Variation in Bacterial Community Structure in Rhizosphere and Bulk Soils of Different Halophytes in the Yellow River Delta

Soil microorganisms play the important role in driving biogeochemical cycles. However, it is still unclear on soil microbial community characteristics and microbial driving mechanism in rhizosphere and bulk soils of different halophyte species. In this study, we analyzed bacterial communities in the rhizosphere and bulk soils of three typical halophytes in the Yellow River Delta, i.e., Phragmites communis, Suaeda salsa, and Aeluropus sinensis, by high-throughput sequencing. The contents of total carbon, total nitrogen, and available phosphorus in rhizosphere soils of the three halophytes were significantly higher than those in bulk soils, which suggested a nutrient enrichment effect of the rhizosphere. Rhizosphere soil bacterial α-diversity of P. communis was higher than that in bulk soil, whereas bacterial α-diversity in rhizosphere soil of S. salsa and A. sinensis was lower than those in bulk soil. The dominant bacterial phyla were Proteobacteria, Actinobacteria, Chloroflexi, and Bacteroidetes, which accounted for 31, 20.5, 16.3, and 10.3%, respectively. LDA effect size (LEfSe) analysis showed that the bacterial species with significant differences in expression abundance was obviously different in the rhizosphere and bulk soil of three halophytes. The principal component analysis (PCoA) showed that bacterial community composition was greatly different between rhizosphere and bulk soils of P. communis and S. salsa, while no difference in A. sinensis. Changed bacterial community composition was mainly ascribed to salinity in rhizosphere and bulk soils. Additionally, salinity was positively correlated with Bacteroidetes and negatively correlated with Actinobacteria and Acidobacteria. Our study clarified the variation in bacterial community structure between rhizosphere and bulk soils with soil physicochemical properties, which proved a biological reference to indicate the characteristics of saline and alkaline land.

Effects of Allelochemicals, Soil Enzyme Activities, and Environmental Factors on Rhizosphere Soil Microbial Community of Stellera chamaejasme L. along a Growth-Coverage Gradient

Allelochemicals released from the root of Stellera chamaejasme L. into rhizosphere soil are an important factor for its invasion of natural grasslands. The aim of this study is to explore the interactions among allelochemicals, soil physicochemical properties, soil enzyme activities, and the rhizosphere soil microbial communities of S. chamaejasme along a growth-coverage gradient. High-throughput sequencing was used to determine the microbial composition of the rhizosphere soil sample, and high-performance liquid chromatography was used to detect allelopathic substances. The main fungal phyla in the rhizosphere soil with a growth coverage of 0% was Basidiomycetes, and the other sample plots were Ascomycetes. Proteobacteria and Acidobacteria were the dominant bacterial phyla in all sites. RDA analysis showed that neochamaejasmin B, chamaechromone, and dihydrodaphnetin B were positively correlated with Ascomycota and Glomeromycota and negatively correlated with Basidiomycota. Neochamaejasmin B and chamaechromone were positively correlated with Proteobacteria and Actinobacteria and negatively correlated with Acidobacteria and Planctomycetes. Allelochemicals, soil physicochemical properties, and enzyme activity affected the composition and diversity of the rhizosphere soil microbial community to some extent. When the growth coverage of S. chamaejasme reached the primary stage, it had the greatest impact on soil physicochemical properties and enzyme activities.

Microbial Responses to the Reduction of Chemical Fertilizers in the Rhizosphere Soil of Flue-Cured Tobacco

The overuse of chemical fertilizers has resulted in the degradation of the physicochemical properties and negative changes in the microbial profiles of agricultural soil. These changes have disequilibrated the balance in agricultural ecology, which has resulted in overloaded land with low fertility and planting obstacles. To protect the agricultural soil from the effects of unsustainable fertilization strategies, experiments of the reduction of nitrogen fertilization at 10, 20, and 30% were implemented. In this study, the bacterial responses to the reduction of nitrogen fertilizer were investigated. The bacterial communities of the fertilizer-reducing treatments (D10F, D20F, and D30F) were different from those of the control group (CK). The alpha diversity was significantly increased in D20F compared to that of the CK. The analysis of beta diversity revealed variation of the bacterial communities between fertilizer-reducing treatments and CK, when the clusters of D10F, D20F, and D30F were separated. Chemical fertilizers played dominant roles in changing the bacterial community of D20F. Meanwhile, pH, soil organic matter, and six enzymes (soil sucrase, catalase, polyphenol oxidase, urease, acid phosphatase, and nitrite reductase) were responsible for the variation of the bacterial communities in fertilizer-reducing treatments. Moreover, four of the top 20 genera (unidentified JG30-KF-AS9, JG30-KF-CM45, Streptomyces, and Elsterales) were considered as key bacteria, which contributed to the variation of bacterial communities between fertilizer-reducing treatments and CK. These findings provide a theoretical basis for a fertilizer-reducing strategy in sustainable agriculture, and potentially contribute to the utilization of agricultural resources through screening plant beneficial bacteria from native low-fertility soil.

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.

Maize/peanut intercropping improves nutrient uptake of side-row maize and system microbial community diversity

Background Intercropping, a diversified planting pattern, increases land use efficiency and farmland ecological diversity. We explored the changes in soil physicochemical properties, nutrient uptake and utilization, and microbial community composition in wide-strip intercropping of maize and peanut. Results The results from three treatments, sole maize, sole peanut and intercropping of maize and peanut, showed that intercropped maize had a marginal advantage and that the nutrient content of roots, stems and grains in side-row maize was better than that in the middle row of intercropped maize and sole maize. The yield of intercropped maize was higher than that of sole cropping. The interaction between crops significantly increased soil peroxidase activity, and significantly decreased protease and dehydrogenase activities in intercropped maize and intercropped peanut. The diversity and richness of bacteria and fungi decreased in intercropped maize rhizosphere soil, whereas the richness of fungi increased intercropped peanut. RB41, Candidatus-udaeobacter, Stropharia, Fusarium and Penicillium were positively correlated with soil peroxidase activity, and negatively correlated with soil protease and dehydrogenase activities. In addition, intercropping enriched the functional diversity of the bacterial community and reduced pathogenic fungi. Conclusion Intercropping changed the composition and diversity of the bacterial and fungal communities in rhizosphere soil, enriched beneficial microbes, increased the nitrogen content of intercropped maize and provided a scientific basis for promoting intercropping in northeastern China.