Abundance In Rhizosphere Soil Research Articles

Intercropping improves maize yield and nitrogen uptake by regulating nitrogen transformation and functional microbial abundance in rhizosphere soil

Intercropping-driven changes in nitrogen (N)-acquiring microbial genomes and functional expression regulate soil N availability and plant N uptake. However, present data seem to be limited to a specific community, obscuring the viewpoint of entire N-acquiring microbiomes and functions. Taking maize intercropped with legumes (peanut and soybean) and non-legumes (gingelly and sweet potato) as models, we studied the effects of intercropping on N transformations and N-acquiring microbiomes in rhizosphere soil across four maize growth stages. Meanwhile, we compiled promising strategies such as random forest analysis and structural equation model for the exploitation of the associations between microbe-driven N dynamics and soil-plant N trade-offs and maize productivity. Compared with monoculture, maize intercropping significantly increased the denitrification rate of rhizosphere soils across four maize growth stages, net N mineralization in the elongation and flowering stages, and the nitrification rate in the seedling and mature stages. The abundance of most N-acquiring microbial populations was influenced significantly by intercropping patterns and maize growth stages. Soil available N components (NH4+-N, NO3−-N, and dissolved organic N content) showed a highly direct effect on plant N uptake, which mainly mediated by N transformations (denitrification rate) and N-acquiring populations (amoB, nirK3, and hzsB genes). Overall, the adaptation of N-acquiring microbiomes to changing rhizosphere micro-environments caused by intercropping patterns and maize development could promote soil N transformations and dynamics to meet demand of maize for N nutrient. This would offer another unique perspective to manage the benefits of the highly N-effective and production-effective intercropping ecosystems.

Deciphering core microbiota in rhizosphere soil and roots of healthy and Rhizoctonia solani-infected potato plants from various locations.

Black scurf caused by Rhizoctonia solani severely affects potato production. Through amplification of V3-V4 and ITS1-5f variable regions of 16S and internal transcribed spacer (ITS) rRNA, the study was based on the location (Kunming, Qujing, and Zhaotong), plant components (rhizosphere soil and roots), and sample types (healthy and diseased) to assess the diversity of bacterial and fungal communities. We found plant components significantly influence microbial diversity, with rhizosphere soil being more diverse than roots, and the microbial community in the root is mainly derived from the rhizosphere soil. Moreover, the rhizosphere soil and roots of healthy potato plants exhibit greater microbial diversity compared to those of potato plants infected by Rhizoctonia solani. Bacterial phyla Actinobacteriota and Acidobacteriota were enriched in rhizosphere soil compared to that of roots, whereas Proteobacteria and Cyanobacteria showed the opposite trend. Fungal phylum Ascomycota was found in low relative abundance in rhizosphere soil than in roots, whereas Basidiomycota showed the opposite trend. Bacterial genera including Streptomyces, Lysobacter, Bacillus, Pseudomonas, Ensifer, Enterobacter, and the Rhizobium group (Allorhizobium, Neorhizobium, Pararhizobium, Rhizobium), along with fungal genera such as Aspergillus, Penicillium, Purpureocillium, and Gibberella moniliformis, have the potential ability of plant growth promotion and disease resistance. However, most fungal species and some bacterial species are pathogenic to potato and could provide a conducive environment for black scurf infection. Interaction within the bacterial network increased in healthy plants, contrasting with the trend in the fungal network. Our findings indicate that R. solani significantly alters potato plant microbial diversity, underscoring the complexity and potential interactions between bacterial and fungal communities for promoting potato plant health and resistance against black scurf.

Mycorrhizal diversity and community composition in co-occurring Cypripedium species.

Orchids commonly rely on mycorrhizal fungi to obtain the necessary resources for seed germination and growth. Whereas most photosynthetic orchids typically associate with so-called rhizoctonia fungi to complete their life cycle, there is increasing evidence that other fungi may be involved as well and that the mycorrhizal communities associated with orchids may be more diverse. Coexisting orchid species also tend to associate with different fungi to reduce competition for similar resources and to increase long-term population viability. However, few studies have related the mycorrhizal communities in the rhizosphere to communities found in the roots of closely related coexisting orchid species. In this study, we used high-throughput sequencing to investigate the diversity and community composition of orchid mycorrhizal fungi in the roots and the rhizosphere of four Cypripedium species growing in forests in Northeast China. The results showed that the investigated Cypripedium species associated with a wide variety of fungi including members of Tulasnellaceae, Psathyrellaceae, and Herpotrichiellaceae, whereas members of Russulaceae, Cortinariaceae, Thelephoraceae, and Herpotrichiellaceae showed high abundance in rhizosphere soils. The diversity of fungi detected in the rhizosphere soil was much higher than that in the roots. The observed variation in fungal communities in Cypripedium roots was not related to forest site or orchid species. On the other hand, variation in mycorrhizal communities of rhizosphere soil was significantly related to sampling site. These results indicate that orchid mycorrhizal communities in the rhizosphere display considerable variation among sites and that orchids use only a subset of the locally available fungi. Future studies focusing on the fine-scale spatial distribution of orchid mycorrhizal fungi and more detailed assessments of local environmental conditions will provide novel insights into the mechanisms explaining variation of fungal communities in both orchid roots and the rhizosphere.

Root Functional Trait and Soil Microbial Coordination: Implications for Soil Respiration in Riparian Agroecosystems.

Predicting respiration from roots and soil microbes is important in agricultural landscapes where net flux of carbon from the soil to the atmosphere is of large concern. Yet, in riparian agroecosystems that buffer aquatic environments from agricultural fields, little is known on the differential contribution of CO2 sources nor the systematic patterns in root and microbial communities that relate to these emissions. We deployed a field-based root exclusion experiment to measure heterotrophic and autotrophic-rhizospheric respiration across riparian buffer types in an agricultural landscape in southern Ontario, Canada. We paired bi-weekly measurements of in-field CO2 flux with analysis of soil properties and fine root functional traits. We quantified soil microbial community structure using qPCR to estimate bacterial and fungal abundance and characterized microbial diversity using high-throughput sequencing. Mean daytime total soil respiration rates in the growing season were 186.1 ± 26.7, 188.7 ± 23.0, 278.6 ± 30.0, and 503.4 ± 31.3 mg CO2-C m–2 h–1 in remnant coniferous and mixed forest, and rehabilitated forest and grass buffers, respectively. Contributions of autotrophic-rhizospheric respiration to total soil CO2 fluxes ranged widely between 14 and 63% across the buffers. Covariation in root traits aligned roots of higher specific root length and nitrogen content with higher specific root respiration rates, while microbial abundance in rhizosphere soil coorindated with roots that were thicker in diameter and higher in carbon to nitrogen ratio. Variation in autotrophic-rhizospheric respiration on a soil area basis was explained by soil temperature, fine root length density, and covariation in root traits. Heterotrophic respiration was strongly explained by soil moisture, temperature, and soil carbon, while multiple factor analysis revealed a positive correlation with soil microbial diversity. This is a first in-field study to quantify root and soil respiration in relation to trade-offs in root trait expression and to determine interactions between root traits and soil microbial community structure to predict soil respiration.

Ryegrass (Lolium multiflorum L.) and Indian mustard (Brassica juncea L.) intercropping can improve the phytoremediation of antibiotics and antibiotic resistance genes but not heavy metals

Lolium multiflorum and Brassica juncea display phytoremediation potential for heavy metals and antibiotics pollution. However, there is limited understanding of their function in removing combined pollutants (heavy metals, antibiotics and antibiotic resistance genes (ARGs)) under different cropping patterns. Sole cropping had little effect on heavy metals, but reduced antibiotics by 2.46%–84.88% and increased ARGs by 15.96%–33.82%. Intercropping was more beneficial to soil remediation and plant accumulation of L. multiflorum, and further increased the remediation of antibiotics by 2.38%–54.40%. Members of phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) were mainly responsible for most antibiotics removal. Compared with sole cropping, intercropping reduced more ARGs abundance in rhizosphere soil for L. multiflorum (20.43%) and in bulk soil for B. juncea (23.22%). Mobile genetic elements (MGEs) played a significant role in the variation of ARGs. Further, sample type showed a higher indirect negative impact on ARGs by mainly affecting soil properties and bacterial community, and the co-occurrence between the bacterial community and ARGs in bulk soil was more complex than that in rhizosphere soil. Together these results suggest that phytoremediation of combined soil pollution was positive but limited, and intercropping resulted in enhanced removal efficiency when compared with sole cropping.

Effect of wheat cultivars with different resistance to Fusarium head blight on rhizosphere Fusarium graminearum abundance and microbial community composition

Wheat (Triticum aestivum L.) cultivars vary in their resistance to Fusarium head blight (FHB), while it is poorly understood how different cultivars influence FHB-causing Fusarium graminearum abundance in rhizosphere soil. A field experiment was conducted to investigate the influence of three wheat cultivars on FHB index, rhizosphere soil F. graminearum abundance, chemical properties, and microbial community composition and metabolic profiles. The cultivars were Sumai3 (SM), Yangmai13 (YM), and Annong8455 (AN), representing high, intermediate, and low resistance to FHB, respectively. Both wheat FHB index and rhizosphere F. graminearum abundance were ranked as SM < YM < AN (p < 0.05). Wheat cultivar influenced community composition with a higher fungal Shannon index in the SM and YM rhizosphere than in the AN rhizosphere. The relative abundances of Arthrobacter, Pseudomonas, Acremonium and Guehomyces that contain microbes with potential to have beneficial effects on pathogen suppression were higher in the rhizosphere soil of SM, relative to AN. Microorganisms in the SM rhizosphere used less carboxylic acids and phenolic acids but more amino acids than those in the AN rhizosphere. Rhizosphere F. graminearum abundance was positively correlated to utilization of carboxylic acids, but negatively correlated with NH4+-N content, fungal Shannon index, and relative abundance of Arthrobacter, Pseudomonas, Acremonium and Guehomyces. The different F. graminearum abundance in rhizosphere soil of wheat cultivars with different resistance to FHB may be associated with the changes in rhizosphere soil chemical properties and microbial community composition and function.

Calla lily intercropping in rubber tree plantations changes the nutrient content, microbial abundance, and enzyme activity of both rhizosphere and non-rhizosphere soil and calla lily growth

Rubber is a globally important crop species and is widely grown in Hainan, China; the development of efficient agricultural practices is essential when attempting to maximize productivity. The effects of interspecific competition for nutrients and calla lily (Alocasia macrorrhizos L.) intercropping on calla lily growth, development, and nutrient uptake were investigated in rubber tree (Hevea brasiliensis Müll. Arg.) plantations. The nutrient abundances, enzyme activity, and number of microbes present in rhizosphere and non-rhizosphere soil were determined. Barriers were inserted between the crops to separate their root systems and nullify belowground competition to facilitate the analysis of intercrop competition. We found that in the rubber tree/calla lily intercropping system, nutrient content and soil urease activities in rhizosphere and non-rhizosphere soil significantly decreased, and nitrogen (N) and potassium (K) taken up by calla lilies, and the growth and biomasses of calla lilies significantly decreased. In contrast, soil sucrase, acid phosphatase, and catalase activities and the quantity of fungi in rhizosphere and non-rhizosphere soil significantly increased, and phosphorus (P) uptake, root length, and the ratio of root to shoot dry weights in calla lilies also significantly increased. Intercropping significantly decreased the abundances of both bacteria and actinomycetes and decreased total microbial abundance in rhizosphere soil, but significantly increased their abundances in non-rhizosphere soil. The nutrient content (excluding organic matter content and pH) in rhizosphere soil was lower than in non-rhizosphere soil. These findings indicate that nutrient competition between rubber trees and calla lilies was significant in this intercropping system, with rubber trees holding a competitive advantage. Intercropping significantly inhibited calla lily growth by significantly decreasing soil nutrient content. The abundances of soil microbes and changes in root architectures correspond to the responses of calla lilies to nutrient competition, allowing the adjustment of the plants’ nutritional needs during growth and development.

Illumina Miseq sequencing-based fungal community of rhizosphere soils along root orders of poplar plantation

The study on microbial community composition in rhizosphere soils surrounding different order roots is of great significance for understanding the interactions between roots and microbes. Using Illumina Miseq sequencing technology, this study analyzed the differences of fungal community structure in bulk soils and rhizosphere soils surrounding different root orders of poplar (Populus × euramericana 'Neva') tree. The microbial species annotation showed that 128, 124, 130 and 101 fungal genera were classified in the rhizosphere soils around 1-2 order roots (R1), 3 order roots (R2), 4-5 order roots (R3) and in the bulk soils (NR), respectively. The differences of present fungal genera indicated a selectivity mechanism driving fungal community assembly in poplar rhizosphere soils. There were seven fungal genera with more than 1% of relative abundance in rhizosphere soils. Trichoderma was the dominant fungal genus in R1. Trichosporon and Aspergillus were the dominant fungal genera in R2 and R3, respectively. Alpha (α) diversity indices showed that the fungal diversity was significantly different among root orders. Specifically, the diversity of soil fungal community in the rhizosphere soils around lower order roots was significantly higher than that of higher order roots (P＜0.05). Beta (β) diversity indices showed that the dissimilarity of fungal community composition increased along with the root orders. All these results implied the different composition and structure of fungal community are closely related with the function of fine root orders.

Elevated atmospheric CO2 affected photosynthetic products in wheat seedlings and biological activity in rhizosphere soil under cadmium stress.

The objective of this study was to investigate the effects of elevated CO2 (700 ± 23μmolmol(-1)) on photosynthetic products in wheat seedlings and on organic compounds and biological activity in rhizosphere soil under cadmium (Cd) stress. Elevated CO2 was associated with decreased quantities of reducing sugars, starch, and soluble amino acids, and with increased quantities of soluble sugars, total sugars, and soluble proteins in wheat seedlings under Cd stress. The contents of total soluble sugars, total free amino acids, total soluble phenolic acids, and total organic acids in the rhizosphere soil under Cd stress were improved by elevated CO2. Compared to Cd stress alone, the activity of amylase, phenol oxidase, urease, L-asparaginase, β-glucosidase, neutral phosphatase, and fluorescein diacetate increased under elevated CO2 in combination with Cd stress; only cellulase activity decreased. Bacterial abundance in rhizosphere soil was stimulated by elevated CO2 at low Cd concentrations (1.31-5.31mgCdkg(-1)dry soil). Actinomycetes, total microbial abundance, and fungi decreased under the combined conditions at 5.31-10.31mgCdkg(-1)dry soil. In conclusion, increased production of soluble sugars, total sugars, and proteins in wheat seedlings under elevated CO2 + Cd stress led to greater quantities of organic compounds in the rhizosphere soil relative to seedlings grown under Cd stress only. Elevated CO2 concentrations could moderate the effects of heavy metal pollution on enzyme activity and microorganism abundance in rhizosphere soils, thus improving soil fertility and the microecological rhizosphere environment of wheat under Cd stress.

Integrating irrigation management for improved grain yield of winter wheat and rhizosphere AM fungal diversity in a semi-arid cropping system

Irrigation of farmland is a popular agricultural practice in semi-arid areas in China. However, little is known about the impacts of different irrigation strategies on grain yield and soil microbial communities, particularly economically-important arbuscular mycorrhizal (AM) fungi. The aim of this study was to optimize irrigation strategies to integrate maximized grain yield, AM fungal diversity and water productivity (defined here as grain yield per unit water supplied). Six irrigation strategies consisting of different amounts of water supplied and time of supply were imposed for field-grown winter wheat (Triticum aestivum) in a typical cropping system in northern China. Results showed that all irrigation strategies significantly increased grain yield compared with the non-irrigation practice (P < 0.01). Irrigation strategy (treatment WJF180) with a total of 180-mm water supplied at Wintering, Jointing, and Grain filling stages (60 mm each) achieved maximal grain yield and water productivity than other treatments. Irrigation strategies also significantly influenced mycorrhizal colonization on roots, fungal species and spore abundance in rhizosphere soil. A total of 17 AM fungal species belonging to Glomus, Acaulopora, Scutellospora and Entrophospora were detected in the soil. The relative abundance of Glomus was the highest and Entrophospora the lowest among the four fungal genera. WJF180-treated plots had the largest species richness and spore abundance in various sampling times with plant growth. Fungal diversity differed greatly among different plant phenological stages. There were significant interactions between irrigation treatments and plant growth stages on both grain yield and AM fungi (species diversity and spore abundance). Irrigation strategies in terms of water amount and watering time integrated with biological, environmental and crop management could have potential for improved grain yield and mycorrhizal diversity leading to maximized farmers' economic productivity and water-use efficiency.

Effects of variation in precipitation on the distribution of soil bacterial diversity in the primitive Korean pine and broadleaved forests.

Patterns of precipitation have changed as a result of climate change and will potentially keep changing in the future. Therefore, it is critical to understand how ecosystem processes will respond to the variation of precipitation. However, compared to aboveground processes, the effects of precipitation change on soil microorganisms remain poorly understood. Changbai Mountain is an ideal area to study the responses of temperate forests to the variations in precipitation. In this study, we conducted a manipulation experiment to simulation variation of precipitation in the virgin, broad-leaved Korean pine mixed forest in Changbai Mountain. Plots were designed to increase precipitation by 30 % [increased (+)] or decrease precipitation by 30 % [decreased (-)]. We analyzed differences in the diversity of the bacterial community in surface bulk soils (0-5 and 5-10 cm) and rhizosphere soils between precipitation treatments, including control. Bacteria were identified using the high-throughput 454 sequencing method. We obtained a total 271,496 optimized sequences, with a mean value of 33,242 (±1,412.39) sequences for each soil sample. Being the same among the sample plots with different precipitation levels, the dominant bacterial communities were Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, and Chloroflexi. Bacterial diversity and abundance declined with increasing soil depth. In the bulk soil of 0-5 cm, the bacterial diversity and abundance was the highest in the control plots and the lowest in plots with reduced precipitation. However, in the soil of 5-10 cm, the diversity and abundance of bacteria was the highest in the plots of increased precipitation and the lowest in the control plots. Bacterial diversity and abundance in rhizosphere soils decreased with increased precipitation. This result implies that variation in precipitation did not change the composition of the dominant bacterial communities but affected bacterial abundance and the response patterns of the dominant communities to variation in precipitation.

The effects of different disease-resistant cultivars of banana on rhizosphere microbial communities and enzyme activities

To understand the mechanism of soil microbial ecosystem and biochemical properties in suppressing soilborne plant diseases, the relationship between the soil rhizosphere microbial communities, hydrolase activities, and different disease-resistant cultivars was investigated. There were statistically significant differences in microbial diversity in the rhizosphere soil between the disease-tolerant cultivar Fj01 and susceptible cultivar Baxi. The rhizosphere soil of Fj01 showed a trend of higher microbial diversity than that of Baxi. At the same growth stage, the similar trends of variation in microbial community diversity between the two different cultivars were observed. The bacterial community abundance in rhizosphere soil from the two banana cultivars was quantified by real-time PCR assays. The size of the rhizosphere bacterial population from the Fj01 was significantly larger than that from the Baxi during the growing stage from July to September. The activities of urease and phosphatase were analyzed to study the effects of the two banana cultivars to soil ecosystem functioning. Urease activity was significantly higher in the rhizosphere soil of Fj01 than that of Baxi in the period from July to September. However, phosphatase activity showed no significant difference between the two different rhizosphere soils.

Aluminum tolerance of wheat does not induce changes in dominant bacterial community composition or abundance in an acidic soil

Aluminum-tolerant wheat plants often produce more root exudates such as malate and phosphate than aluminum-sensitive ones under aluminum (Al) stress, which provides environmental differences for microorganism growth in their rhizosphere soils. This study investigated whether soil bacterial community composition and abundance can be affected by wheat plants with different Al tolerance. Two wheat varieties, Atlas 66 (Al-tolerant) and Scout 66 (Al-sensitive), were grown for 60 days in acidic soils amended with or without CaCO3. Plant growth, soil pH, exchangeable Al content, bacterial community composition and abundance were investigated. Atlas 66 showed better growth and lower rhizosphere soil pH than Scout 66 irrespective of CaCO3 amendment or not, while there was no significant difference in the exchangeable Al content of rhizosphere soil between the two wheat lines. The dominant bacterial community composition and abundance in rhizosphere soils did not differ between Atlas 66 and Scout 66, although the bacterial abundance in rhizosphere soil of both wheat lines was significantly higher than that in bulk soil. Sphingobacteriales, Clostridiales, Burkholderiales and Acidobacteriales were the dominant bacteria phylotypes. The difference in wheat Al tolerance does not induce the changes in the dominant bacterial community composition or abundance in the rhizosphere soils.

Quantitative real-time PCR assay for rapid detection of plant and human pathogenic Macrophomina phaseolina from field and environmental samples

A real-time qPCR assay was developed to detect and quantify Macrophomina phaseolina abundance in rhizosphere soil and plant tissue. Both TaqMan and SYBR green techniques were targeted on ~ 1 kb sequence characterized amplified region (SCAR) of M. phaseolina and two sets of specific primers were designed for SYBR green (MpSyK) and TaqMan (MpTqK) assays. No cross-hybridization and no fluorescent signal exceeding the baseline threshold was observed in TaqMan and SYBR green assays, respectively. The minimum detection limit or sensitivity of TaqMan assay was 30 fg/μL of M. phaseolina DNA and limit of quantification of M. phaseolina viable population was estimated as 0.66 × 105 CFU/g soil−1 equivalent to 10 pg/μL of target DNA. This is the first report which demonstrated real-time qPCR assays with greater specificity and sensitivity to detect M. phaseolina population in soil and plant materials.

Defoliation‐induced changes in carbon allocation and root soluble carbon concentration in field‐grown Lolium perenne plants: do they affect carbon availability, microbes and animal trophic groups in soil?

Summary It is hypothesized that defoliation‐induced changes in plant carbon allocation and root soluble C concentration modify rhizosphere C availability and, further, the abundance and activity of soil microbes and their grazers. To test this hypothesis, field‐grown Lolium perenne swards were defoliated twice during their second growing season at two nitrogen availabilities (added N or no added N). Plant, soil and microbial attributes were measured 2 and 4 days after the last defoliation, and nematode abundance was measured 6 days after the last defoliation. Defoliation decreased shoot production in plots where N was added, but had no significant effect in plots where N was not added. Root biomass and the ratio of root mass to shoot production were not affected. Defoliation increased root soluble C concentration by 26% at the first harvest (2 days after defoliation) and by 18% at the second harvest (4 days after defoliation). Leaf N concentration was 27% lower in defoliated than in non‐defoliated swards at the first harvest, while that of stems was 14% higher in defoliated swards at both harvests, and that of roots was not affected. Defoliation increased root C : N ratio, decreased stem C : N ratio, and did not have a statistically significant effect on leaf C : N ratio. Soil attributes (soil soluble C concentration and soil C and N concentrations) were not affected by defoliation. Similarly, microbial attributes such as microbial C and N content, bacterial abundance in rhizosphere soil, and diversity of C sources utilized by the rhizosphere microbial community, did not differ between defoliated and non‐defoliated swards. Among nematode trophic groups, defoliation reduced the abundance of fungivorous and herbivorous nematodes by 70 and 47%, respectively, but did not affect the abundance of bacterivorous, omnivorous and predatory nematodes. Although defoliation altered plant C allocation and root soluble C concentration, these changes did not influence C availability, soil microbial growth or the abundance of bacteria‐feeding nematodes in the plant rhizosphere. Instead, the effects on root‐ and fungus‐feeding nematodes suggest that the effects of defoliation on soil communities were propagated not through the effects of root‐released C on bacteria and bacterial grazers, but through effects of root quality on root‐feeders and possibly through effects of mycorrhizal fungi on fungus‐feeders.