Rhizobacterial Community Structure Research Articles

Orfamide production in Pseudomonas protegens CHA0T promotes rhizospheric colonization and influences assemblage of the bacterial community of wheat roots in soil.

Orfamides (Ofa) are a family of closely related cyclic lipopeptides (cLPs) produced by different soil-inhabiting and plant beneficial strains of the Pseudomonas protegens subgroup. Orfamides are required for swarming motility, they mediate toxicity on oomycetes, algae, and insects, and they can act as ISR elicitors. Ofa biosynthesis depends on a non-ribosomal peptide synthetase gene cluster whose expression is tightly controlled by the post-transcriptional regulatory cascade Gac-Rsm. Although the biological properties and physiological role of Ofa have been well characterized in vitro, the role of Ofa in the fitness of the producing bacterium in its niche has not been studied so far. Here, we used an Ofa biosynthesis-deficient mutant (ΔofaABC) derived from the biocontrol model strain P. protegens CHA0T to explore the relevance of this cLP in soil for the survival of strain CHA0T, its contribution to the bacterial competitiveness for colonization of wheat roots, and its impact on the corresponding rhizobacterial community structure. To facilitate CFU counts in non-sterile soil and root samples we used chromosomally tagged versions of CHA0T and its ΔofaABC mutant with mini-Tn7 constructs carrying antibiotic resistance markers. We confirmed that the tagged Ofa− mutant does not show drop-collapse activity neither it can swarm in semi-solid medium. We also confirmed that Ofa can be exploited in vitro as a social good by the Ofa− mutant to resume swarming in the presence of CHA0T cells. We found that Ofa production did not confer any advantage for bacterial survival along a period of 5 weeks after soil inoculation. However, we observed that Ofa production was associated with a higher competitiveness for colonization of the wheat rhizosphere. Expression of the ofa biosynthetic operon, by means of a transcriptional Pofa-gfp reporter fusion, was detected in the rhizoplane of colonized wheat roots, suggesting that Ofa is produced in situ on the surface of colonized wheat roots. Finally, we observed that seed inoculation with the wild type Ofa producer strain CHA0T resulted in a differential assemblage of the bacterial community of the wheat rhizosphere with respect to that of seeds bacterized with the Ofa deficient mutant. Overall, we provide evidence that Ofa is important for the competitiveness of P. protegens CHA0T cells to colonize the surface of wheat roots and that Ofa production in the rhizosphere can impact the structure of the assembled bacterial microbiome.

Plant diversity and functional identity drive grassland rhizobacterial community responses after 15 years of CO2 and nitrogen enrichment

Abstract Improved understanding of bacterial community responses to multiple environmental filters over long time periods is a fundamental step to develop mechanistic explanations of plant–bacterial interactions as environmental change progresses. This is the first study to examine responses of grassland root‐associated bacterial communities to 15 years of experimental manipulations of plant species richness, functional group and factorial enrichment of atmospheric CO2 (eCO2) and soil nitrogen (+N). Across the experiment, plant species richness was the strongest predictor of rhizobacterial community composition, followed by +N, with no observed effect of eCO2. Monocultures of C3 and C4 grasses and legumes all exhibited dissimilar rhizobacterial communities within and among those groups. Functional responses were also dependent on plant functional group, where N2‐fixation genes, NO3−‐reducing genes and P‐solubilizing predicted gene abundances increased under resource‐enriched conditions for grasses, but generally declined for legumes. In diverse plots with 16 plant species, the interaction of eCO2+N altered rhizobacterial composition, while +N increased the predicted abundance of nitrogenase‐encoding genes, and eCO2+N increased the predicted abundance of bacterial P‐solubilizing genes. Synthesis: Our findings suggest that rhizobacterial community structure and function will be affected by important global environmental change factors such as eCO2, but these responses are primarily contingent on plant species richness and the selective influence of different plant functional groups.

Biological inoculants and chemical fertilizers application produce differential effects on rhizobacterial community structure associated to peanut (Arachis hypogaea L.) and maize (Zea mays L.) plants

Biological inoculants and chemical fertilizers application produce differential effects on rhizobacterial community structure associated to peanut (Arachis hypogaea L.) and maize (Zea mays L.) plants

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 < 0.01), while the TT was not affected in group B (ciprofloxacin). For group C (tobramycin), the TT significantly decreased (p < 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.

Rhizobacterial compositions and their relationships with soil properties and medicinal bioactive ingredients in Cinnamomum migao.

Rhizobacterial communities and their metabolites can affect plant growth, development, and stress resistance, as well as the biosynthesis and accumulation of bioactive compounds in medicinal plants. This relationship has been well-characterized in many medicinal herbs, although much less commonly in medicinal trees. Here, we analyzed the composition and structure of Cinnamomum migao rhizobacterial communities across nine growing regions in Yunnan, Guizhou and Guangxi, China, as well as differences in soil properties and fruit bioactive compounds. Results showed that the C. migao rhizobacterial communities exhibited high species richness, but location-specific differences in structure. Site-specific differences in soil properties and bioactive compounds were also observed. Furthermore, rhizobacterial community compositions were correlated with both soil properties and fruit bioactive compounds, metabolism-related functions were most common in C. migao rhizobacteria. Several bacterial genera, including Acidothermus, Acidibacter, Bryobacter, Candidatus_Solibacter, and Acidimicrobiales, potentially promote the biosynthesis and accumulation of 1,8-cineole, cypressene, limonene, and α-terpineol, Nitrospira and Alphaproteobacteria may play an inhibitory role. Finally, our results emphasized the critical role that soil pH and nitrogen levels play in driving rhizobacterial community structure, and specific functional bacteria can also counteract with soil properties, Acidibacter and Nitrospira can affect soil pH and nitrogen effectiveness. Overall, this study provides additional insight into the complex correlation of rhizosphere microorganisms with bioactive ingredients and soil properties of medicinal plants.

The structure and assembly of rhizobacterial communities are influenced by poplar genotype.

The interaction between plants and microbes dominates plant growth and fitness in specific environments. The study of the relationship between plant genotypes and rhizobacterial community structure would provide a deep insight into the recruitment strategies of plants toward soil bacteria. In this study, three genotypes of 18-year-old mature poplar (H1, H2, and H3) derived from four different parents were selected from a germplasm nursery of Populus deltoides. Rhizosphere soil carbon, nitrogen, and phosphorus properties as well as the 16S rDNA sequences of rhizobacterial communities were analyzed to determine the relationship between poplar genotypes and rhizobacterial communities assembly. The results showed there were significant differences in the diversity (Chao1, ACE index, and Shannon index) of rhizobacterial communities between H1 and H2, as well as between H2 and H3, but no difference between H1 and H3. Principal component analysis also revealed a similar structure of rhizobacterial communities between H1 and H3, whereas the rhizobacterial communities of H2 demonstrated significant differences from H1 and H3. Linear discriminant effect size analysis indicated that there were 11 and 14 different biomarkers in the H1 and H3 genotype, respectively, but 42 in the H2 genotype. Co-occurrence network analysis indicated that the rhizobacterial communities of H2 had a distinct network structure compared to those of the other two genotypes, whereas H1 and H3 had a similar pattern of co-occurrence network. Threshold indicator taxa analysis revealed that 63 genera responded significantly to NO3 --N content and 58 genera to NH4 +-N/NO3 --N ratio. Moreover, the stochastic assembly process was found to be decreased with increasing NO3 --N content and fluctuated with increasing NH4 +-N/NO3 --N ratio. All results indicated that the structure of poplar rhizobacterial communities were influenced by host genotypes, and available nitrogen might play a dominant role in the assembly of rhizobacterial communities. This study would promote the future selection and utilization of rhizobacteria in poplar breeding.

Identification of root bacteria associated with different stripe rust resistance in wheat cultivars

AbstractThe plant rhizosphere bacterial community influences plant stress resistance. Stripe rust causes severe damage to wheat (Triticum aestivum L.) production. To reveal the composition and function of root bacterial communities in wheat cultivars with different stripe rust resistance, rhizosphere soil samples were collected from four wheat cultivars. High‐throughput 16S rRNA gene sequencing was used to study the rhizobacterial community structure and function in stripe rust‐resistant (Guinong 19 and Huamai 1223) and ‐susceptible (Mingxian 169 and Taichung 29) wheat cultivars. A total of 6,392 operational taxonomic units (OTUs) were detected, belonging to 29 bacterial phyla. Analysis showed the susceptible and resistant wheat cultivars had different microbial communities. Principal coordinate analysis showed that all wheat rhizosphere bacterial samples could be divided into two groups, according to different disease resistance. Linear discriminant analysis effect size analysis showed that different bacterial taxa were enriched in the rhizosphere soil between resistant and susceptible wheat cultivars. Functional analysis showed that the bacterial community in stripe rust‐resistant wheat had greater amino acid transport and metabolic functions. Our research not only provides basic knowledge of the composition of wheat‐related microbiota but also reveals the microbial taxa that could be integrated into the management strategy of wheat stripe rust.

Changes in diversity and composition of rhizosphere bacterial community during natural restoration stages in antimony mine.

BackgroundOpen pit antimony (Sb) mining causes serious soil pollution, and phytoremediation is a low-cost approach to remediate heavy metal contaminated soil. Rhizosphere bacteria play an important role in ecological restoration in mining areas. There is a knowledge gap on how to find suitable rhizosphere microorganisms to improve the phytoremediation effect. Understanding the differences of rhizosphere bacterial diversity in different restoration stages is helpful to find suitable bacteria for ecological restoration.MethodsA method of the substitution of “space” for “time” was used to study the effect of natural restoration on rhizosphere bacterial community. According to the dominant vegetation types (herb, shrub, and tree) in the natural restoration area of Sb mining, the early restoration (ER), middle restoration (MR), and later restoration (LR) from the largest Sb mine (Xikuangshan mine) in the world were selected to evaluate the differences in the composition and diversity of rhizosphere bacteria during three natural restoration stages. Each restoration stage had five samples. To determine the relationship between restoration stages and bacterial diversity in the rhizosphere, high throughput sequencing of PCR amplified were used.ResultsAlpha diversity, as assessed by Chao indices, appeared lowest in ER but this trend was not seen with other diversity metrics, including the Simpson and Shannon. Beta diversity analysis suggested there were differences in rhizobacterial community structure associate with restoration stage. At the phylum level, natural restoration led to a significant increase in the relative abundance of Actinobacteria in the MR, and a significant decrease in the relative abundance of Patescibacteria in the LR. Additionally, Calditrichaeota, Deferribacteres and Epsilonbacteraeota were only found in ER. At the genus level, the relative abundance of RB41 and Haliangium were highest in LR plots, while that of Bacillus and Gaiella were highest in ER plots. Additionally, the Azorhizobium genus was only detected in the ER phase. Overall, our findings suggested that several rhizosphere microbial communities had significant differences among three natural restoration stages (ER, MR, and LR) and the rhizosphere bacterial communities mainly appeared in the early restoration stage can be preferred for remediation of pollution soil in Xikuangshan.

Plant beneficial rhizobacteria community structure changes through developmental stages of peanut and maize

Our objective in this study was to analyze the structure of the rhizobacterial community during different growth stages of peanut and maize plants. Microcosm assays were performed using pots containing unsterile soil from the peanut growing area of Argentina in which peanut and maize plants were grown during 120 and 100 days, respectively. Four to five samples of rhizospheric soil were obtained at the beginning of the assay, at an early growth stage of each plant and at the end of the assay. Two replicate DNA extractions from rhizospheric soil samples were realized per treatment on both microcosm assays to analyze rhizobacterial community structure by high-throughput sequencing of 16S rRNA gene.We observed changes in rhizobacteria community structure with crop developmental stages. Community structure changes occurred at several bacteria taxonomic levels, and major changes were observed in later stages. In particular, plant growth promoting bacteria genera were promoted in later stages. Our results indicate plant rhizospheric selection for growth enhancing rhizobacteria during stages of high nutrient demand. In conclusion, the structure of the rhizobacterial communities of peanut and maize are influenced by plant phenological stages, and beneficial bacteria are favoured in late phenological stages.

Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure

Microorganisms residing on root surfaces play a central role in plant development and performance and may promote growth in agricultural settings. Studies have started to uncover the environmental parameters and host interactions governing their assembly. However, soil microbial communities are extremely diverse and heterogeneous, showing strong variations over short spatial scales. Here, we quantify the relative effect of meter-scale variation in soil bacterial community composition among adjacent field microsites, to better understand how microbial communities vary by host plant genotype as well as soil microsite heterogeneity. We used bacterial 16S rDNA amplicon sequencing to compare rhizosphere communities from four Brassica rapa cultivars grown in three contiguous field plots (blocks) and evaluated the relative contribution of resident soil communities and host genotypes in determining rhizosphere community structure. We characterize concomitant meter-scale variation in bacterial community structure among soils and rhizospheres and show that this block-scale variability surpasses the influence of host genotype in shaping rhizosphere communities. We identified biomarker amplicon sequence variants (ASVs) associated with bulk soil and rhizosphere habitats, each block, and three of four cultivars. Numbers and percent abundances of block-specific biomarkers in rhizosphere communities far surpassed those from bulk soils. These results highlight the importance of fine-scale variation in the pool of colonizing microorganisms during rhizosphere assembly and demonstrate that microsite variation may constitute a confounding effect while testing biotic and abiotic factors governing rhizosphere community structure.

Shifts in the structure of rhizosphere bacterial communities of avocado after Fusarium dieback

The rhizosphere microbiome is critical for plant growth and protection against plant pathogens. However, rhizosphere microbial communities are likely to be restructured upon plant infection by fungal pathogens. Our objective was to determine the shifts in rhizosphere bacterial communities of avocado trees (Persea americana Mill.) after Fusarium dieback (FD), a disease triggered by the symbiotic fungi of invasive ambrosia beetles (Euwallacea kuroshio and Euwallacea sp. nr. fornicatus), using 16S rDNA gene amplicon sequencing and a culture-dependent approach. Rhizosphere soil samples were collected from five asymptomatic and five FD-symptomatic avocado trees in a Californian orchard. Sequence analysis showed that diversity metrics of the rhizosphere bacterial communities associated with asymptomatic avocado trees were larger than those of communities from FD-symptomatic trees. Moreover, FD produced significant shifts in rhizobacterial community structure, which were mainly caused by rare OTUs. Bacterial taxa such as Armatimonadetes, Sporocytophaga or Cellvibrio were exclusively associated with the rhizosphere of asymptomatic trees and may act as an insurance mechanism against fungal invasions. Conversely, genera such as Myxococcus or Lysobacter, which have been described as effective biocontrol agents against Fusarium oxysporum, Colletotrichum gloeosporioides or Rhizoctonia spp., among other phytopathogens, were only found in the rhizosphere of FD-symptomatic trees. The culturable bacterial communities in the rhizosphere of both FD-symptomatic and asymptomatic trees were dominated by isolates from the Bacillus and Pseudomonas genera, indicating that potential biocontrol agents against FD may be isolated from healthy and diseased avocado trees. Altogether, our results showed that FD elicited shifts in the avocado rhizosphere microbiome, which could potentially affect soil microbial processes, and provide a basis for the selection of biocontrol agents that could be used for FD prevention.

Rhizobacterial community structure in grafted tomato plants infected by Ralstonia solanacearum

Abstract. Navitasari L, Joko T, Murti RH, Arwiyanto T. 2020. Rhizobacterial community structure in grafted tomato plants infected by Ralstonia solanacearum. Biodiversitas 21: 4888-4895. Bacterial wilt disease caused by Ralstonia solanacearum is a devastating soil-borne vascular disease of tomato leading to a 100% yield loss. One of the alternatives to suppress the infestation of R. solanacearum infestation is the application of grafting techniques, which has been studied and successfully practiced by tomato growers. However, the infestation mode of R. solanacearum and the rhizobacterial community structure in grafted tomato plants are poorly reported. In this study, the rhizobacterial community structure in grafted tomato plants infected by R. solanacearum was investigated. The experiment was conducted on tomato germplasms with the implementation of tube grafting using resistant rootstocks (Amelia from Indonesia, H.7996 from Asian Vegetable Research Development Center/AVRDC) and susceptible scion (Servo from Indonesia). The rhizobacterial community structure was analyzed by metagenomic study under 16S rRNA genes sequencing with a distinct region (16SV3-V4) that was amplified using a specific primer (16SV4: 515F-806R) 5’-GTGCCAGCMGCCGCGGTAA and 5’GGACTACHVHHHTWTCTAAT. The results indicated that the grafted tomato plants and resistant rootstocks that were infected by R. solanacearum showed significantly lower intensity of bacterial wilt disease compared to the susceptible scion. The rhizobacterial community structure in the grafted tomato plants infected by R. solanacearum was indicated by predominant phyla of Proteobacteria, Firmicutes, and Actinobacteria with dominant genera of Pseudomonas and Bacillus. Besides, significant difference was also indicated by species of Geitlerinema sp. in the grafted tomatoes infected by R. solanacearum.

Rhizobacterial communities and fine root traits together reveal variations in growth performance of Quercus acutissima in different provenances

It is important to understand the variations in intraspecific growth performance for forest management. We evaluated the relationships among fine root traits, rhizobacterial community structure, and growth variables in different oak (Quercus acutissima) provenances. Four oak provenances with different growth performances were studied. In each provenance, growth variables, fine root traits, rhizosphere soil chemical properties, and rhizobacterial abundance were measured. The structure of rhizobacterial communities was assessed by 16S rRNA gene sequencing. The co-occurrence patterns of bacterial taxa were analyzed by network analysis. The relative contribution of fine root traits and rhizobacterial communities to variations in growth performance was evaluated by hierarchical partitioning analysis. Growth performance of the four oak provenances was positively correlated with the specific root length. The β-diversity of rhizobacterial communities, but not α-diversity, was positively correlated with the growth variables. The relative abundance of Actinobacteria (e.g., Actinospica and Conexibacter genera) increased with aboveground biomass. The co-occurrence network analysis showed more clusters with highly interconnected taxa in the high-yielding provenances. Variation in growth performance of oak in different provenances was significantly affected by the rhizobacterial community structure and fine root traits, with the former being a more prominent factor.

High Aluminum Drives Different Rhizobacterial Communities Between Aluminum-Tolerant and Aluminum-Sensitive Wild Soybean.

Aluminum (Al)-resistant plant cultivars can recruit beneficial microbes to alleviate the stresses. However, the mechanism of how rhizobacterial communities strengthen Al tolerance of wild soybean has not been addressed. The aim of this study was to investigate the bacterial community structure in the rhizosphere of Al-tolerant (BW69) and Al-sensitive (W270) wild soybean germplasm subjected to three Al concentrations. We analyzed the rhizobacterial communities of the two genotypes by high-throughput sequencing of 16S rRNA genes. The results showed that high Al stress recruited different rhizobacterial communities between two genotypes. In total, 49 OTUs, such as OTU15 (Gammaproteobacteria_KF-JG30-C25_norank), OTU23 (Mizugakiibacter), and OTU93 (Alkanibacter), were enriched in the rhizosphere of BW69 at the low and high Al concentrations. Moreover, bacterial community in the rhizosphere of BW69 had a more complex co-occurrence network than did W270 at the high Al concentration. Overall, our findings highlighted that high Al concentration magnified the difference in rhizobacterial community structure between two genotypes. However, the lower modularity of the co-occurrence network in rhizosphere of BW69 than W270 under Al stress may cause the rhizobacterial community to be less resistant and more influenced by disturbance. This study emphasizes the possibility of using rhizobacteria as an improved crop breeding or gene to produce crops that are more resistant to the toxicity of heavy metal.

Heavy metal-immobilizing bacteria combined with calcium polypeptides reduced the uptake of Cd in wheat and shifted the rhizosphere bacterial communities

In situ stabilization techniques for the “remediation” of heavy metal-contaminated soil are a novel and inexpensive technology. However, the mechanisms underlying the interaction of exogenous passivators with the bacterial community in wheat rhizosphere soil remain unclear. Soil static culture and pot experiments were conducted to evaluate the effects and mechanisms of the heavy metal-immobilizing bacterium Enterobacter bugandensis TJ6 and calcium polypeptides (CPPs) and their association with Cd uptake in wheat, soil quality and the rhizobacterial community structure. The results showed that compared with the control treatment (CK), the TJ6, CPP, and TJ6+CPP treatments significantly decreased the diethylenetriaminepentaacetic acid (DTPA)-extractable Cd (25.2%–60.1%) content and increased the pH, organic matter content and urease activity in the wheat rhizosphere soil, which resulted in decreases in the Cd (21.5%–77.8%) content in wheat tissues (grain, straw, and roots). In particular, the TJ6+CPP treatment was more effective at decreasing Cd accumulation in grains. Furthermore, the TJ6+CPP treatment improved the diversity of the soil bacterial community in the wheat rhizosphere, and the relative abundances of Proteobacteria, Firmicutes, Arthrobacter, Microvirga, Ensifer, Brevundimonas, Devosia and Pedobacter were enriched. These results suggest that the TJ6+CPP treatment decreased the uptake of Cd in wheat by i) providing essential elements (N and C sources), ii) increasing the pH and reducing the bioavailable Cd content in wheat rhizosphere soil, iii) allowing colonization to promote plant growth and Cd-resistant bacteria, and iv) increasing the abundance of genes associated with ABC transporters, carbon metabolism and oxidative phosphorylation in the rhizosphere bacterial community. Our results showed that the heavy metal-immobilizing bacterium TJ6 combined with CPPs decreased the Cd content and increased the bacterial community diversity of wheat rhizosphere soil. Our results also highlight the potential of using heavy metal-immobilizing bacteria and CPPs to ensure the safe production of crops growing on heavy metal-polluted soils.

Pakchoi Antioxidant Improvement and Differential Rhizobacterial Community Composition under Organic Fertilization

A high level of antioxidants in organic-produced vegetables has been attributed to soil conditions; however, little is known about the relationships between antioxidants and rhizobacteria under different fertilization treatments. A pot trial for pakchoi (Brassica campestris ssp. chinensis L.) was conducted under greenhouse conditions with: (1) control; (2) chemical fertilizer; and (3) organic fertilizer. The responses of the plant, soil properties, and rhizobacterial community were measured after 45 days of cultivation. Fertilization increased soil nutrient levels and pakchoi productivity and the reshaped rhizobacterial community structure, while no differences in rhizobacterial abundance and total diversity were observed. Generally, most plant antioxidants were negatively correlated with inorganic nitrogen (N) and positively correlated to organic N in soil. The genera of Arthrospira and Acutodesmus contained differential rhizobacteria under chemical fertilizer treatment, which are known as copiotrophs. In addition, the addition of a chemical fertilizer may stimulate organic substance turnover by the enrichment of organic compound degraders (e.g., Microbacterium and Chitinophaga) and the promotion of predicted functional pathways involved in energy metabolism. Several beneficial rhizobacteria were associated with organic fertilizer amended rhizosphere including the genera Bacillus, Mycobacterium, Actinomycetospora, and Frankia. Furthermore, Bacillus spp. were positively correlated with plant biomass and phenolic acid. Moreover, predictive functional profiles of the rhizobacterial community involved in amino acid metabolism and lipid metabolism were significantly increased under organic fertilization, which were positively correlated with plant antioxidant activity. Overall, our study suggests that the short-term application of chemical and organic fertilizers reshapes the rhizobacterial community structure, and such changes might contribute to the plant’s performance.

Rhizobacterial community structure in response to nitrogen addition varied between two Mollisols differing in soil organic carbon

Excessive nitrogen (N) fertilizer input to agroecosystem fundamentally alters soil microbial properties and subsequent their ecofunctions such as carbon (C) sequestration and nutrient cycling in soil. However, between soils, the rhizobacterial community diversity and structure in response to N addition is not well understood, which is important to make proper N fertilization strategies to alleviate the negative impact of N addition on soil organic C and soil quality and maintain plant health in soils. Thus, a rhizo-box experiment was conducted with soybean grown in two soils, i.e. soil organic C (SOC)-poor and SOC-rich soil, supplied with three N rates in a range from 0 to 100 mg N kg−1. The rhizospheric soil was collected 50 days after sowing and MiSeq sequencing was deployed to analyze the rhizobacterial community structure. The results showed that increasing N addition significantly decreased the number of phylotype of rhizobacteria by 12.3%, and decreased Shannon index from 5.98 to 5.36 irrespective of soils. Compared to the SOC-rich soil, the increases in abundances of Aquincola affiliated to Proteobacteria, and Streptomyces affiliated to Actinobacteria were greater in the SOC-poor soil in response to N addition. An opposite trend was observed for Ramlibacter belong to Proteobacteria. These results suggest that N addition reduced the rhizobacterial diversity and its influence on rhizobacterial community structure was soil-specific.

Rhizobacterial community structure differences among sorghum cultivars in different growth stages and soils

Plant genotype selects the rhizosphere microbiome. The success of plant-microbe interactions is dependent on factors that directly or indirectly influence the plant rhizosphere microbial composition. We investigated the rhizosphere bacterial community composition of seven different sorghum cultivars in two different soil types (abandoned (CF) and agricultural (VD)). The rhizosphere bacterial community was evaluated at four different plant growth stages: emergence of the second (day 10) and third leaves (day 20), the transition between the vegetative and reproductive stages (day 35), and the emergence of the last visible leaf (day 50). At early stages (days 10 and 20), the sorghum rhizosphere bacterial community composition was mainly driven by soil type, whereas at late stages (days 35 and 50), the bacterial community composition was also affected by the sorghum genotype. Although this effect of sorghum genotype was small, different sorghum cultivars assembled significantly different bacterial community compositions. In CF soil, the striga-resistant cultivar had significantly higher relative abundances of Acidobacteria GP1, Burkholderia, Cupriavidus (Burkholderiaceae), Acidovorax and Albidiferax (Comamonadaceae) than the other six cultivars. This study is the first to simultaneously investigate the contributions of plant genotype, plant growth stage and soil type in shaping sorghum rhizosphere bacterial community composition.

Bacterial community structure and detection of putative plant growth-promoting rhizobacteria associated with plants grown in Chilean agro-ecosystems and undisturbed ecosystems

Soil microorganisms with phytase- and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activities are widely studied as plant growth-promoting rhizobacteria (PGPR). Here, we explored the bacterial community structure and occurrence of putative PGPR in plants grown in agro-ecosystems and undisturbed ecosystems from northern, central, and southern Chile. Total rhizobacterial community structure was evaluated by denaturing gradient gel electrophoresis, and dominant bands present in diverse ecosystems were sequenced. Significant differences in total bacterial communities were shown with some bacterial orders (Enterobacteriales, Actinomycetales, and Rhizobiales) being highly similar to both ecosystems. Twenty-nine putative PGPR, showing phytate- and ACC-degrading activities and production of auxin, were selected from across the sites. Based on 16S rRNA gene sequencing, the putative PGPR were characterized as Enterobacteriales (Enterobacter, Serratia, Pantoea, Rahnella, Leclercia), Pseudomonas, and Bacillus, consistent with previously reported PGPR and endophytic bacteria. Beta-propeller phytase genes with similarity to Bacillus were also identified. PGPR from agro-ecosystems appeared to show higher auxin production compared to those from undisturbed ecosystems. This study demonstrates that putative PGPR are widely distributed across Chilean soils. Further understanding of their contribution to the growth and adaptation of plant hosts to local soil conditions may provide opportunity for development of new PGPR in Chilean agriculture.

Pyrosequencing reveals how pulses influence rhizobacterial communities with feedback on wheat growth in the semiarid Prairie

Background and Aims Evidence shows that plants modify their microbial environment leading to the “crop rotation effect”, but little is known about the changes in rhizobacterial community structure and functionality associated with beneficial rotation effects. Methods Polymerase chain reaction (PCR) and 454 GS FLX amplicon pyrosequencing were used to describe the composition of the rhizobacterial community evolving under the influence of pea, a growth promoting rotation crop, and the influence of three genotypes of chickpea, a plant known as an inferior rotation crop. The growth promoting properties of these rhizobacterial communities were tested on wheat in greenhouse assays. Results The rhizobacterial communities selected by pea and the chickpea CDC Luna in 2008, a wet year, promoted durum wheat growth, but those selected by CDC Vanguard or CDC Frontier had no growthpromoting effect. In 2009, a dry year, the influence of plants was mitigated, indicated that moisture availability is a major driver of soil bacterial community dynamics. Conclusion The effect of pulse crops on soil biological quality varies with the crop species and genotypes, and certain chickpea genotypes may induce positive rotation effects on wheat. The strength of a rotation effect on soil biological quality is modulated by the abundance of precipitation.