Diversity of Culturable Bacteria Isolated from Root Domains of Moso Bamboo (Phyllostachys edulis)

The distribution of culturable bacteria in the rhizosphere, rhizoplane, and interior root tissues of moso bamboo plants was investigated in this study. Of the 182 isolates showing different colony characteristics on Luria–Bertani and King B plates, 56 operational taxonomic units of 22 genera were identified by 16S ribosomal RNA gene sequence analysis. The majority of root endophytic bacteria were Proteobacteria (67.5%), while the majority of rhizospheric and rhizoplane bacteria were Firmicutes (66.3% and 70.4%, respectively). The most common genus in both the rhizosphere and on the rhizoplane was Bacillus (42.4% and 44.4%, respectively), while Burkholderia was the most common genus inside the roots, comprising 35.0% of the isolates from this root domain. The endophytic bacterial community was less diverse than the rhizoplane and rhizospheric bacterial communities. Members of Lysinibacillus, Bacillus, and Burkholderia were found in all three root domains, whereas many isolates were found in only a single domain. Our results show that the population diversity of culturable bacteria is abundant in the root domains of moso bamboo plants and that obvious differences exist among the rhizospheric, rhizoplane, and endophytic bacterial communities.     

Influence of Two Plant Species (Flax and Tomato) on the Distribution of Nitrogen Dissimilative Abilities within Fluorescent Pseudomonas spp

The distribution of nitrogen-dissimilative abilities among 317 isolates of fluorescent pseudomonads was studied. These strains were isolated from an uncultivated soil and from the rhizosphere, rhizoplane, and root tissue of two plant species (flax and tomato) cultivated on this same soil. The isolates were distributed into two species, Pseudomonas fluorescens (45.1%) and Pseudomonas putida (40.4%), plus an intermediate type (14.5%). P. fluorescens was the species with the greatest proportion of isolates in the root compartments and the greatest proportion of dissimilatory and denitrifying strains. According to their ability to dissimilate nitrogen, the isolates have been distributed into nondissimilatory and dissimilatory strains, nitrate reducers and true denitrifiers with or without N(inf2)O reductase. The proportion of dissimilatory isolates was significantly enhanced in the compartments affected by flax and tomato roots (55% in uncultivated soil and 90 and 82% in the root tissue of flax and tomato, respectively). Among these strains, the proportion of denitrifiers gradually and significantly increased in the root vicinity of tomato (44, 68, 75, and 94% in uncultivated soil, rhizosphere, rhizoplane, and root tissue, respectively) and was higher in the flax rhizoplane (66%) than in the uncultivated soil. A higher proportion of N(inf2)O reducers was also found in the root compartments. This result was particularly clear for tomato. It is hypothesized that denitrification could be a selective advantage for the denitrifiers in the root environment and that this process could contribute to modify the specific composition of the bacterial communities in the rhizosphere.     

Enterococcus faecalis sufCDSUB complements Escherichia coli sufABCDSE

A total of 985 bacterial strains with different colony characteristics were isolated from the root of tree peony plants (variety 'Fengdan' and 'Lan Furong'); 69 operational taxonomic units were identified by amplified ribosomal DNA restriction analysis. Representatives of each group were selected for partial 16S rRNA gene sequencing and phylogenetic analysis. The major groups in the bulk soil, rhizosphere, and rhizoplane of Fengdan were Firmicutes (63.2%), Actinobacteria (36.3%), and Betaproteobacteria (53.0%), respectively. The major bacteria groups in the bulk soil, rhizosphere, and rhizoplane of Lan Furong were Actinobacteria (34.8%), Gammaproteobacteria (45.2%), and Betaproteobacteria (49.1%), respectively. In total, the bacterial isolates comprised 26 genera--14 in the bulk soil, 14 in the rhizosphere, and 11 in the rhizoplane. The most common genus in the bulk soil of Fengdan and Lan Furong was Bacillus (49.6% and 32.6%, respectively), in the rhizosphere Microbacterium (21.1%) and Pseudomonas (42.0%), and in the rhizoplane Variovorax (53.0% and 49.1%, respectively). The results show that there are obvious differences in the bacterial communities in the three root domains of the two varieties, and the plants exerted selective pressures on their associated bacterial populations. The host genotypes also influenced the distribution pattern of the bacterial community.     

Rhizobacteria of Cotton and Their Repression of Seedling Disease Pathogens

During the 1983 field season, the rhizobacteria (including organisms from rhizosphere soil and the root rhizoplane) of cotton plants at one location in Mississippi were inventoried at different plant growth stages. Isolates (1,000) were identified to the genus level and characterized for repression of Pythium ultimum and Rhizoctonia solani. Cotton seedlings were initially colonized by bacteria of many different genera, and populations quickly reached 10⁸ CFU/g of root tissue. As the season progressed, the bacterial populations declined as root mass increased and the roots became more woodlike in consistency. Fluorescent pseudomonads were the most numerous gram-negative rhizobacterial isolates of those that were randomly collected and identified, and they provided the largest number of isolates with fungal repressive activity. Several other gram-negative bacterial genera were recovered throughout the growing season, and some gram-positive bacteria were also isolated routinely, but at lower numbers. There was no correlation between the proportion of rhizobacterial isolates that possessed fungal repressive activity and the plant growth stage from which the isolates were obtained. Approximately twice as many bacterial isolates demonstrated fungal repression in the agar assay compared with the inplanta assay, and isolates were found more frequently with fungal repressive activity against P. ultimum than against R. solai.     

Isolation and characterization of bacteria associated with two sand dune plant species, Calystegia soldanella and Elymus mollis

Little is known about the bacterial communities associated with the plants inhabiting sand dune ecosystems. In this study, the bacterial populations associated with two major sand dune plant species, Calystegia soldanella (beach morning glory) and Elymus mollis (wild rye), growing along the costal areas in Tae-An, Chungnam Province, were analyzed using a culture-dependent approach. A total of 212 bacteria were isolated from the root and rhizosphere samples of the two plants, and subjected to further analysis. Based on the analysis of the 16S rDNA sequences, all the bacterial isolates were classified into six major phyla of the domain Bacteria. Significant differences were observed between the two plant species, and also between the rhizospheric and root endophytic communities. The isolates from the rhizosphere of the two plant species were assigned to 27 different established genera, and the root endophytic bacteria were assigned to 21. Members of the phylum Gammaproteobacteria, notably the Pseudomonas species, comprised the majority of both the rhizospheric and endophytic bacteria, followed by members of Bacteroidetes and Firmicutes in the rhizosphere and Alphaproteobacteria and Bacteroidetes in the root. A number of isolates were recognized as potentially novel bacterial taxa. Fifteen out of 27 bacterial genera were commonly found in the rhizosphere of both plants, which was comparable to 3 out of 21 common genera in the root, implying the host specificity for endophytic populations. This study of the diversity of culturable rhizospheric and endophytic bacteria has provided the basis for further investigation aimed at the selection of microbes for the facilitation of plant growth.     

Microbial Complexes Occurring on the Apogeotropic Roots and in the Rhizosphere of Cycad Plants

The microbial complexes of soil, the rhizosphere, and the rhizoplane of the apogeotropic (coralloid) roots of cycad plants were comparatively studied. The aseptically prepared homogenates of the surface-sterilized coralloid roots did not contain bacterial microsymbiont, indicating that in the root tissues the symbiosis is a two-component one (plant–cyanobacteria). At the same time, associated bacteria belonging to different taxonomic groups were detected in increasing amounts in the cycad rhizoplane, rhizosphere, and the surrounding soil. The bacterial communities found in the cycad rhizoplane and the surrounding soil were dominated by bacteria from the genus Bacillus. The saprotrophic bacteria and fungi colonizing the cycad rhizosphere and rhizoplane were dominated by microorganisms capable of degrading the plant cell walls. The local degradation of the cell wall was actually observed on the micrographs of the thin sections of cycad roots in the form of channels through which symbiotic cyanobacterial filaments can penetrate into the cortical parenchyma.     

Diversity of root-associated bacteria associated with field-grown canola (Brassica napus L.) and wheat (Triticum aestivum L.)

Little is known about the composition and diversity of the bacterial community associated with plant roots. The purpose of this study was to investigate the diversity of bacteria associated with the roots of canola plants grown at three field locations in Saskatchewan, Canada. Over 300 rhizoplane and 220 endophytic bacteria were randomly selected from agar-solidified trypticase soy broth, and identified using fatty acid methyl ester (FAME) profiles. Based on FAME profiles, 18 bacterial genera were identified with a similarity index >0.3, but 73% of the identified isolates belonged to four genera: Bacillus (29%), Flavobacterium (12%), Micrococcus (20%) and Rathayibacter (12%). The endophytic community had a lower Shannon-Weaver diversity index (1.35) compared to the rhizoplane (2.15), and a higher proportion of Bacillus, Flavobacterium, Micrococcus and Rathayibacter genera compared to rhizoplane populations. Genera identified in the endophytic isolates were also found in the rhizoplane isolates. Furthermore, principal component analysis indicated three clusters of bacteria regardless of their site of origin, i.e., rhizoplane or endophytic. In addition, the rhizoplane communities of canola and wheat grown at the same site differed significantly. These results indicate that diverse groups of bacteria are associated with field-grown plants and that endophytes are a subset of the rhizoplane community.     

Microbial complexes from apogeotropic roots and from rhizosphere of cycad plants

The microbial complexes of soil, the rhizosphere, and the rhizoplane of the apogeotropic (coralloid) roots of cycad plants were comparatively studied. The aseptically prepared homogenates of the surface-sterilized coralloid roots did not contain bacterial microsymbiont, indicating that it was absent in the root tissues. At the same time, associated bacteria belonging to different taxonomic groups were detected in increasing amounts in the cycad rhizoplane, rhizosphere, and the surrounding soil. The bacterial communities found in the cycad rhizoplane and the surrounding soil were dominated by bacteria from the genus Bacillus. The saprotrophic bacteria and fungi colonizing the cycad rhizosphere and rhizoplane were dominated by microorganisms capable of degrading the plant cell walls. The local degradation of the cell wall was actually observed on the micrographs of the thin sections of cycad roots in the form of channels, through which symbiotic cyanobacterial filaments can penetrate into the cortical parenchyma.     

Preferential Promotion of Lycopersicon esculentum (Tomato) Growth by Plant Growth Promoting Bacteria Associated with Tomato

A total of 74 morphologically distinct bacterial colonies were selected during isolation of bacteria from different parts of tomato plant (rhizoplane, phylloplane and rhizosphere) as well as nearby bulk soil. The isolates were screened for plant growth promoting (PGP) traits such as production of indole acetic acid, siderophore, chitinase and hydrogen cyanide as well as phosphate solubilization. Seven isolates viz., NR4, NR6, RP3, PP1, RS4, RP6 and NR1 that exhibited multiple PGP traits were identified, based on morphological, biochemical and 16S rRNA gene sequence analysis, as species that belonged to four genera Aeromonas, Pseudomonas,Bacillus and Enterobacter. All the seven isolates were positive for 1-aminocyclopropane-1-carboxylate deaminase. Isolate NR6 was antagonistic to Fusarium solani and Fusarium moniliforme, and both PP1 and RP6 isolates were antagonistic to F. moniliforme. Except RP6, all isolates adhered significantly to glass surface suggestive of biofilm formation. Seed bacterization of tomato, groundnut, sorghum and chickpea with the seven bacterial isolates resulted in varied growth response in laboratory assay on half strength Murashige and Skoog medium. Most of the tomato isolates positively influenced tomato growth. The growth response was either neutral or negative with groundnut, sorghum and chickpea. Overall, the results suggested that bacteria with PGP traits do not positively influence the growth of all plants, and certain PGP bacteria may exhibit host-specificity. Among the isolates that positively influenced growth of tomato (NR1, RP3, PP1, RS4 and RP6) only RS4 was isolated from tomato rhizosphere. Therefore, the best PGP bacteria can also be isolated from zones other than rhizosphere or rhizoplane of a plant.

Electronic supplementary material

The online version of this article (doi:10.1007/s12088-014-0470-z) contains supplementary material, which is available to authorized users.     

Development of rhizosphere and rhizoplane microflora of Aristida coerulescens in the Libyan desert

Summary Microflora of rhizosphere soil, rhizoplane and macerated root-portions of Aristida coerulescens, naturally occurring in the Libyan desert, were different in count and isolates, in the different root zones. A rhizosphere effect characteristic of each zone is shown. The root base contained the lowest numbers of microflora (bacteria and fungi) whilst the root tip included the highest counts. Distribution of most of the individual fungal species in the different root zones and root-surfaces is given in text.     

Effect of Two Plant Species, Flax (Linum usitatissinum L.) and Tomato (Lycopersicon esculentum Mill.), on the Diversity of Soilborne Populations of Fluorescent Pseudomonads

Suppression of soilborne disease by fluorescent pseudomonads may be inconsistent. Inefficient root colonization by the introduced bacteria is often responsible for this inconsistency. To better understand the bacterial traits involved in root colonization, the effect of two plant species, flax (Linum usitatissinum L.) and tomato (Lycopersicon esculentum Mill.), on the diversity of soilborne populations was assessed. Fluorescent pseudomonads were isolated from an uncultivated soil and from rhizosphere, rhizoplane, and root tissue of flax and tomato cultivated in the same soil. Species and biovars were identified by classical biochemical and physiological tests. The ability of bacterial isolates to assimilate 147 different organic compounds and to show three different enzyme activities was assessed to determine their intraspecific phenotypic diversity. Numerical analysis of these characteristics allowed the clustering of isolates showing a high level (87.8%) of similarity. On the whole, the populations isolated from soil were different from those isolated from plants with respect to their phenotypic characteristics. The difference in bacteria isolated from uncultivated soil and from root tissue of flax was particularly marked. The intensity of plant selection was more strongly expressed with flax than with tomato plants. The selection was, at least partly, plant specific. The use of 10 different substrates allowed us to discriminate between flax and tomato isolates. Pseudomonas fluorescens biovars II, III, and V and Pseudomonas putida biovar A and intermediate type were well distributed among the isolates from soil, rhizosphere, and rhizoplane. Most isolates from root tissue of flax and tomato belonged to P. putida bv. A and to P. fluorescens bv. II, respectively. Phenotypic characterization of bacterial isolates was well correlated with genotypic characterization based on repetitive extragenic palindromic PCR fingerprinting.     

Identification and Characterization of Rhizosphere-Competent Bacteria of Wheat

To obtain rhizosphere-competent bacteria which could subsequently be modified for the development of biological control agents, bacteria were isolated from the rhizosphere and rhizoplane of wheat and barley plants by standard techniques. Of these isolates, 60 were selected for field testing as spring wheat seed inoculants in 1985. Isolates were marked genetically for resistance to antibiotics via selection of spontaneous mutants to detect and monitor isolates in the field. Forty-three days after planting, the average log₁₀ CFU/mg (dry weight) of roots and rhizosphere soil for the mutant isolates sampled ranged from 0 to 3.4. Twenty mutant isolates were retested in 1986. A total of 4 isolates were not detected, but the other 16 had an average root colonization value of log₁₀ 2.1 CFU and a range of log₁₀ 0.9 CFU to log₁₀ 3.2 CFU when sampled 32 days after planting. The average colonization value dropped to log₁₀ 1.1 CFU 51 days later. Some isolates detected previously were not detected in the second sampling; others had root colonization values similar to those obtained in the first sampling. Mutant isolates of rhizosphere bacteria included Bacillus pumilus, Bacillus subtilis, Pseudomonas fluorescens, Streptomyces spp., Xanthomonas maltophilia, and a saprophytic coryneform. Mixtures of isolates from different genera and species were compatible on seeds and roots.     

The rhizosphere effect on bacteria antagonistic towards the pathogenic fungus Verticillium differs depending on plant species and site

Rhizobacteria with antagonistic activity towards plant pathogens play an essential role in root growth and plant health and are influenced by plant species in their abundance and composition. To determine the extent of the effect of the plant species and of the site on the abundance and composition of bacteria with antagonistic activity towards Verticillium dahliae, bacteria isolated from the rhizosphere of two Verticillium host plants, oilseed rape and strawberry, and from bulk soil were analysed at three different locations in Germany over two growing seasons. A total of 6732 bacterial isolates screened for in vitro antagonism towards Verticillium resulted in 560 active isolates, among which Pseudomonas (77%) and Serratia (6%) were the most dominant genera. The rhizosphere effect on the antagonistic bacterial community was shown by an enhanced proportion of antagonistic isolates, by enrichment of specific amplified ribosomal DNA restriction analysis types, species and genotypes, and by a reduced diversity in the rhizosphere in comparison to bulk soil. Such an effect was influenced by the plant species and by the site of its cultivation. Altogether, 16S rRNA gene sequencing of 66 isolates resulted in the identification of 22 different species. Antagonists of the genus Serratia were preferentially isolated from oilseed rape rhizosphere, with the exception of one site. For isolates of Pseudomonas and Serratia, plant-specific and site-specific genotypes were found.     

元阳梯田地方水稻品种根部内生菌及根际微生物的分离与鉴定

采用组织分离法和土壤稀释涂板法,对元阳哈尼梯田2个地方品种‘月亮谷’和‘红脚老粳’的根部内生细菌及根际土壤细菌进行了分离,研究元阳梯田传统水稻品种特殊的内生菌组成.结果表明: 试验共得到399个菌株.经形态特征及生理生化鉴定,月亮谷根部和其根际土壤分别分离到8和5个属,其中5个属是共有的;红脚老粳的根部和其根际土壤中分别分离到10和7个属,其中6个属是共有的.经分子生物学鉴定,月亮谷根部分离到11个种和5个属,根际土壤分离到8个种和4个属,其中5个种和4个属是共有的;红脚老粳根部分离到9个种和5个属,根际土壤分离到10个种和3个属,其中4个种和2个属是共有的.通过分子生物学鉴定,大部分菌株都可以鉴定到种,而通过形态及生理生化特性只能初步鉴定到属,但两种方法在属层次上的鉴定结果基本一致.元阳地方水稻根部内生细菌及根际土壤细菌具有一定的种属同源性与特异性.     

Growth of bacteria in the rhizoplane and the rhizosphere of rape seedlings

Abstract The growth of 10 isolates of rhizosphere bacteria was compared in the rhizoplane (RP), rhizosphere (RS) and non-rhizosphere soil of a model system with rape seedlings growing in sterile sand. The colonization of the RP differed little among isolates. However, the bacterial isolates differed according to their degree of dependence on the root for growth, as judged by RS:RP and plant:non-plant ratios for CFU. These two ratios were correlated with changes in viability and 'physiological status' (as judged by γ values, Hattori, T. (1983) J. Gen. Appl. Microbiol. 29, 9–16).     

Bacterial diversity in roots of conventional and genetically modified hybrid maize

Cultivated surfaces of genetically modified (GM) crops increased year by year, becoming in 2012 more extensive in developed than in industrialized countries. Furthermore, it has been postulated that the plant is which leads to the selection of the microorganisms on its root exudates, creating specific conditions which in turn regulate the specific microbial structure of each plant. In this study, our main objective was to examine whether the introduction of transgenic maize herbicide-tolerant plants will impact the microbial structures that inhabit at the rhizosphere and rhizoplane with respect to conventional hybrid maize plants. Bacterial populations were determined (CFU/g) using four different semi-selective media. The bacterial genera isolated from the rhizoplane and rhizosphere were identified by sequencing its 16S ribosomal DNA. Although minor differences were found in bacterial populations, our results indicated that there was not a strong change of the microorganisms populations that interact at the rhizosphere of an either conventional hybrid or genetically modified maize. However, we found some bacteria that were only isolated in the either genetically modified [Chryseobacterium sp. (4.39%) and Micrococcus sp. (3.72%)] or conventional maize [Sphingobium sp. (13.17%) and Microbacterium sp. (14.81%)].     

Isolation and characterization of pyrene metabolizing microbial consortia from the plant rhizoplane

Most research on the ecology of PAH degrading bacteria in the rhizosphere has focused on individual strains that grow on specific PAHs. Thus, there are fundamental questions as to importance of microbial consortia for PAH degradation in the plant rhizosphere. The study reported here characterized cultivable pyrene degrading rhizoplane microbial communities from two different plant species using a root printing technique on agar plates. Colonies were revealed by formation of clearing zones on medium containing a thin film of pyrene on the surface of a mineral nutrient agar. Prints of the rhizoplane colonies were obtained from roots of Melilotus officinalis (sweet yellow clover) and Andropogon gerardii (big bluestem) plants. Phylogenetic characterizations of selected pyrene degrading colonies were assessed by PCR-DGGE and DNA sequencing. Results showed that different populations of cultivable pyrene degraders were obtained from representative consortia that were examined. Many of the PAH degrading consortia consisted of mixtures of bacterial species that were unable to degrade pyrene by themselves. While this study focused on culturable PAH degraders, the results suggest that pyrene degradation in the rhizosphere commonly involves the activity of bacterial consortia in which various species of bacteria interact to achieve PAH degradation.     

Assessment of microbial diversity in the rhizosphere of Pinus roxburghii (Sarg.) and bio‐inoculant potential of selected pine bacterial isolates for wheat varieties based on cultureindependent and culture‐dependent techniques

• Evidence is lacking regarding compatibility of pine bacteria as bio‐inoculants for crops. The diversity and abundance of rhizosphere bacteria of Pinus roxburghii has never been investigated with simultaneous application of culture‐dependent and culture‐independent techniques. The present study was aimed to isolate, characterise, check the bio‐inoculant potential of pine bacteria and assess rhizosphere bacterial diversity using culture‐independent advanced approaches.
• Forty bacteria isolated from the rhizoplane of P. roxburghii growing in a cold climate at high altitude in Murree, were morphologically characterised; nine were identified by 16S rRNA sequence analyses and used in experiments. Diversity and abundance of the 16S rRNA gene and nif H gene in the rhizosphere was assessed by cloning, RFLP analysis, 454‐amplicon pyrosequencing and qPCR.
• The bacterial isolates significantly improved dry weight of shoot, root, root area, IAA and GA₃ content, number of grains plant^?1, weight of grains plant^?1 in wheat varieties Chakwal‐50 and Fareed‐06 under axenic and field conditions. The number of 16S rRNA sequences (2979) identified by pyrosequencing shared similarity with 13 phyla of bacteria and archaea.
• The results confirm the existence of diverse bacteria of agricultural and industrial importance in the rhizosphere and compatibility of rhizoplane bacteria as bio‐inoculants for wheat varieties.

     

Bacterial origin and community composition in the barley phytosphere as a function of habitat and presowing conditions

An understanding of the factors influencing colonization of the rhizosphere is essential for improved establishment of biocontrol agents. The aim of this study was to determine the origin and composition of bacterial communities in the developing barley (Hordeum vulgare) phytosphere, using denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes amplified from extracted DNA. Discrete community compositions were identified in the endorhizosphere, rhizoplane, and rhizosphere soil of plants grown in an agricultural soil for up to 36 days. Cluster analysis revealed that DGGE profiles of the rhizoplane more closely resembled those in the soil than the profiles found in the root tissue or on the seed, suggesting that rhizoplane bacteria primarily originated from the surrounding soil. No change in bacterial community composition was observed in relation to plant age. Pregermination of the seeds for up to 6 days improved the survival of seed-associated bacteria on roots grown in soil, but only in the upper, nongrowing part of the rhizoplane. The potential occurrence of skewed PCR amplification was examined, and only minor cases of PCR bias for mixtures of two different DNA samples were observed, even when one of the samples contained plant DNA. The results demonstrate the application of culture-independent, molecular techniques in assessment of rhizosphere bacterial populations and the importance of the indigenous soil population in colonization of the rhizosphere.