial diversity after treatment was similar to that of the control community structure, indicating its regulating effect on the soil microbial community. The abundance of Domibacillus, Pedosphaeraceae, and Enterococcus decreased due to the MP treatment, whereas Achromobacter, Massilia, Ralstonia, and Nitrosospira increased (P < 0.05). Furthermore, functional prediction indicated that MP treatment resulted in the enrichment of microbial functions, such as an AraC-type DNA-binding domain, etc. The microbial communities exposed to different sizes and concentrations of MPs had their own unique functions in response to the effects of the MPs. This study provided novel insights into the effects of different particle sizes and concentrations of MPs on the rhizosphere microbial community and agronomic traits of highland barley. It could be used to improve the understanding of the impact of MPs on the rhizosphere soil microecology and enhance bioremediation of MPs.

Rotational strip peanut/cotton intercropping improves agricultural production through modulating plant growth, root exudates, and soil microbial communities

Legume-based intercropping is widely used by smallholder farmers; however, there is scarce information governing the long-term effects of interspecific interactions on the crop growth performance. Here, we present data of 5 years field experimentation on a rotational strip peanut/cotton intercropping system to uncover its beneficial effects on crop production and decipher the underlying mechanisms. Treatments included monoculture of peanut (MP), monoculture of cotton (MC), peanut/cotton intercropping (IC), and peanut/cotton intercropping with solid root barrier (SC). Averaged for 5 years, intercropping did not alter the peanut pods yield whereas the seed cotton yield was significantly increased by 52.63% compared with monoculture. Moreover, the net economic return of IC was significantly increased by 59.49%. Physiological data indicated that the leaf net photosynthetic rate, total biomass, and the accumulation of total nitrogen in peanut pods and cotton buds were significantly increased in IC compared with MP and MC. Meanwhile, the contents of total protein and oleic acid in peanut kernels were also increased by intercropping. Metabolomics evidence showed that differential metabolites from “Tryptophan” and “Carbon” pathways were significantly enriched in peanut and cotton strips of IC. Additionally, IC significantly altered the rhizosphere soil bacterial abundance composition and diversity, and the metabolic functional features of “carbohydrate” and “amino acid” were significantly enriched. Strikingly, the beneficial effects of intercropping were partially counteracted by SC as indicated by the reduction of crop production and net return. Our results demonstrated that rotational strip peanut/cotton intercropping increases production, net economic returns, and peanut quality parameters via the interspecific interactions by enhancing plant growth, regulating root exudates, and modulating soil microbial communities.

Metagenomics offers insights into the rhizospheric bacterial diversity of mushrooms from a tropical forest and temperate forest of India

Bacteria promote mushroom growth by providing growth factors and vitamins, preventing pathogen growth, and enhancing spore distribution. Soil bacteria involved in the nitrogen cycle showed association with the abundance of ectomycorrhizal fungi. Uncultured microorganisms comprise a significant proportion of complex soil ecosystem. Nanopore sequencing Technologies used a genome-resolved metagenomics approach to evaluate the rhizospheric bacterial diversity of these mushrooms from the tropical forests of West Bengal (India) and the temperate forests of West Kameng districts in Arunachal Pradesh, India. The ectomycorrhizosphere soil of tropical forest has higher abundance of nitrogen fixing bacteria such as Bradyrhizobium diazoefficiens, B. erythrophlei, and B. elkanii whereas the ectomycorrhizosphere soil of temperate forest has higher abundance of Candidatus Solibacter usitatus, Rhodoplanes sp. Z2-YC6860, Candidatus Koribacter versatilis, Bacillus cereus, Granulicella tundricola, G. mallensis, Bradyrhizobium icense, Bradyrhizobium sp. SK17, Acidobacterium capsulatum, Bacillus weihaiensis, Terriglobus saanensis, Planococcus sp. MB-3u-03, Bradyrhizobium sp. CCGE-LA001, and Bradyrhizobium japonicum These microorganisms have deep impact in the growth and development of ectomycorrhizal partners (trees and mushrooms) and be called as mycorrhiza helper bacteria (MHB).

Arbuscular mycorrhizal fungi alter rhizosphere bacterial diversity, network stability and function of lettuce in barren soil

Arbuscular mycorrhizal fungi (AMF) play an important role in plant growth and rhizosphere microbiome composition. However, how the plant-AMF-rhizosphere microbiome continuum interacts in barren soils to efficiently promote the plant's growth is still an area of little research. Here, we present the results of a controlled environment experiment to reveal the effect of AMF on the rhizosphere bacterial community of lettuce. Compared with the control group, AMF significantly increased plant biomass, mycorrhizal colonization, and affected the rhizosphere microbial community composition. AMF inoculation changed the function of the rhizosphere bacterial community, reduced the complexity of the bacterial network, and improved its stability. In addition, SEM showed that the composition and structure of rhizosphere soil bacterial community were significantly positively correlated with soil carbon, nitrogen, and phosphorus content after adding AMF. Our findings provide new information for exploring the positive effects of plant-microbe interactions.

Response of Nicandra physalodes (Linn.) Gaertn. and Its Rhizospheric Organisms to the Selective Pressures of High-Concentration Oxytetracycline, Ciprofloxacin, and Tobramycin

Antibiotics play an essential role in the treatment of infectious diseases in humans and animals. Despite their benefits, the release of an increasing amount of various antibiotics into the environment poses a potential threat to plants, soils, animals, and microorganisms. Here, an outdoor pot experiment was conducted to preliminarily evaluate high concentrations of three antibiotics (oxytetracycline, ciprofloxacin, and tobramycin) on Nicandra physalodes (Linn.) Gaertn. and its rhizospheric organisms. The results showed that the three antibiotics had different effects on the growth behavior (germination uniformity, average growing height gain per week, and thousand seed weight) and biomass (aboveground biomass and belowground biomass) of Nicandra physalodes (Linn.) Gaertn. After adding high concentrations of the three antibiotics to the soil of each test group, the earthworm extract in group A (oxytetracycline) significantly increased the coagulation parameters prothrombin time (PT) and thrombin time (TT). The PT significantly decreased (p &lt; 0.01), while the TT was not affected in group B (ciprofloxacin). For group C (tobramycin), the TT significantly decreased (p &lt; 0.01) and the PT was not affected compared to the CK group (control group). The application of the three antibiotics caused alterations in the general activity of enzymes, such as soil sucrase (SC), urease (UE), acid phosphatase (ACP), alkaline phosphatase (AKP), and nitrate reductase (NR). Different antibiotic groups influenced the rhizosphere bacterial diversity and community structure of Nicandra physalodes (Linn.) Gaertn. At the phylum level, Ignavibacteriae was only found in group C, and Parcubacteria and Ignavibacteriae were not present in the CK group. At the genus level, Parcubacteria_norank was not present in the CK group, and BSV40_norank was found in group C. Ultimately, the results suggested that high concentrations of oxytetracycline, ciprofloxacin, and tobramycin could affect the growth behavior and biomass of Nicandra physalodes (Linn.) Gaertn. and alter its rhizobacterial community structure, providing the scientific basis for the rational use of antibiotics in animal husbandry and veterinary science.