Metagenomic analysis of rhizosphere microbiome provides insights into occurrence of iron deficiency chlorosis in field of Asian pears

Background Fe-deficiency chlorosis (FDC) of Asian pear plants is widespread, but little is known about the association between the microbial communities in the rhizosphere soil and leaf chlorosis. The leaf mineral concentration, leaf subcellular structure, soil physiochemical properties, and bacterial species community and distribution had been analysed to gain insights into the FDC in Asian pear plant. Results The total Fe in leaves with Fe-deficiency was positively correlated with total K, Mg, S, Cu, Zn, Mo and Cl contents, but no differences of available Fe (AFe) were detected between the rhizosphere soil of chlorotic and normal plants. Degraded ribosomes and degraded thylakloid stacks in chloroplast were observed in chlorotic leaves. The annotated microbiome indicated that there were 5 kingdoms, 52 phyla, 94 classes, 206 orders, 404 families, 1,161 genera, and 3,043 species in the rhizosphere soil of chlorotic plants; it was one phylum less and one order, 11 families, 59 genera, and 313 species more than in that of normal plant. Bacterial community and distribution patterns in the rhizosphere soil of chlorotic plants were distinct from those of normal plants and the relative abundance and microbiome diversity were more stable in the rhizosphere soils of normal than in chlorotic plants. Three (Nitrospira defluvii, Gemmatirosa kalamazoonesis, and Sulfuricella denitrificans) of the top five species (N. defluvii, G. kalamazoonesis, S. denitrificans, Candidatus Nitrosoarchaeum koreensis, and Candidatus Koribacter versatilis). were the identical and aerobic in both rhizosphere soils, but their relative abundance decreased by 48, 37, and 22%, respectively, and two of them (G. aurantiaca and Ca. S. usitatus) were substituted by an ammonia-oxidizing soil archaeon, Ca. N. koreensis and a nitrite and nitrate reduction related species, Ca. K. versatilis in that of chlorotic plants, which indicated the adverse soil aeration in the rhizosphere soil of chlorotic plants. A water-impermeable tables was found to reduce the soil aeration, inhibit root growth, and cause some absorption root death from infection by Fusarium solani. Conclusions It was waterlogging or/and poor drainage of the soil may inhibit Fe uptake not the amounts of AFe in the rhizosphere soil of chlorotic plants that caused FDC in this study.

Bioavailability of selected trace and rare earth elements to Juncus effusus L.: the potential role of de-icing chlorides in the roadside environment

Background and aim The presence of chlorides in soils, e.g., from de-icing salts may change metal availability to plants. Methods To assess the role of de-icing chlorides on bioavailability of metals, the samples of the rhizosphere soils, roots and shoots of Juncus effusus L. were collected monthly from April to June of 2019 in the vicinity of roads and analyzed for trace (Ag, Cd, Co, Cu, Pb, Zn) and rare earth elements (from La to Lu). Results Concentrations of Cl− were distinctly higher in the shoots than in the roots. Apart from Cd, the concentration sequence of the other metals was as follows: rhizosphere soils>roots>shoots. The bioaccumulation and translocation factors indicated that Cd was the most preferably transported to the shoots as opposed to Ag, Co, Pb and REEs that showed a very low translocation potential. Negative correlations, which were noted between Cu and Co in the shoots and Cl− in soils, revealed their role in salinity stress alleviation. All soil samples showed a positive anomaly of Ce and a negative anomaly of Eu, whereas the shoots showed in turn a negative anomaly of Ce and a distinct positive anomaly of Eu. The lowest salinity factors (K/Na, Ca/Na) of the shoots resulted from an increase of salinity in J. effusus by higher sodium concentrations derived from de-icing NaCl. Conclusions De-icing agents may change the uptake of other elements. In natural habitats, the factors affecting this process include: type of element, soil metal concentrations and interactions, and individual plant features.

Diversity and structure of the rhizosphere microbial communities of wild and cultivated ginseng

Background The resources of wild ginseng have been reducing sharply, and it is mainly dependent on artificial cultivation in China, Korea and Japan. Based on cultivation modes, cultivated ginseng include understory wild ginseng (the seeds or seedlings of cultivated ginseng were planted under the theropencedrymion without human intervention) and farmland cultivated ginseng (grown in farmland with human intervention). Cultivated ginseng, can only be planted on the same plot of land consecutively for several years owing to soilborne diseases, which is mainly because of the variation in the soil microbial community. In contrast, wild ginseng can grow for hundreds of years. However, the knowledge of rhizosphere microbe communities of the wild ginseng is limited. Result In the present study, the microbial communities in rhizosphere soils of the three types of ginseng were analyzed by high-throughput sequencing of 16 S rRNA for bacteria and internal transcribed spacer (ITS) region for fungi. In total, 4,381 bacterial operational taxonomic units (OTUs) and 2,679 fungal OTUs were identified in rhizosphere soils of the three types of ginseng. Among them, the shared bacterial OTUs was more than fungal OTUs by the three types of ginseng, revealing fungal communities were to be more affected than bacterial communities. In addition, the composition of rhizosphere microbial communities and bacterial diversity were similar between understory wild ginseng and wild ginseng. However, higher bacterial diversity and lower fungal diversity were found in rhizosphere soils of wild ginseng compared with farmland cultivated ginseng. Furthermore, the relative abundance of Chloroflexi, Fusarium and Alternaria were higher in farmland cultivated ginseng compared to wild ginseng and understory wild ginseng. Conclusions Our results showed that composition and diversity of rhizosphere microbial communities were significantly different in three types of ginseng. This study extended the knowledge pedigree of the microbial diversity populating rhizospheres, and provided insights into resolving the limiting bottleneck on the sustainable development of P. ginseng crops, and even the other crops of Panax.

Risks for Using FeCl3 Under a Submerged Condition, and Different Water Management to Reduce Uptake of Antimony and Cadmium in a Rice Plant

Soil pollution by multiple metal(loid)s is a common problem, and it is not easy to synchronously reduce their uptake in crops. Compounds containing iron (Fe) are often used to efficiently remediate soil metal(loid) pollution; however, its associated risks did not receive much attention especially under unsuitable soil water conditions. Pot experiments were set up using an antimony (Sb) and cadmium (Cd) co-contaminated soil treated with a continued submergence condition plus 5, 10, or 20 mg kg−1 FeCl3 (Experiment I), or treated with different water management including submergence, intermittent irrigation, and dry farming (Experiment II). Our results showed that the continued submergence resulted in excessive accumulation of arsenic (As) in different tissues of rice plants even if the soil As background concentration is low. High soil moisture content increased the available concentrations of Sb and As, but reduced that of Cd in rhizosphere soils, which was in line with their concentrations in different tissues of rice plants (Experiment II). Under a continued submergence condition, FeCl3 significantly stimulated As concentration in the shoots, roots (excluded Fe20 treatment), and husks, but reduced it in the grains. FeCl3 reduced Sb concentration only in the roots and grains, and reduced Cd concentration only in the husks, suggesting a limited efficiency of FeCl3 to reduce Cd uptake under a submergence condition. In this study, the dynamic changes of As, Sb, and Cd concentrations in soil solution, their available concentrations in rhizosphere soils, their accumulation in root iron/manganese plaques, and the relationships among the above parameters were also discussed. We suggested that if FeCl3 would be used to remediate the contaminated soils by Sb and Cd, dry farming for a short time is needed to avoid As accumulation, and intermittent irrigation is a potential choice to avoid the excessive accumulation of As, Sb, and Cd in the edible parts of rice plants.

Effect of Bacillus mesonae H20-5 Treatment on Rhizospheric Bacterial Community of Tomato Plants under Salinity Stress

Plant growth-promoting bacteria improve plant growth under abiotic stress conditions. However, their effects on microbial succession in the rhizosphere are poorly understood. In this study, the inoculants of Bacillus mesonae strain H20-5 were administered to tomato plants grown in soils with different salinity levels (EC of 2, 4, and 6 dS/m). The bacterial communities in the bulk and rhizosphere soils were examined 14 days after H20-5 treatment using Illumina MiSeq sequencing of the bacterial 16S rRNA gene. Although the abundance of H20-5 rapidly decreased in the bulk and rhizosphere soils, a shift in the bacterial community was observed following H20-5 treatment. The variation in bacterial communities due to H20-5 treatment was higher in the rhizosphere than in the bulk soils. Additionally, the bacterial species richness and diversity were greater in the H20-5 treated rhizosphere than in the control. The composition and structure of the bacterial communities varied with soil salinity levels, and those in the H20-5 treated rhizosphere soil were clustered. The members of Actinobacteria genera, including Kineosporia, Virgisporangium, Actinoplanes, Gaiella, Blastococcus, and Solirubrobacter, were enriched in the H20-5 treated rhizosphere soils. The microbial co-occurrence network of the bacterial community in the H20-5 treated rhizosphere soils had more modules and keystone taxa compared to the control. These findings revealed that the strain H20-5 induced systemic tolerance in tomato plants and influenced the diversity, composition, structure, and network of bacterial communities. The bacterial community in the H20-5 treated rhizosphere soils also appeared to be relatively stable to soil salinity changes.

Clover Species Specific Influence on Microbial Abundance and Associated Enzyme Activities in Rhizosphere and Non-Rhizosphere Soils

Legume cultivation, especially the clover species, has shown promoting effects on soil biological properties. However, the ways in which various clover species contribute to beneficial plant-rhizosphere soil interactions have remained neglected in the past. Therefore, we performed a field experiment to assess and compare the species-specific influence of five different clover species on plant traits, microbial soil health indicators, namely soil enzymes, microbial biomass and abundance and their potential nutrient cycling abilities under rhizosphere and non-rhizosphere soils. For this, soil samples from bulk soil and rhizosphere of each clover species were collected and analyzed for soil enzymes including β-glucosidase, arylsulfatase, phosphatase, N-acetyl-β-D-glucosaminidase, and urease and microbial communities’ abundance. Results revealed that the soil biological properties were more affected in the rhizosoil than in the bulk soil, although the individual legume crop variants differed in the rate and extent of the differential impact on either rhizosoil or bulk soil. The most significantly affected species-specific properties were ammonium oxidizing bacteria and phosphorus-solubilizing microbiota in the rhizosoil of white clover and alsike clover variants, whereas the least impact was exerted by sweet clover. The biological properties of rhizosoil showed a significant effect on the plant qualitative and quantitative properties. We further detected antagonism among N and P + K transfer from the rhizosoil to plants, which influenced above ground and root biomass. Overall, these results suggest that the positive effects of clover species cultivation on rhizosphere soil properties are species specific.