Rhizosphere Ecosystem Research Articles

Correlation between physico-chemical parameters with soil of Citrus rhizosphere microbes

The population dynamics of microorganisms in soil are extremely difficult to assess due to the complex nature of the soil environment. The diverse nutritional requirements of microorganisms in soil may not be easily estimated; hence, isolation of the soil microorganisms and studying them in the laboratory, as pure or mixed culture cannot be easily attained. The growth and colonization of soil microorganisms can be influenced by chemical, physical and biological properties of the soil. The availability of macro and micro nutrient element can limit microbial population growth in the particular soil ecosystem. Essential soil elements for plant growth such as nitrogen, phosphorous, sulfur and micronutrients influences the microbial population as these nutrient elements are also needed for microbial growth and activity. The prospect of manipulating crop rhizosphere microbial populations by inoculation of beneficial organisms i.e. Pseudomonas fluorescence and Trichoderma spp. and managing soil physico-chemical properties of soil, increases plant growth and control of many soil borne diseases has shown considerable promise in laboratory and field. Present investigation was carried out during 2014 - 2015 at Department of Plant Pathology, All India Co-ordinated Research Project on Fruits, Dr. P. D. K. V. Akola and Department of Soil Science and Agricultural Chemistry, Post Graduate Institute. Dr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola (M.S.) by collecting soil samples from Akola (AK), Amravati (AM1 & AM2), Wardha(WR), Washim (WA), Yavatmal (YA), Nagpur (NA1&NA2) and Buldhana (BU) sampling site of Vidarbha region to know the correlation between physico-chemical parameters with soil rhizosphere microbes for which isolation of different microbes like bacteria, fungi was carried out. The result showed that in healthy rhizosphere, moisture, Organic carbon, Copper and Phosphorous are positively correlated with bacterial and fungal population whereas Temperature, Manganese, EC, Iron, Zinc, pH, and Potassium were negatively correlated. In diseased rhizosphere of citrus, Temperature, Manganese, Phosphorous, Nitrogen, Iron and Moisture were positively correlated whereas PH, Zn, Organic carbon and Potassium negatively correlated. The PCA analysis was carried out to see the influencing factor of Physio-chemical properties with microbial population at different locations. The result reported that the sampling sites Akola (AK) was influenced by Temperature, Moisture, Nitrogen, Copper and Zinc and Amravati (AM1) by Organic carbon, Moisture, Copper, Temperature, EC, Iron, Nitrogen, Potassium and Zinc. Whereas, Amravati (AM2) by Zinc, Nitrogen, Phosphorous, EC for microbial population in citrus rhizosphere ecosystem. In case of Wardha (WR) and Washim (WA), Temperature, Moisture, Nitrogen, Zinc, Iron, pH, are the most influencing factors whereas in Nagpur region NA1 and NA2, pH, Organic carbon, Moisture and Manganese are the factor which are responsible for the microbial population in the rhizosphere region of citrus. In Buldhana (BU) sampling sites, EC and Manganese whereas in Yavatmal (YA) sampling site pH, Iron and EC are the soil properties which influenced the microbial population in rhizosphere region of citrus.

Hydrological and soil physiochemical variables determine the rhizospheric microbiota in subtropical lakeshore areas.

BackgroundDue to intensive sluice construction and other human disturbances, lakeshore vegetation has been destroyed and ecosystems greatly changed. Rhizospheric microbiota constitute a key part of a functioning rhizosphere ecosystem. Maintaining rhizosphere microbial diversity is a central, critical issue for sustaining these rhizospheric microbiota functions and associated ecosystem services. However, the community composition and abiotic factors influencing rhizospheric microbiota in lakeshore remain largely understudied.MethodsThe spatiotemporal composition of lakeshore rhizospheric microbiota and the factors shaping them were seasonally investigated in three subtropical floodplain lakes (Lake Chaohu, Lake Wuchang, and Lake Dahuchi) along the Yangtze River in China through 16S rRNA amplicon high-throughput sequencing.ResultsOur results showed that four archaeal and 21 bacterial phyla (97.04 ± 0.25% of total sequences) dominated the rhizospheric microbiota communities of three lakeshore areas. Moreover, we uncovered significant differences among rhizospheric microbiota among the lakes, seasons, and average submerged depths. The Acidobacteria, Actinobacteria, Bacteroidetes, Bathyarchaeota, Gemmatimonadetes, and Proteobacteria differed significantly among the three lakes, with more than half of these dominant phyla showing significant changes in abundance between seasons, while the DHVEG-6, Ignavibacteriae, Nitrospirae, Spirochaetes, and Zixibacteria varied considerably across the average submerged depths (n = 58 sites in total). Canonical correspondence analyses revealed that the fluctuation range of water level and pH were the most important factors influencing the microbial communities and their dominant microbiota, followed by total nitrogen, moisture, and total phosphorus in soil. These results suggest a suite of hydrological and soil physiochemical variables together governed the differential structuring of rhizospheric microbiota composition among different lakes, seasons, and sampling sites. This work thus provides valuable ecological information to better manage rhizospheric microbiota and protect the vegetation of subtropical lakeshore areas.

Effects of Lentil Genotype on the Colonization of Beneficial Trichoderma Species and Biocontrol of Aphanomyces Root Rot.

Trichoderma species are opportunistic plant symbionts that are common in the root and rhizosphere ecosystems. Many Trichoderma species may enhance plant growth, nutrient acquisition, and disease resistance, and for these reasons, they are widely used in agriculture as biofertilizers or biocontrol agents. Host plant genotype and other microorganisms, such as root pathogens, may influence the efficacy of Trichoderma inoculants. Aphanomyces euteiches is an important soil-borne oomycete in western Canada that causes root rot in legume crops such as lentil and pea, and there is not yet any significantly resistant varieties or effective treatments available to control the disease. In this study, the composition of root-associated fungal communities and the abundance of Trichoderma species, T. harzianum strain T-22 and T. virens strain G41, was determined in the roots of eight Lens genotypes based on internal transcribed spacer (ITS) Illumina MiSeq paired-end sequencing, both in the presence and the absence of the root rot pathogen Aphanomyces euteiches. Biocontrol effects of T. harzianum on A. euteiches was also examined. Significant genotypic variations were observed in the composition of root-associated fungal communities and the abundance of the different Trichoderma species in the lentil roots. The presence of A. euteiches altered the composition of Trichoderma found associated to the lentil genotypes. Biocontrol of A. euteiches by T. harzianum T22 species was observed in vitro and positive correlations between the abundance of Trichoderma and plant root and shoot biomass were observed in vivo. These findings revealed that lentil genotype and infection by the phytopathogen A. euteiches greatly influenced the colonization of root-associated fungi and the abundance of the Trichoderma species, as well as the effect on plant growth promotion. The multipartite interactions observed among lentil genotypes, Trichoderma species and A. euteiches suggest possibilities to select compatible host-beneficial microbe combinations in lentil breeding programs and to develop application strategies to harness the beneficial effects of Trichoderma inoculants in sustainable crop production systems.

Effects of Long-Term exposure to Heavy Metals upon Rhizosphere Bacteria from Baia Mare Area (Maramureş County, Romania)

The aim of this study was to investigate the extent of heavy metal (HM) pollution and its effect on microorganisms from rhizosphere soil in Baia Mare area (Maramureş County, Romania). Two sites with different contamination degrees were included in the study: one with a long history of mining activities and one within a drinking water safeguard zone. Rhizosphere soil samples were characterized with respect to physico-chemical parameters and the Cd, Cu, Pb and Zn contents. Native bacteria were investigated for HM tolerance and biofilm formation under toxic exposure by the microdilution assay. The most resistant strains were identified and the minimum inhibitory concentrations for HMs were determined. Cd, Cu, Pb and Zn exceeded the intervention threshold in Bozânta tailings site, while Pb content exceeded the intervention level within the area of the drinking water treatment plant. Cd showed a very high potential ecological risk in Bozânta area. The long-term exposure to HMs contributed to the selection of HM-tolerant and weakly adherent strains. Biofouling was significantly reduced under the influence of copper ions. Arthrobacter, Rhodococcus and Acidovorax strains with exceptional resistant profiles were isolated from the tailings site, indicating the important role of native microorganisms in rhizosphere ecosystems of contaminated sites.

OsPAL2-1 Mediates Allelopathic Interactions Between Rice and Specific Microorganisms in the Rhizosphere Ecosystem.

The use of plant allelopathy to control weeds in the field has been generally recognized as a win-win strategy because it is an environmentally friendly and resource-saving method. The mechanism of this natural weed-control method relies on allelochemicals, the rhizosphere microbiome, and their bio-interaction, and exploring the link between allelochemicals and specific microbes helps accelerate the application of allelopathic characteristics in farming. In this study, we used allelopathic rice PI312777 (PI), its genetically modified OsPAL2-1 repression (PR) or overexpression (PO) lines, and non-allelopathic rice Lemont (Le) as donor plants to reveal the bio-interaction between rice allelochemicals and rhizosphere specific microorganisms. The results showed a higher content of phenolic acid exudation from the roots of PI than those of Le, which resulted in a significantly increased population of Myxococcus in the rhizosphere soil. Transgenic PO lines exhibited increasing exudation of phenolic acid, which led to the population of Myxococcus xanthus in the rhizosphere soil of PO to be significantly increased, while PR showed the opposite result in comparison with wild type PI. Exogenous application of phenolic acid induced the growth of M. xanthus, and the expressions of chemotaxis-related genes were up-regulated in M. xanthus. In addition, quercetin was identified in the culture medium; according to the bioassay determination, a quercetin concentration of 0.53 mM inhibited the root length by 60.59%. Our study indicates that OsPAL2-1 is among the efficient genes that regulate rice allelopathy by controlling the synthesis of phenolic acid allelochemicals, and phenolic acid (ferulic acid, FA) induces the chemotactic aggregation of M. xanthus, which promoted the proliferation and aggregation of this microbe. The potential allelochemical, quercetin was generated from the FA-induced M. xanthus cultured medium.

Taxonomic Characterization and Secondary Metabolite Analysis of NEAU-wh3-1: An Embleya Strain with Antitumor and Antibacterial Activity.

Cancer is a serious threat to human health. With the increasing resistance to known drugs, it is still urgent to find new drugs or pro-drugs with anti-tumor effects. Natural products produced by microorganisms have played an important role in the history of drug discovery, particularly in the anticancer and anti-infective areas. The plant rhizosphere ecosystem is a rich resource for the discovery of actinomycetes with potential applications in pharmaceutical science, especially Streptomyces. We screened Streptomyces-like strains from the rhizosphere soil of wheat (Triticum aestivum L.) in Hebei province, China, and thirty-nine strains were obtained. Among them, the extracts of 14 isolates inhibited the growth of colon tumor cell line HCT-116. Strain NEAU-wh-3-1 exhibited better inhibitory activity, and its active ingredients were further studied. Then, 16S rRNA gene sequence similarity studies showed that strain NEAU-wh3-1 with high sequence similarities to Embleya scabrispora DSM 41855T (99.65%), Embleya hyalina MB891-A1T (99.45%), and Streptomyces lasii 5H-CA11T (98.62%). Moreover, multilocus sequence analysis based on the five other house-keeping genes (atpD, gyrB, rpoB, recA, and trpB) and polyphasic taxonomic approach comprising chemotaxonomic, phylogenetic, morphological, and physiological characterization indicated that the isolate should be assigned to the genus Embleya and was different from its closely related strains, therefore, it is proposed that strain NEAU-wh3-1 may be classified as representatives of a novel species of the genus Embleya. Furthermore, active substances in the fermentation broth of strain NEAU-wh-3-1 were isolated by bioassay-guided analysis and identified by nuclear magnetic resonance (NMR) and mass spectrometry (MS) analyses. Consequently, one new Zincophorin analogue together with seven known compounds was detected. The new compound showed highest antitumor activity against three human cell lines with the 50% inhibition (IC50) values of 8.8–11.6 μg/mL and good antibacterial activity against four pathogenic bacteria, the other known compounds also exhibit certain biological activity.

Nitrogen Fertilizer Amendment Alter the Bacterial Community Structure in the Rhizosphere of Rice (Oryza sativa L.) and Improve Crop Yield.

Availability of nitrogen (N) in soil changes the composition and activities of microbial community, which is critical for the processing of soil organic matter and health of crop plants. Inappropriate application of N fertilizer can alter the rhizosphere microbial community and disturb the soil N homeostasis. The goal of this study was to assess the effect of different ratio of N fertilizer at various early to late growth stages of rice, while keeping the total N supply constant on rice growth performance, microbial community structure, and soil protein expression in rice rhizosphere. Two different N regimes were applied, i.e., traditional N application (NT) consists of three sessions including 60, 30 and 10% at pre-transplanting, tillering and panicle initiation stages, respectively, while efficient N application (NF) comprises of four sessions, i.e., 30, 30, 30, and 10%), where the fourth session was extended to anthesis stage. Soil metaproteomics combined with Terminal Restriction Fragment Length Polymorphism (T-RFLP) were used to determine the rhizosphere biological process. Under NF application, soil enzymes, nitrogen utilization efficiency and rice yield were significantly higher compared to NT application. T-RFLP and qPCR analysis revealed differences in rice rhizosphere bacterial diversity and structure. NF significantly decreased the specific microbes related to denitrification, but opposite result was observed for bacteria associated with nitrification. Furthermore, soil metaproteomics analysis showed that 88.28% of the soil proteins were derived from microbes, 5.74% from plants, and 6.25% from fauna. Specifically, most of the identified microbial proteins were involved in carbohydrate, amino acid and protein metabolisms. Our experiments revealed that NF positively regulates the functioning of the rhizosphere ecosystem and further enabled us to put new insight into microbial communities and soil protein expression in rice rhizosphere.

Hydrolyzed Organic Fish Fertilizer and Poultry Litter Influence Yield and Rhizosphere Ecology of Sweetpotato

Organic fertilization techniques have become an attractive alternative to conventional techniques, but there remains interest in their impact on rhizosphere ecology. This study was aimed at assessing the impacts of various organic fertilizer amendments on storage root yield, chemical, biochemical, and microbial factors in the rhizosphere ecosystem and the bacterial community composition in the rhizosphere ecosystem. Four sweetpotato cultivars (J6/66, NCC-58, TU Purple, and Whatley/Loretan) and four organic fertilizer treatments [poultry litter, Megabloom (fish protein), NPK, and an untreated control] were used in the study. The experiments were conducted as a randomized complete block design with a 4 × 4 factorial treatment arrangement and three replications. Fertilizer treatments were split-applied at the rate of 134–67–67 kg·ha−1 NPK equivalent based on soil test recommendations 1 and 4 weeks after planting as single bands 15 cm from the plants and organic amendments were calculated based on total N content. Rhizosphere soil samples were collected at harvest and analyzed for soil pH, soil organic carbon (SOC), bacterial 16S rDNA, and selected soil enzymes. Organic amendments did not affect storage root yield or percent dry matter but enhanced both the mass and number of US#1 storage roots. Rhizosphere pH varied depending on cultivar and cultivar response varied with pH and ranged from 6.1 to 6.8, whereas SOC was similar regardless of the amendment. The impact of fertilizers was evident as Megabloom (fish protein) treatment suppressed the relative abundance (RA) of nitrifiers (Nitrosococcus and Nitrosomonadaceae). Also, the rhizosphere of ‘Whatley/Loretan’ seemed to have been a beneficial habitat for populations of common nitrogen-fixing bacteria Bradyrhizobium elkanii, and Rhodospirillaceae sp. as their RA increased significantly in the rhizosphere. That bacteria associated with carbon and nitrogen cycling under aerobic conditions were found to be ubiquitous in the rhizosphere of sweetpotato, suggesting that certain amendments positively impacted the populations of nitrogen-cycling bacteria, thus making them a viable alternative to NPK when considering increasing or sustaining yield while promoting long-term soil health.

Impact of root system architecture on rhizosphere and root microbiome

The root system influences plant fitness, health, and productivity via its phenotypic traits (phenes) such as root length, biomass, density, volume, and surface area. Although these traits differentially impact the release of 20 to 80% of total photosynthates as root exudates, their role in influencing microbial communities in the rhizosphere and root environments is not clear. The root phenes or architecture significantly alter soil biophysical and edaphic properties such as aggregation, structure, pH, moisture, temperature, and nutrient stoichiometry (C:N, C:P, and N:P ratios, etc.). Meantime, the exteriors and interiors of various root types demonstrate a tremendous phenotypic plasticity in their cellular structure, anatomy, cell types, shapes, metabolisms and biochemical profiles. These heterogeneities in the rhizosphere and endosphere create micro-environments and ecological niches for diverse microbial species to foster beneficial rhizospheric interactions. Results from the root systems of some agricultural, forest and model plants suggest that root phenes selectively filter and recruit different microbial communities. However, microbial colonization of root and rhizosphere environments may also occur through vertical transmission. We suggest that plant breeders should nevertheless consider root phenome and biota while developing new cultivars. Linking root phenome to microbiome (or its functional traits) and crop management practices may enhance our understanding of rhizospheric interactions, and their role in developing climate-resilient rhizosphere ecosystems.

Isolation, identification, and the growth promoting effects of two antagonistic actinomycete strains from the rhizosphere of Mikania micrantha Kunth

Actinomycetes are an important group of gram-positive bacteria that play an essential role in the rhizosphere ecosystem. The confrontation culture and Oxford cup method were used to evaluate the antagonistic activities of strains, which were isolated from the rhizosphere soil of Mikania micrantha. The two isolates were identified using morphological and physiological tests combined with 16S rRNA-based molecular analysis, respectively. The type I polyketone synthase (PKS-I) was amplified. The constituents of fermentation metabolites were analyzed by gas chromatography mass spectrometry. The plant growth promoting effect was determined. Finally, the growth of wheat seedlings was assessed using the Petri dish method. Overall, of the isolated twelve strains, WZS1-1 and WZS2-1 could significantly inhibit target fungi. Isolate WZS1-1 was identified as Streptomyces rochei, and WZS2-1 was identified as Streptomyces sundarbansensis. In particular, Fusarium graminearum (FG) from wheat was inhibited by more than 80%, and the inhibitory bandwidths against FG were 31 ± 0.3 mm and 19 ± 0.5 mm, respectively. The genes PKS-I were successfully amplified, confirming that these strains are capable of producing biosynthetic secondary metabolites. Major component analysis revealed aliphatic ketones, carboxylic acids, and esters, with n-hexadecanoic acid being the most abundant compound. Plant growth promoting test indicated that both strains produced IAA, presented with orange loops on CAS plates, dissolved phosphorus and potassium, fixed nitrogen, but did not generate organic acids; both strains colonized in soil, while only WZS1-1 colonized in wheat roots. Additionally, the fermentation broth significantly promoted the growth of wheat.

Trichoderma harzianum MTCC 5179 impacts the population and functional dynamics of microbial community in the rhizosphere of black pepper (Piper nigrum L.).

Employing Illumina Hiseq whole genome metagenome sequencing approach, we studied the impact of Trichoderma harzianum on altering the microbial community and its functional dynamics in the rhizhosphere soil of black pepper (Piper nigrum L.). The metagenomic datasets from the rhizosphere with (treatment) and without (control) T. harzianum inoculation were annotated using dual approach, i.e., stand alone and MG-RAST. The probiotic application of T. harzianum in the rhizhosphere soil of black pepper impacted the population dynamics of rhizosphere bacteria, archae, eukaryote as reflected through the selective recruitment of bacteria [Acidobacteriaceae bacterium (p = 1.24e−12), Candidatus koribacter versatilis (p = 2.66e−10)] and fungi [(Fusarium oxysporum (p = 0.013), Talaromyces stipitatus (p = 0.219) and Pestalotiopsis fici (p = 0.443)] in terms of abundance in population and bacterial chemotaxis (p = 0.012), iron metabolism (p = 2.97e−5) with the reduction in abundance for pathogenicity islands (p = 7.30e−3), phages and prophages (p = 7.30e−3) with regard to functional abundance. Interestingly, it was found that the enriched functional metagenomic signatures on phytoremediation such as benzoate transport and degradation (p = 2.34e−4), and degradation of heterocyclic aromatic compounds (p = 3.59e−13) in the treatment influenced the rhizosphere micro ecosystem favoring growth and health of pepper plant. The population dynamics and functional richness of rhizosphere ecosystem in black pepper influenced by the treatment with T. harzianum provides the ecological importance of T. harzianum in the cultivation of black pepper.

Distribution of 2,4-Diacetylphloroglucinol Biosynthetic Genes among the Pseudomonas spp. Reveals Unexpected Polyphyletism.

Fluorescent pseudomonads protecting plant roots from phytopathogens by producing 2,4-diacetylphloroglucinol (DAPG) are considered to form a monophyletic lineage comprised of DAPG+ Pseudomonas strains in the “P. corrugata” and “P. protegens” subgroups of the “Pseudomonas fluorescens” group. However, DAPG production ability has not been investigated for many species of these two subgroups, and whether or not the DAPG+ Pseudomonas are truly monophyletic remained to be verified. Thus, the distribution of the DAPG biosynthetic operon (phlACBD genes) in the Pseudomonas spp. was investigated in sequenced genomes and type strains. Results showed that the DAPG+ Pseudomonas include species of the “P. fluorescens” group, i.e., P. protegens, P. brassicacearum, P. kilonensis, and P. thivervalensis, as expected, as well as P. gingeri in which it had not been documented. Surprisingly, they also include bacteria outside the “P. fluorescens” group, as exemplified by Pseudomonas sp. OT69, and even two Betaproteobacteria genera. The phl operon-based phylogenetic tree was substantially congruent with the one inferred from concatenated housekeeping genes rpoB, gyrB, and rrs. Contrariwise to current supposition, ancestral character reconstructions favored multiple independent acquisitions rather that one ancestral event followed by vertical inheritance. Indeed, based on synteny analyses, these acquisitions appeared to vary according to the Pseudomonas subgroup and even the phylogenetic groups within the subgroups. In conclusion, our study shows that the phl+ Pseudomonas populations form a polyphyletic group and suggests that DAPG biosynthesis might not be restricted to this genus. This is important to consider when assessing the ecological significance of phl+ bacterial populations in rhizosphere ecosystems.

Bio-protective microbial agents from rhizosphere eco-systems trigger plant defense responses provide protection against sheath blight disease in rice (Oryza sativa L.)

Sheath blight of rice (Oryza sativa L.) caused by Rhizoctonia solani is a major disease and attempts are being made to develop microbe based technologies for biocontrol of this pathogen. However, the mechanisms of biocontrol are not fully understood and still require indepth study in the backdrop of emerging concepts in biological systems. The present investigation was aimed at deciphering the mechanisms of biocontrol of sheath blight of rice employing Pseudomonas fluorescens and Trichoderma harzianum as model agents for biocontrol. Initially 25, 5 and 5 strains of P. fluorescens, T. viride and T. harzianum, respectively, were screened for their biocontrol potential. Out of which, six strains with higher value of percent inhibition of fungal mycelium in dual plate assay were selected. The role of P. fluorescens, T. viride and T. harzianum were investigated in induction and bioaccumulation of natural antioxidants, defence-related biomolecules and other changes in plant which lead not only to growth promotion but also protection from pathogenic stress conditions in rice. The two most promising strains, P. fluorescens PF-08 and T. harzianum UBSTH-501 selected on the basis of in planta evaluation, when applied individually or in combination, significantly enhanced the accumulation of defence-related biomolecules, enzymes and exhibited biocontrol potential against R. solani. A modified/newly developed delivery system was applied for the first time in the experiments involving inoculation of plants with both bioagents, viz. P. fluorescens PF-08 and T. harzianum UBSTH-501. Results suggested that application of P. fluorescens PF-08 and T. harzianum UBSTH-501 alone or in combination, not only helps in control of the disease but also increases plant growth along with reduction in application of toxic chemical pesticides.

Indole-3-Acetic Acid Produced by Burkholderia heleia Acts as a Phenylacetic Acid Antagonist to Disrupt Tropolone Biosynthesis in Burkholderia plantarii.

Burkholderia heleia PAK1-2 is a potent biocontrol agent isolated from rice rhizosphere, as it prevents bacterial rice seedling blight disease caused by Burkholderia plantarii. Here, we isolated a non-antibacterial metabolite from the culture fluid of B. heleia PAK1-2 that was able to suppress B. plantarii virulence and subsequently identified as indole-3-acetic acid (IAA). IAA suppressed the production of tropolone in B. plantarii in a dose-dependent manner without any antibacterial and quorum quenching activity, suggesting that IAA inhibited steps of tropolone biosynthesis. Consistent with this, supplementing cultures of B. plantarii with either L-[ring-2H5]phenylalanine or [ring-2H2~5]phenylacetic acid revealed that phenylacetic acid (PAA), which is the dominant metabolite during the early growth stage, is a direct precursor of tropolone. Exposure of B. plantarii to IAA suppressed production of both PAA and tropolone. These data particularly showed that IAA produced by B. heleia PAK1-2 disrupts tropolone production during bioconversion of PAA to tropolone via the ring-rearrangement on the phenyl group of the precursor to attenuate the virulence of B. plantarii. B. heleia PAK1-2 is thus likely a microbial community coordinating bacterium in rhizosphere ecosystems, which never eliminates phytopathogens but only represses production of phytotoxins or bacteriocidal substances.

Assessing bacterial communities in the rhizosphere of 8-year-old genetically modified poplar (Populus spp.)

Microbe communities in rhizosphere ecosystems are important for plant health but there is limited knowledge of them in the rhizospheres of genetically modified (GM) plants, especial for tree species. We used the amplitude sequencing method to analyze the V4 regions of the 16S rRNA gene to identify changes in bacterial diversity and community structure in two GM lines (D520 and D521), one non-genetically modified (non-GM) line and in uncultivated soil. After chimera filtering, 468.133 sequences in the domain Bacteria remained. There were ten dominant taxonomic groups (with >1 % of all sequences) across the samples. 241 of 551 genera (representing a ratio of 97.33 %) were common to all samples. A Venn diagram showed that 1.926 operational taxonomic units (OTUs) were shared by all samples. We found a specific change, a reduction in Chloroflexi, in the microorganisms in the rhizosphere soil planted with poplars. Taken together, the results showed few statistical differences in the bacterial diversity and community structure between the GM line and non-GM line, this suggests that there was no or very limited impact of this genetic modification on the bacterial communities in the rhizosphere.

English

The purpose of this study was to assay the cultivable microorganisms of Davidia involucrate in rhizosphere soil and to analyze their diversity using colony and individual morphology and genetic profiling methods. A total of 118 strains were obtained after colony characterization and a microscopic examination, including 52 bacteria strains, 27 actinomycetes strains and 39 fungi strains. Fifty-seven (57) of these strains were randomly selected for rDNA analysis and phylogenetic identification, including 23 rhizobaceria isolates, 29 fungi isolates, and five streptomyces isolates. The selected isolates were accurately identified at the genus level with consistent results using a morphology examination and phylogenetic identification. From the study, we concluded the following: (1) Bacillus, Lactobacillus, Azotobacter, and Streptomyces are predominant microorganisms of D. involucrate in rhizophere soil and Bacillus is a dominant rhizobacteria that might have potential in host growth promotion; (2) the physiological activity of dovetree could significantly influence the microorganism biomass of the rhizophere soil; and (3) the dovetree is a highly complex rhizosphere ecosystem, and additional research on this topic should be carried out in the future. Key words: Rhizosphere microorganism, Davidia involucrate, plant growth promotion, soil.

Metaproteomic analysis of ratoon sugarcane rhizospheric soil

BackgroundThe current study was undertaken to elucidate the mechanism of yield decline in ratoon sugarcane using soil metaproteomics combined with community level physiological profiles (CLPP) analysis.ResultsThe available stalk number, stalk diameter, single stalk weight and theoretical yield of ratoon cane (RS) were found to be significantly lower than those of plant cane (NS). The activities of several carbon, nitrogen and phosphorus processing enzymes, including invertase, peroxidase, urease and phosphomonoesterase were found to be significantly lower in RS soil than in NS soil. BIOLOG analysis indicated a significant decline in average well-color development (AWCD), Shannon’s diversity and evenness indices in RS soil as compared to NS soil. To profile the rhizospheric metaproteome, 109 soil protein spots with high resolution and repeatability were successfully identified. These proteins were found to be involved in carbohydrate/energy, amino acid, protein, nucleotide, auxin and secondary metabolisms, membrane transport, signal transduction and resistance, etc. Comparative metaproteomics analysis revealed that 38 proteins were differentially expressed in the RS soil as compared to the control soil or NS soil. Among these, most of the plant proteins related to carbohydrate and amino acid metabolism and stress response were up-regulated in RS soil. Furthermore, several microbial proteins related to membrane transport and signal transduction were up-regulated in RS soil. These proteins were speculated to function in root colonization by microbes.ConclusionsOur experiments revealed that sugarcane ratooning practice induced significant changes in the soil enzyme activities, the catabolic diversity of microbial community, and the expression level of soil proteins. They influenced the biochemical processes in the rhizosphere ecosystem and mediated the interactions between plants and soil microbes.

Isolation and characterization of bacteriophages infecting Xanthomonas arboricola pv. juglandis, the causal agent of walnut blight disease

Walnut orchards suffer from a blight caused by the bacteria Xanthomonas arboricola pv. juglandis. These bacteria can be infected by viral bacteriophages and this study was carried out to isolate and characterize bacteriophages from walnut orchards located throughout the South Island of New Zealand. Twenty six X. arboricola phages were isolated from three hundred and twenty six samples of plant material representing phyllosphere and rhizosphere ecosystems. The phage isolates were characterized by host-range, plaque and particle morphology, restriction digest and phylogenetic analysis and stability under various storage conditions. From capsid and tail dimensions the bacteriophages were considered to belong to the double-stranded DNA families Podoviridae and Siphoviridae. Of the twenty six bacteriophages, sixteen belonged to Podoviridae and were found both in the phyllosphere and rhizosphere. In contrast, Siphoviridae were present only in the rhizosphere isolates. Phage genome sizes ranged from 38.0 to 52.0 kb from a Hind III restriction digestion and had in common a 400 kb fragment that was identical at the DNA level. Despite the similar restriction patterns, maximum parsimony bootstrap analysis showed that the phage were members of different groups. Finally, we hypothesise that these phage might have use in a biocontrol strategy and therefore storage stability and efficacy was tested. Titres declined more than 50% over a 12-months storage period. Deep-freezing temperatures (-34°C) increased while chloroform decreased the stability.

Diversity of streptomycetes among specific Greek terrestrial ecosystems

The diversity of streptomycetes isolated from different Greek terrestrial ecosystems using phenotypic identification, and the relationship between the number of species and the number of isolates as a diversity index, was studied. A total of 344 Streptomyces strains have been isolated and identified from diverse sites in the Greek territory, such as heavily disturbed agricultural areas and preserved forest areas, and from specific rhizosphere ecosystems. According to phenotypic identification, these strains belonged to 19 different cluster groups with a Willcox probability > 0·8. Streptomyces cyaneus, Strep. albidoflavus, Strep. diastaticus and Strep. exfoliatus were the most common cluster groups isolated from at least six different habitats. On the other hand, there were cluster groups that appeared in only one or two habitats, such as Strep. griseoflavus, Strep. rimosus, Streptoverticillium blastmyceticum, Nocardia mediterranea and Strep. fulvissimus. The diversity indices among the different cluster groups of each sampling area indicated that the different habitats can be sub-divided into two main groups: rhizosphere habitats and non-rhizosphere habitats, showing that the rhizosphere is one of the most important factors which determines the population structure of a specific soil area.

Microbiological Evaluation and Improvement of Rhizosphere Ecosystem of Upland Plants

Microbiological Evaluation and Improvement of Rhizosphere Ecosystem of Upland Plants