Diversity Of Rhizosphere Bacterial Communities Research Articles

Effects of Nitrogen Application Rate on Rhizosphere Microbial Diversity in Oilseed Rape (Brassica napus L.)

Nitrogen is one of the essential nutrients for rape growth and development, of which the demand is large. In order to reveal the response of rhizosphere microbial diversity on oilseed rape to the nitrogen fertilizer, four nitrogen application rates of N (170 kgN/hm2), N50% (85 kgN/hm2), N70% (119 kgN/hm2) and N150% (255 kgN/hm2) were set. The diversity and community structure of soil bacteria and fungi in seedling, flowering and mature stages of oilseed rape were analyzed based on the high-throughput sequencing technology. The results of rhizosphere soil microbial analysis showed that the dominant bacteria phyla were Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes and Cyanobacteria. The dominant fungi phyla were Ascomycota, Olpidiomycota and Basidiomycota. NMDS analysis showed that the community structure of soil bacteria and fungi changed significantly under nitrogen treatment. Cluster analysis showed that the bacteria at seedling and flowering stage had little effect under the condition of less nitrogen application, while the fungi had little effect on the rhizosphere soil microbial flora at flowering stage. At seedling stage, the diversity and richness of bacterial community in the rhizosphere of oilseed rape were lower under low nitrogen application (85 kgN/hm2). Bacteria and fungi in the rhizosphere soil of flowering oilseed rape maintained a higher community diversity under the condition of high nitrogen (255 kgN/hm2). The diversity of rhizosphere bacterial community was higher under conventional N application than under other N application.

Combined foliar and soil selenium fertilizer improves selenium transport and the diversity of rhizosphere bacterial community in oats.

Agronomic selenium (Se) biofortification of grain crops is considered the best method for increasing human Se intake, which may help people alleviate Se-deficiency. To investigate the efficiency of agronomic Se biofortification of oat, four Se fertilizer application treatments were tested: topsoil (T), foliar (S), the combination of T and S (TS), and control without Se application (CK). Compared with CK, TS significantly increased the 1000-grain weight, grain yield, Se contents in all parts of oats, contents of soil available N, K, and organic matter by 18%, 8.70%, 19.7-60.2%, 6.00%, 8.02%, and 17.95%, respectively. Leaves, roots, and ears had the highest conversion rate of exogenous Se in S (644.63%), T (416.00%), and TS (273.20%), respectively. TS also increased the activities of soil urease, alkaline phosphatase, and sucrose and the diversity of soil bacterial communities. TS and T increased the relative abundance of bacteria involved in the decomposition of organic matter, such as Actinobacteria, Gemmatimonadetes, Chloroflexi, and Bacteroidetes positively correlated with soil nutrients and enzyme activities, and reduced Proteobacteria and Firmicutes negatively correlated with them, Granulicella, Bacillus, Raoultella, Lactococcus, Klebsiella, and Pseudomonas. Furthermore, TS significantly increased the relative abundance of Planctomycetes, Chlorobi, Nitrospinae, Nitrospirae, Aciditeromonas, Gemmatimonas, Geobacter, and Thiobacter. T significantly increased the abundance of Lysobacter, Holophaga, Candidatus-Koribacter, Povalibacter, and Pyrinomonas. S did not significantly change the bacterial communities. Thus, a combined foliar and soil Se fertilizer proved conducive for achieving higher yield, grain Se content, and improving Se transport, the diversity of rhizosphere bacterial community, and bacterial functions in oats.

Bacterial composition, function and the enrichment of plant growth promoting rhizobacteria (PGPR) in differential rhizosphere compartments of Al-tolerant soybean in acidic soil.

Low pH with aluminum (Al) toxicity are the main limiting factors affecting crop production in acidic soil. Selection of legume crops with acid tolerance and nitrogen-fixation ability should be one of the effective measures to improve soil quality and promote agricultural production. The role of the rhizosphere microorganisms in this process has raised concerns among the research community. In this study, BX10 (Al-tolerant soybean) and BD2 (Al-sensitive soybean) were selected as plant materials. Acidic soil was used as growth medium. The soil layers from the outside to the inside of the root are bulk soil (BS), rhizosphere soil at two sides (SRH), rhizosphere soil after brushing (BRH) and rhizosphere soil after washing (WRH), respectively. High-throughput sequencing of 16S rDNA amplicons of the V4 region using the Illumina MiSeq platform was performed to compare the differences of structure, function and molecular genetic diversity of rhizosphere bacterial community of different genotypes of soybean. The results showed that there was no significant difference in alpha diversity and beta diversity in rhizosphere bacterial community among the treatments. PCA and PCoA analysis showed that BRH and WRH had similar species composition, while BS and SRH also had similar species composition, which indicated that plant mainly affected the rhizosphere bacterial community on sampling compartments BRH and WRH. The composition and abundance of rhizosphere bacterial community among the treatments were then compared at different taxonomic levels. The ternary diagram of phylum level showed that Cyanobacteria were enriched in WRH. Statistical analysis showed that the roots of Al-tolerant soybean BX10 had an enrichment effect on plant growth promoting rhizobacteria (PGPR), which included Cyanobacteria, Bacteroides, Proteobacteria and some genera and species related to the function of nitrogen fixation and aluminum tolerance. The rhizosphere bacterial community from different sampling compartments of the same genotype soybean also were selectively enriched in different PGPR. In addition, the functional prediction analysis showed that there was no significant difference in the classification and abundance of COG (clusters of orthologous groups of proteins) function among different treatments. Several COGs might be directly related to nitrogen fixation, including COG0347, COG1348, COG1433, COG2710, COG3870, COG4656, COG5420, COG5456 and COG5554. Al-sensitive soybean BD2 was more likely to be enriched in these COGs than BX10 in BRH and WRH, and the possible reason remains to be further investigated in the future.

Crop development has more influence on shaping rhizobacteria of wheat than tillage practice and crop rotation pattern in an arid agroecosystem

Root-associated bacteria are studied under a single agricultural measure, but the responses of rhizosphere bacterial communities toward agricultural management, in an arid agroecosystem, are unclear. Here, we evaluated the effects of tillage practice, crop rotation pattern, and crop development on rhizobacteria in a field experiment in the dryland region of northern China. Three tillage [chisel plow tillage (conservation), zero tillage (conservation), and plow tillage (conventional)] practices and two crop rotation (maize–wheat rotation and soybean–wheat rotation) patterns were been combined to assess changes in rhizosphere bacterial communities during wheat development. Our results showed that conservation tillage practices had considerable effects on soil physicochemical properties compared with conventional tillage, thus changing the rhizosphere microenvironment. Spearman's correlation analysis also indicated that soil physicochemical properties were closely related to the relationships among the rhizosphere bacterial communities and taxa. Furthermore, the composition and α-diversity of the rhizosphere bacterial communities were substantially affected by the crop growth stage and tillage practices; however, the legacy effect of the previous crop had different effects on the rhizosphere bacterial communities owing to the short period of implementing crop rotation. The phylogenetic diversity and taxonomic composition of rhizosphere bacterial communities were mainly explained by the crop growth stage and tillage practice, respectively. Additionally, conservation tillage practices and soybean–wheat rotation pattern both delayed rhizobacteria successions. Co-occurrence networks also showed that the differential modules among the rhizosphere bacterial communities decreased with wheat development, whereas the soybean–wheat rotation pattern increased their degree of co-occurrence. The differences in taxonomic compositions and phylogenetic diversities of the rhizosphere bacterial communities may affect their potential functions and alter crop growth and development.

Effects of mancozeb on citrus rhizosphere bacterial community

Multiple and consecutive application of fungicide might damage the rhizosphere bacterial community of citrus. In order to evaluated effect of mancozeb on the chemical properties of citrus-cultivated soil and the richness and diversity of rhizosphere bacterial community. The abundance response of rhizosphere bacterial groups without application or with application of 1.333 g mg−1 mancozeb for 2, 4, 6 and 8 times were investigated, and further studied the relationship between the rhizosphere bacterial community and chemical properties of citrus-cultivated soil. We found the rhizosphere bacterial composition and diversity were distinct between soil planted with citrus and without citrus, in addition, the abundance of rhizosphere-associated bacterial species in the soil planted with citrus increased significantly. Meanwhile, the chemical properties and the richness and diversity of rhizosphere bacterial community of the soil planted with citrus did not significantly change among different application frequence of mancozeb. Moreover, with the increased applying times of mancozeb, the relative abundance of Candidatus, Saccharibacteria, Parcubacteria, and Proteobacteria increased but the abundance of Nitrospirae decreased. In our one-year trial, there were less adverse effects of mancozeb on the citrus-cultivated rhizosphere by the repeated application of mancozeb. Therefore, mancozeb, as a fungicide, could be used multiple times to control citrus disease.

Bacterial community diversity and functional roles in the rhizosphere of Rinorea cf. bengalensis and Phyllanthus rufuschaneyi under a nickel concentration gradient

The tropical nickel (Ni) hyperaccumulator plants, Rinorea cf. bengalensis and Phyllanthus rufuschaneyi, are locally common on ultramafic soils in the Malaysian state of Sabah on the island of Borneo. The aim of this study was to determine whether the structure and diversity of R. cf. bengalensis rhizosphere microbial communities were dependant on the Ni concentrations in the different rhizosphere soils studied. Rinorea cf. bengalensis and Phyllanthus rufuschaneyi were subjected to a randomized block design experiment in which four Ni dose levels were applied (0, 60, 240, 600 mg Ni kg−1) × 5 replicates per level for 12 months cultivation. At the end of the trial foliar elemental concentrations were measured. In addition, rhizosphere soils were collected for elemental and microbial analyses. The microbial analysis consisted of measuring microbial enzymatic activities and a diversity analysis based on Illumina sequencing. The Illumina sequencing analysis yielded 2,649,138 sequences grouped under 2430 different Operational Taxonomic Units (OTUs) belonging to 25 phyla. No impact of the Ni amendments was shown for the four microbial enzymatic activities tested, even at the highest Ni dose level (600 mg Ni kg−1). Higher microbial enzymatic activities were found in the rhizosphere of R. cf. bengalensis relative to P. rufuschaneyi. Nickel concentrations appeared to have a high impact on the P. rufuschaneyi rhizosphere soils, whereas no effect was found for the rhizosphere bacterial community diversity of R. cf. bengalensis. There may be a significant role of rhizodeposits associated with R. cf. bengalensis that protect and preserve the microbial communities in the rhizosphere, regardless of the prevailing nickel concentrations.

Variation of rhizosphere bacterial community diversity in the desert ephemeral plant Ferula sinkiangensis across environmental gradients

Ferula sinkiangensis (F. sinkiangensis) is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in plant growth and adaptability. However, F. sinkiangensis rhizosphere bacterial communities and the soil physicochemical factors that drive the bacterial community distribution are currently unclear. On this study, based on high-throughput sequencing, we explored the diversity, structure and composition of F. sinkiangensis rhizosphere bacterial communities at different slope positions and soil depths and their correlation with soil physicochemical properties. Our results revealed the heterogeneity and changed trend of F. sinkiangensis rhizosphere bacterial community diversity and abundance on slope position and soil depth and found Actinobacteria (25.5%), Acidobacteria (16.9%), Proteobacteria (16.6%), Gemmatimonadetes (11.5%) and Bacteroidetes (5.8%) were the dominant bacterial phyla in F. sinkiangensis rhizosphere soil. Among all soil physicochemical variables shown in this study, there was a strong positive correlation between phosphorus (AP) and the diversity of rhizosphere bacterial community in F. sinkiangensis. In addition, Soil physicochemical factors jointly explained 24.28% of variation in F. sinkiangensis rhizosphere bacterial community structure. Among them, pH largely explained the variation of F. sinkiangensis rhizosphere bacterial community structure (5.58%), followed by total salt (TS, 5.21%) and phosphorus (TP, 4.90%).

Exogenous application of signaling molecules to enhance the resistance of legume-rhizobium symbiosis in Pb/Cd-contaminated soils

Being signaling molecules, nitric oxide (NO) and hydrogen sulfide (H2S) can mediate a wide range of physiological processes caused by plant metal toxicity. Moreover, legume-rhizobium symbiosis has gained increasing attention in mitigating heavy metal stress. However, systematic regulatory mechanisms used for the exogenous application of signaling molecules to alter the resistance of legume-rhizobium symbiosis under metal stress are currently unknown. In this study, we examined the exogenous effects of sodium nitroprusside (SNP) as an NO donor additive and sodium hydrosulfide (NaHS) as a H2S donor additive on the phytotoxicity and soil quality of alfalfa (Medicago sativa)-rhizobium symbiosis in lead/cadmium (Pb/Cd)-contaminated soils. Results showed that rhizobia inoculation markedly promoted alfalfa growth by increasing chlorophyll content, fresh weight, and plant height and biomass. Compared to the inoculated rhizobia treatment alone, the addition of NO and H2S significantly reduced the bioaccumulation of Pb and Cd in alfalfa-rhizobium symbiosis, respectively, thus avoiding the phytotoxicity caused by the excessive presence of metals. The addition of signaling molecules also alleviated metal-induced phytotoxicity by increasing antioxidant enzyme activity and inhibiting the level of lipid peroxidation and reactive oxygen species (ROS) in legume-rhizobium symbiosis. Also, signaling molecules improved soil nutrient cycling, increased soil enzyme activities, and promoted rhizosphere bacterial community diversity. Both partial least squares path modeling (PLS-PM) and variation partitioning analysis (VPA) identified that using signaling molecules can improve plant growth by regulating major controlling variables (i.e., soil enzymes, soil nutrients, and microbial diversity/plant oxidative damage) in legume-rhizobium symbiosis. This study offers integrated insight that confirms that the exogenous application of signaling molecules can enhance the resistance of legume-rhizobium symbiosis under metal toxicity by regulating the biochemical response of the plant-soil system, thereby minimizing potential health risks.

High abundance of Ralstonia solanacearum changed tomato rhizosphere microbiome and metabolome

BackgroundRhizosphere microbiome is dynamic and influenced by environment factors surrounded including pathogen invasion. We studied the effects of Ralstonia solanacearum pathogen abundance on rhizosphere microbiome and metabolome by using high throughput sequencing and GC-MS technology.ResultsThere is significant difference between two rhizosphere bacterial communities of higher or lower pathogen abundance, and this difference of microbiomes was significant even ignoring the existence of pathogen. Higher pathogen abundance decreased the alpha diversity of rhizosphere bacterial community as well as connections in co-occurrence networks. Several bacterial groups such as Bacillus and Chitinophaga were negatively related to the pathogen abundance. The GC-MS analysis revealed significantly different metabolomes in two groups of rhizosphere soils, i.e., the rhizosphere soil of lower harbored more sugars such as fructose, sucrose and melibiose than that in high pathogen abundance.ConclusionsThe dissimilar metabolomes in two rhizosphere soils likely explained the difference of bacterial communities with Mantel test. Bacillus and Chitinophaga as well as sugar compounds negatively correlated with high abundance of pathogen indicated their potential biocontrol ability.

Artificial soil aeration increases soil bacterial diversity and tomato root performance under greenhouse conditions

AbstractSoil aeration can enhance soil enzyme activity and plant growth. These effects may be caused by variations in soil microbial diversity and plant root development. However, little is known about the responses of soil microbial composition, structure, and diversity and plant root development to artificial soil aeration. The aims of this study were to examine the composition, structure, and diversity of rhizosphere bacterial communities and tomato root morphology under four aeration volumes in combination with drip‐tubing placed at two different soil depths. The aeration volumes (V) were 0, 0.5, 1, and 1.5 times (CK, V1, V2, and V3, respectively) the standard aeration volume. The drip irrigation tube burial depths were 15 (D15) and 40 cm (D40). The results demonstrated that soil aeration had a significant influence on root performance (root morphology and activity) and soil bacterial diversity in the tomato root zone. In comparison with the CK treatment, V3 soil aeration increased root length, surface area, tip number, and activity by 7.9%, 6.3%, 14.5%, and 7.0%, respectively. The abundance‐based coverage estimator, Chao index, and Shannon diversity increased by 5.3%, 4.7%, and 3.5%, respectively. The abundance of Acidobacteria increased and that of Gammaproteobacteria decreased in response to the soil aeration treatments; conversely, Geobacteraceae and Halanaerobiaceae were eliminated. Moreover, different subsurface tubing placement depths changed the rhizosphere bacterial community. The results indicate that soil aeration ameliorates hypoxic conditions and provides benefits to soil bacterial communities and root morphology.

Effects of Different Fertilizers on Rhizosphere Bacterial Communities of Winter Wheat in the North China Plain

The application of bioorganic fertilizer affects rhizosphere microbes and further improves soil fertility in farmlands. However, the effects of different fertilizers on rhizosphere bacterial community diversity and structure of winter wheat remains unclear. In this study, we explored the effects of different fertilization treatments (no fertilizer added, CK; nitrogen fertilizer, NF; bioorganic fertilizer, BOF) on the rhizosphere bacterial community of winter wheat in the North China Plain. Rhizosphere soil treated with BOF had a higher Shannon index than that of CK and NF. The relative abundance of the Proteobacteria treated with BOF was significantly higher than that of NF, while the Acidobacteria and Planctomycetes were significantly lower. The redundancy analysis (RDA) and Mantel test showed that soil bacterial communities were significantly correlated with pH, nitrate, available phosphorus (AP), and available potassium (AK). Our findings indicated that BOF increased bacterial diversity and the relative abundance of copiotrophic bacteria in rhizosphere soil, while NF reduced bacterial diversity and increased the relative abundance of oligotrophic bacteria. The increase in copiotrophic bacteria in the rhizosphere of winter wheat could indicate an increase in soil nutrient availability, which might have positive implications for soil fertility and crop production.

Do metal contamination and plant species affect microbial abundance and bacterial diversity in the rhizosphere of metallophytes growing in mining areas in a semiarid climate?

Mining areas are low-quality habitats for macro- and microorganisms’ development, mainly due to the degradation of the soil quality by metal pollution. The present work aimed to analyze the influence of metal contamination and of plant species on the rhizospheric microbial communities of four indigenous metallophytes (Ononis natrix, Haloxylon scoparium, Peganum harmala, and Aizoon canariense) growing along a metal contamination gradient in Kettara mine near Marrakech, Morocco. In pyrrhotite mining areas (Kettara mine, Morocco), rhizosphere soil samples were collected from four predominant indigenous metallophytes (O. natrix, H. scoparium, P. harmala, and A. canariense) growing along a metal contamination gradient (ZC, control zone; Z1, high metal contamination; Z2, moderate metal contamination; Z3, low metal contamination). Microbial communities were analyzed by using microbial counts and by denaturing gradient gel electrophoresis (DGGE). The physicochemical properties (pH, conductivity, total organic carbon, nitrogen, P Olsen, and metal concentrations) of soils were also determined. The physicochemical analysis revealed that rhizospheric soils from Z1, Z2, and Z3 were relatively poor in nutrients as they presented low levels of total organic carbon and nitrogen, organic matter and available P. Moreover, these rhizospheric soils showed high concentrations of metals, especially Cu and Pb, which significantly reduced the abundance of the different groups of soil microorganisms (bacteria, fungi, and actinomycetes) and the activity of soil dehydrogenase. The analysis of bacterial communities by DGGE revealed that bacterial diversity was not negatively affected by metal contamination being higher in the most contaminated area (Z1). Overall, the microbial abundance, the composition, and the diversity of rhizospheric bacterial communities were more influenced by the environmental factors in sampling zones than by plant cover. Microbial counts and enzymatic activity were both systematically affected throughout the metal gradient, evidencing as good indicators of the harmful effects of anthropogenic disturbances in soils. H. scorparium and P. harmala proved to be good candidates for the development of phytotechnological programs aiming the revegetation of mining degraded areas.

Rhizosphere bacterial community in watermelon-wheat intercropping was more stable than in watermelon monoculture system under Fusarium oxysporum f. sp. niveum invasion

Although intercropping and pathogen invasion can affect the plant rhizosphere bacterial community, how intercropping affects the rhizosphere bacterial community in response to pathogen invasion is poorly understood. The root system of watermelon was separated into two halves and placed in separate pots for Fusarium oxysporum f. sp. niveum(FON) inoculation and wheat intercropping. Responses of the watermelon rhizosphere bacterial community to wheat intercropping and FON inoculation were analyzed by high-throughput sequencing. Wheat intercropping did not affect the diversity but altered the composition of rhizosphere bacterial community on both sides of watermelon roots. In watermelon monoculture, FON inoculation increased the diversity of the rhizosphere bacterial community and stimulated certain potentially plant beneficial bacteria. The effects of FON inoculation on the watermelon rhizosphere bacterial community diversity and composition in watermelon-wheat intercropping were weaker than those in watermelon monoculture. No contact between wheat and FON was required to decrease the disease index of Fusarium wilt. The effects of wheat intercropping and FON inoculation on the watermelon rhizosphere bacterial community were mostly plant-mediated, and under FON invasion the rhizosphere bacterial community was more stable in watermelon-wheat intercropping than in watermelon monoculture.

High aluminum stress drives different rhizosphere soil enzyme activities and bacterial community structure between aluminum-tolerant and aluminum-sensitive soybean genotypes

Aluminum is a major deleterious factor for soybean productivity in acidic soils. Soil enzyme activities and bacteria play important roles in improving the stress tolerance of soybean. We assessed soil enzyme activities and bacterial structure and functions in Al-tolerant (Al-T) and Al-sensitive (Al-S) soybean genotypes subjected to different Al stress. We used a pot experiment system and determined plant biomass, urease, acid phosphatase, catalase, sucrase, and amylase activities, soil chemical properties, and the rhizosphere bacterial community diversity and structure of Al-T and Al-S soybean genotypes under different Al concentrations (0, 0.2, and 0.4 Al3+ g kg−1). Significant differences in soil enzyme activities and bacterial community structure were only observed between Al-T and Al-S soybeans under high Al stress. We identified 23 operational taxonomic units (OTUs), including OTU46 (Tumebacillus), OTU253 (Granulicella), and OTU180 (Burkholderia), which may improve soybean tolerance to Al toxicity. The results of canonical correspondence analysis (CCA) indicated that NH4+-N was an important factor that drove bacterial community structure differences between the two genotypes. Al stress simplified the network structure in the Al-T soybean, which may cause the soil bacterial community to be easily influenced by biotic and abiotic factors. High Al stress drove different soil enzyme activities and bacterial community structures between Al-T and Al-S soybean genotypes, and NH4+-N was the most important factor that drove the bacterial community structure between the two genotypes. Al-T soybeans recruited Al-tolerant microorganisms, such as Tumebacillus, Granulicella, and Burkholderia, to improve the resistance to Al stress. Nevertheless, Al stress simplified the network structure in the Al-T soybeans, which may allow for the soil bacterial community to be easily influenced by other biotic and abiotic factors.

Effects of an EPSPS-transgenic soybean line ZUTS31 on root-associated bacterial communities during field growth.

The increased worldwide commercial cultivation of transgenic crops during the past 20 years is accompanied with potential effects on the soil microbial communities, because many rhizosphere and endosphere bacteria play important roles in promoting plant health and growth. Previous studies reported that transgenic plants exert differential effects on soil microbial communities, especially rhizobacteria. Thus, this study compared the soybean root-associated bacterial communities between a 5-enolpyruvylshikimate-3-phosphate synthase -transgenic soybean line (ZUTS31 or simply Z31) and its recipient cultivar (Huachun3 or simply HC3) at the vegetative, flowering, and seed-filling stages. High-throughput sequencing of 16S rRNA gene (16S rDNA) V4 hypervariable region amplicons via Illumina MiSeq and real-time quantitative PCR (qPCR) were performed. Our results revealed no significant differences in the overall alpha diversity of root-associated bacterial communities at the three developmental stages and in the beta diversity of root-associated bacterial communities at the flowering stage between Z31 and HC3 under field growth. However, significant differences in the beta diversity of rhizosphere bacterial communities were found at the vegetative and seed-filling stages between the two groups. Furthermore, the results of next generation sequencing and qPCR showed that the relative abundances of root-associated main nitrogen-fixing bacterial genera, especially Bradyrhizobium in the roots, evidently changed from the flowering stage to the seed-filling stage. In conclusion, Z31 exerts transitory effects on the taxonomic diversity of rhizosphere bacterial communities at the vegetative and seed-filling stages compared to the control under field conditions. In addition, soybean developmental change evidently influences the main symbiotic nitrogen-fixing bacterial genera in the roots from the flowering stage to the seed-filling stage.

Microorganisms reveal what plants do not: wheat growth and rhizosphere microbial communities after Azospirillum brasilense inoculation and nitrogen fertilization under field conditions

Azospirillum brasilense is one of plant growth promoting bacteria used to improve plant growth and grain yield of cereal crops. The level of inoculation response is defined by complex plant-microorganism interactions, many of them still unknown. Thus, we evaluated both agronomic response and microbial ecology of wheat crop under A. brasilense inoculation and nitrogen fertilization at field conditions in order to improve inoculation efficiency. Treatments were: control, nitrogen fertilization and inoculation with 40M and 42M strains. Functional and structural diversity of rhizosphere bacterial communities were evaluated by community-level physiological and terminal restriction fragment length polymorphism profiles. Besides, aerial biomass, grain yield and counts of microaerophilic diazotrophic rhizobacteria were determined. Plant ontogeny modified the number of culturable microaerophilic diazotrophic rhizobacteria. Although agronomic response did not show differences, plant ontogeny and the agricultural practices modified both physiology and genetic structure of rhizosphere microbial communities. Interestingly, these differences due to the treatments were observed at jointing stage but not at grain-filling stage of wheat. Our results demonstrate how different management decisions can change plant- microorganism relationships. While wheat could not show differences between some agricultural treatments, under the soil surface microbial communities could show them.

Impact of a Glyphosate-Tolerant Soybean Line on the Rhizobacteria, Revealed by Illumina MiSeq

The global commercial cultivation of transgenic crops, including glyphosate-tolerant soybean, has increased widely in recent decades with potential impact on the environment. The bulk of previous studies showed different results on the effects of the release of transgenic plants on the soil microbial community, especially rhizosphere bacteria. In this study, comparative analyses of the bacterial communities in the rhizosphere soils and surrounding soils were performed between the glyphosate-tolerant soybean line NZL06-698 (or simply N698), containing a glyphosate-insensitive EPSPS gene, and its control cultivar Mengdou12 (or simply MD12), by a 16S ribosomal RNA gene (16S rDNA) amplicon sequencing-based Illumina MiSeq platform. No statistically significant difference was found in the overall alpha diversity of the rhizosphere bacterial communities, although the species richness and evenness of the bacteria increased in the rhizosphere of N698 compared with that of MD12. Some influence on phylogenetic diversity of the rhizosphere bacterial communities was found between N698 and MD12 by beta diversity analysis based on weighted UniFrac distance. Furthermore, the relative abundances of part rhizosphere bacterial phyla and genera, which included some nitrogen-fixing bacteria, were significantly different between N698 and MD12. Our present results indicate some impact of the glyphosate-tolerant soybean line N698 on the phylogenetic diversity of rhizosphere bacterial communities together with a significant difference in the relative abundances of part rhizosphere bacteria at different classification levels as compared with its control cultivar MD12, when a comparative analysis of surrounding soils between N698 and MD12 was used as a systematic contrast study.

Analysis of Tea Rhizosphere Bacterial Community at the Seedling Stage Using Terminal Restriction Fragment Length Polymorphism (TRFLP) Techniques

Bio-imunizer contains an active compound of Chryseobacterium sp. and Bacillus sp. has been developed by PPTK Gambung. This formula has positive effect on the growth of tea plants also potentially increasing resistance of the plant. The purpose of this study was to determine the effects of bacteria in Bio-imunizer to the rhizosphere bacterial communities as well as the consistency of its existence after application on tea plants at the nursery stage. The technique used in this research is Terminal Restriction Fragment Length Polymorphism based on metagenomic and culture dependent approaches. The value of relative abundance, Shannon diversity index, Pielou's evenness index, and Simpson dominance index were calculated. Based on the T-RF profiles of rhizosphere bacterial communities show that Chryseobacterium sp. and Bacillus sp. which is the active compound of Bio-imunizer consistently found in the tea plant rhizosphere. Application of Bio-imunizer can increase the diversity of rhizosphere bacterial community without affecting the communities that already exist.

Impact of Genetically Modified Stacked Maize NK603 × MON810 on the Genetic Diversity of Rhizobacterial Communities

Abstract Field trials with the genetic modified (GM) maize stacked hybrid NK603 × MON810 performed in two different locations in the Czech Republic were used for evaluation of genetic diversity of rhizosphere bacterial communities using the terminal restriction fragment length polymorphism. Statistically significant differences in the number of terminal restriction fragments (i.e. bacterial richness) between GM and non-GM maize were not detected. Diversity indices (Gini-Simpson and Shannon’s) revealed higher bacterial diversity in non-GM sample from location Ivanovice na Hané and in the GM maize from location Probluz, but statistical significant differences between GM and non-GM samples were not detected. Additionally, using principal component analysis and cluster analysis, no substantial variation in the composition of bacterial communities between GM and conventional maize were observed but the differences among individual collection sites were recorded.

Effects of glyphosate on the bacterial community associated with roots of transgenic Roundup Ready® soybean

Introduction of glyphosate-resistant soybean plants into agricultural systems has greatly increased the application frequency of glyphosate. Because glyphosate is able to inhibit 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) not only in plants but also in different microorganisms, its application could lead to shifts in rhizosphere microbial communities in farming soils. In this study, greenhouse experiments were conducted with the objective to evaluate the effects of glyphosate on the composition and diversity of rhizosphere bacterial communities of transgenic soybean. This was especially relevant, because foliar applied glyphosate is transported down to the roots and exuded into the rhizosphere. After two foliar herbicide applications, root samples of treated and untreated plants were analysed by 16S rRNA gene T-RFLP analysis. Multivariate statistical analysis of the data and diversity indices were used to assess changes in the microbial populations in response to glyphosate applications. A comparison of rhizosphere communities revealed that the abundance of a T-RF representing microbes related to Burkholderia sp. significantly decreased under glyphosate application, while the abundance of a T-RF representing uncultured Gemmatimonadetes significantly increased. Interestingly, the bacterial community associated with soybean roots after glyphosate application not only demonstrated effective resilience after the disturbance but in addition, T-RF diversity also increased in comparison to the untreated control samples. The results suggest that bacterial diversity was even stimulated in the rhizosphere after glyphosate application.