Bacterial communities of the rhizosphere and endorhiza associated with field-grown cucumber plants inoculated with a plant growth-promoting rhizobacterium or its genetically modified derivative

Editing Metabolism, Sex, and Microbiome: How Can We Help Poplar Resist Pathogens?

Poplar (Populus) is a genus of woody plants of great economic value. Due to the growing economic importance of poplar, there is a need to ensure its stable growth by increasing its resistance to pathogens. Genetic engineering can create organisms with improved traits faster than traditional methods, and with the development of CRISPR/Cas-based genome editing systems, scientists have a new highly effective tool for creating valuable genotypes. In this review, we summarize the latest research data on poplar diseases, the biology of their pathogens and how these plants resist pathogens. In the final section, we propose to plant male or mixed poplar populations; consider the genes of the MLO group, transcription factors of the WRKY and MYB families and defensive proteins BbChit1, LJAMP2, MsrA2 and PtDef as the most promising targets for genetic engineering; and also pay attention to the possibility of microbiome engineering.

Transgenesis and Genome Engineering: A Historical Review

Our ability to modify DNA molecules and to introduce them into mammalian cells or embryos almost appears in parallel, starting from the 1970s of the last century. Genetic engineering techniques rapidly developed between 1970 and 1980. In contrast, robust procedures to microinject or introduce DNA constructs into individuals did not take off until 1980 and evolved during the following two decades. For some years, it was only possible to add transgenes, de novo, of different formats, including artificial chromosomes, in a variety of vertebrate species or to introduce specific mutations essentially in mice, thanks to the gene-targeting methods by homologous recombination approaches using mouse embryonic stem (ES) cells. Eventually, genome-editing tools brought the possibility to add or inactivate DNA sequences, at specific sites, at will, irrespective of the animal species involved. Together with a variety of additional techniques, this chapter will summarize the milestones in the transgenesis and genome engineering fields from the 1970s to date.

Isolation and characterization of endophytic bacteria from tomato foliage and their in vitro efficacy against root-knot nematodes

Fifteen endophytic bacteria were isolated from leaves and stems of Solanum lycopersicum and Solanum pimpinellifolium collected from different locations of the Jorhat district of Assam and characterized by morphological, cultural, biochemical and molecular approaches. An in vitro study was carried out to evaluate their potentiality as biological control agents against second stage juvenile of the root-knot nematode, Meloidogyne incognita race2. Thirty second stage juveniles (J₂) of M. incognita race 2 were exposed to cell free culture filtrates of all the 15 bacterial endophytes in a sterile cavity block at a concentration of S(100%), S/2(50%), S/4(25%), S/6(17%) and S/10(10%) for a duration of 6, 12, 24, and 48 hr. The results revealed that all the isolates had the potentiality to significantly increase the mortality of the second stage juveniles (J₂). The percent mortality was directly proportional to the duration of exposure time and the concentration of the culture filtrate. The isolate BETL2 showed the best result with 81.47% mortality of juveniles followed by isolates BETL4 (81.43%), BETLI (79.07%), BETS2 (78.87%), and BETL6 (78.17%). The 16S rRNA sequence amplification results indicated that these isolates were Bacillus marisflavi (BETL2), Bacillus altitudinis (BETL4), Microbacterium arborescens (BETL1), Exiguobacterium indicum (BETS2), and Bacillus marisflavi (BETL6). The four most efficient isolates were structurally analyzed using a scanning electron microscope and this revealed that the length and breadth of isolates—BETLI, BETL2, BETL4, and BETS2 were 701.70 nm × 348.30 nm, 954.10 nm × 303.10 nm, 984.10 nm × 332.90 nm and 1422.00 nm × 742.00 nm, respectively. The result of the present study indicated that the above four novel strains of endophytic bacterial isolates enhance the mortality of J₂ of M. incognita race2 and has the potentiality as biological control agents against M. incognita.

Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights

Bacillus subtilis is a model gram-positive bacterium, commonly used to explore questions across bacterial cell biology and for industrial uses. To enable greater understanding and control of proteins in B. subtilis, here we report broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons. We use these systems to achieve click-labelling, photo-crosslinking, and translational titration. These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression, validate a predicted protein-protein binding interface, and begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo. We expect that the establishment of this simple and easily accessible chemical biology system in B. subtilis will help uncover an abundance of biological insights and aid genetic code expansion in other organisms.

Culturable Bacterial Endophytes From Sedimentary Humic Acid-Treated Plants

The global decrease in soil fertility leads to a new agricultural scenario where eco-friendly solutions play an important role. The plant growth promotion through the use of microbes, especially endophytes and rhizosphere microbiota, has been proposed as a useful solution. Several studies have shown that humic substances are suitable vehicles for the inoculation of plant growth promoting bacteria, and that this combination has an enhanced effect on the stimulation of plant development. In this work, cucumber plants grown hydroponically have been pre-treated with a sedimentary humic acid (SHA) with known plant growth-enhancing effects, and culturable bacterial endophytes have been isolated from these plants. The hypothesis was that this pre-treatment with SHA could lead to the isolation of certain endophytic taxa whose proliferation within the plant could have been promoted as a result of the effects of the treatment with SHA, and that could eventually reinforce a potential synergistic effect of a combined application of those endophytic bacteria and SHA. The culturable endophytes that have been isolated from humic acid-treated cucumber plants have been identified as members of four main phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Isolates were characterized according to the following plant growth-promoting traits: nitrogen fixation/scavenging, phosphate solubilization, siderophore production and plant hormone production. Most of the isolates were able to fix/scavenge nitrogen and to produce plant hormones (indole-3-acetic acid and several cytokinins), whereas few isolates were able to solubilize phosphate and/or produce siderophores. The most promising endophyte isolates for its use in futures investigations as plant growth-promoting bacterial inocula were Pseudomonas sp. strains (that showed all traits), Sphingomonas sp., Stenotrophomonas sp. strains, or some Arthrobacter sp. and Microbacterium sp. isolates.

Putative Nitrogen-Fixing Bacteria Associated With the Rhizosphere and Root Endosphere of Wheat Plants Grown in an Andisol From Southern Chile

Acidic ash derived volcanic soils (Andisols) support 50% of cereal production in Chile. Nitrogen (N) is essential for cereal crops and commonly added as urea with consequent environmental concerns due to leaching. Despite the relevance of N to plant growth, few studies have focused on understanding the application, management and ecological role of N2-fixing bacterial populations as tool for improve the N nutrition of cereal crops in Chile. It is known that N2-fixing bacteria commonly inhabits diverse plant compartments (e.g., rhizosphere and root endosphere) where they can supply N for plant growth. Here, we used culture-independent and dependent approaches to characterize and compare the putative N2-fixing bacteria associated with the rhizosphere and root endosphere of wheat plants grown in an Andisol from southern Chile. Our results showed significantly greater bacterial loads in the rhizosphere than the root endosphere. Quantitative PCR results indicated that the copy number of the 16S rRNA gene ranged from 1012~1013 and 107~108 g-1 sample in rhizosphere and root endosphere, respectively. The nifH gene copy number ranged from 105~106 and 105 g-1 sample in rhizosphere and root endosphere, respectively. The total culturable bacteria number ranged from 109~1010 and 107~108 CFU g-1 sample in rhizosphere and 104~105 and 104 CFU g-1 sample in root endosphere using LB and NM-1 media, respectively. Indirect counts of putative N2-fixing bacteria were 103 and 102~103 CFU g-1 sample in rhizosphere and root endosphere using NFb medium, respectively. Sequencing of 16S rRNA genes from randomly selected putative N2-fixing bacteria revealed the presence of members of Proteobacteria (Bosea and Roseomonas), Actinobacteria (Georgenia, Mycobacterium, Microbacterium, Leifsonia, and Arthrobacter), Bacteroidetes (Chitinophaga) and Firmicutes (Bacillus and Psychrobacillus) taxa. Differences in 16S rRNA and putative nifH-containing bacterial communities between rhizosphere and root endosphere were shown by denaturing gradient gel electrophoresis (DGGE). This study shows a compartmentalization between rhizosphere and root endosphere for both the abundance and diversity of total (16S rRNA) and putative N2-fixing bacterial communities on wheat plants grown in Chilean Andisols. This information can be relevant for the design and application of agronomic strategies to enhance sustainable N-utilization in cereal crops in Chile.

Putative Nitrogen-Fixing Bacteria Associated With the Rhizosphere and Root Endosphere of Wheat Plants Grown in an Andisol From Southern Chile

Acidic ash derived volcanic soils (Andisols) support 50% of cereal production in Chile. Nitrogen (N) is essential for cereal crops and commonly added as urea with consequent environmental concerns due to leaching. Despite the relevance of N to plant growth, few studies have focused on understanding the application, management and ecological role of N₂-fixing bacterial populations as tool for improve the N nutrition of cereal crops in Chile. It is known that N₂-fixing bacteria commonly inhabits diverse plant compartments (e.g., rhizosphere and root endosphere) where they can supply N for plant growth. Here, we used culture-independent and dependent approaches to characterize and compare the putative N₂-fixing bacteria associated with the rhizosphere and root endosphere of wheat plants grown in an Andisol from southern Chile. Our results showed significantly greater bacterial loads in the rhizosphere than the root endosphere. Quantitative PCR results indicated that the copy number of the 16S rRNA gene ranged from 10¹²~10¹³ and 10⁷~10⁸ g^-1 sample in rhizosphere and root endosphere, respectively. The nifH gene copy number ranged from 10⁵~10⁶ and 10⁵ g^-1 sample in rhizosphere and root endosphere, respectively. The total culturable bacteria number ranged from 10⁹~10¹⁰ and 10⁷~10⁸ CFU g^-1 sample in rhizosphere and 10⁴~10⁵ and 10⁴ CFU g^-1 sample in root endosphere using LB and NM-1 media, respectively. Indirect counts of putative N₂-fixing bacteria were 10³ and 10²~10³ CFU g^-1 sample in rhizosphere and root endosphere using NFb medium, respectively. Sequencing of 16S rRNA genes from randomly selected putative N₂-fixing bacteria revealed the presence of members of Proteobacteria (Bosea and Roseomonas), Actinobacteria (Georgenia, Mycobacterium, Microbacterium, Leifsonia, and Arthrobacter), Bacteroidetes (Chitinophaga) and Firmicutes (Bacillus and Psychrobacillus) taxa. Differences in 16S rRNA and putative nifH-containing bacterial communities between rhizosphere and root endosphere were shown by denaturing gradient gel electrophoresis (DGGE). This study shows a compartmentalization between rhizosphere and root endosphere for both the abundance and diversity of total (16S rRNA) and putative N₂-fixing bacterial communities on wheat plants grown in Chilean Andisols. This information can be relevant for the design and application of agronomic strategies to enhance sustainable N-utilization in cereal crops in Chile.

Does nature make provision for backups in the modification of bacterial community structures?

Self-balancing is an inherent character in nature in response to community structure modification pressure and modern biotechnology has revolutionized the way such detections are made. Presented here is an overview of the forces and process interactions between released bacteria and indigenous microflora which encompass soil bacterial diversity, community structure, indigenous endorhizosphere micro-organisms, molecular detection methodologies, and transgenic plants and microbes. Issues of soil bacterial diversity and community structure as well as the interpretation of results from various findings are highlighted and discussed as inferred from research articles. An understanding of the factors influencing bio-inoculant modification of bacterial community structure in the colonization of the rhizosphere is essential for improved establishment of biocontrol agents, and is critically reviewed.

Inoculating Helianthus annuus (sunflower) grown in zinc and cadmium contaminated soils with plant growth promoting bacteria--effects on phytoremediation strategies

Plant growth promoting bacteria (PGPR) may help reducing the toxicity of heavy metals to plants in polluted environments. In this work the effects of inoculating metal resistant and plant growth promoting bacterial strains on the growth of Helianthus annuus grown in Zn and Cd spiked soils were assessed. The PGPR strains Ralstonia eutropha (B1) and Chrysiobacterium humi (B2) reduced losses of weight in metal exposed plants and induced changes in metal bioaccumulation and bioconcentration - with strain B2 decreasing up to 67% Zn accumulation and by 20% Zn bioconcentration factor (BCF) in the shoots, up to 64% Zn uptake and 38% Zn BCF in the roots, and up to 27% Cd uptake and 27% Cd BCF in plant roots. The impact of inoculation on the bacterial communities in the rhizosphere of the plant was also assessed. Bacterial community diversity decreased with increasing levels of metal contamination in the soil, but in rhizosphere soil of plants inoculated with the PGPR strains, a higher bacterial diversity was kept throughout the experimental period. Inoculation of sunflower, particularly with C. humi (B2), appears to be an effective way of enhancing the short term stabilization potential of the plant in metal contaminated land, lowering losses in plant biomass and decreasing aboveground tissue contamination.

Endophytic bacteria in the rice plant

Endophytic bacteria are defined as bacteria detected inside surface-sterilized plants or extracted from inside plants and having no visibly harmful effects on the plants. Various kinds of endophytic bacteria, such as Pantoea, Methylobacterium, Azospirillum, Herbaspirillum, Burkholderia and Rhizobium etc., have been found inside rice plants. This minireview summarizes and discusses recent studies of endophytic bacteria residing in rice plants, focusing on flora, origin, movement, and interaction with plants/other microbes and referring to endophytes in other plants. The findings concerning bacterial flora obtained by cultural and non-cultural methods are also compared and discussed. Some attempts to apply endophytes to the rice plant and the resultant effects are introduced. The future perspective to deepen the study of endophytes in terms of both application and basic science is considered.

Genome sequence of the plant growth promoting endophytic bacterium Enterobacter sp. 638

Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpaxdeltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT-PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to improve establishment and sustainable production of poplar as an energy feedstock on marginal, non-agricultural soils using endophytic bacteria as growth promoting agents.

Contrasting patterns of seed and root colonization by bacteria from the genus Chryseobacterium and from the family Oxalobacteraceae

Microbial colonization of plant seeds and roots is a highly complex process in which soil and plant type can influence the composition of the root-associated and rhizosphere microbial communities. Amendment of compost, a common agricultural technique, introduces exogenous nutrients and microorganisms to the soil-plant environment, and can further influence microbial community composition in the plant environment. Although compost amendments can strongly influence soil and rhizosphere microbial communities, there is evidence that with increasing proximity to the root, plant influences predominate over soil effects. We hypothesized that the 'rhizosphere effect' observed with proximity to plant surfaces does not act equally on all microorganisms. To explore this issue, we examined two bacterial taxa that reproducibly colonized seed and root surfaces in an experiment examining the influence of compost amendment on plant-associated bacterial communities. Population-specific analyses revealed striking differences in the ecology of bacteria from the genus Chryseobacterium and the family Oxalobacteraceae in potting mix and plant-associated environments. Seed- and root-colonizing Oxalobacteraceae populations were highly sensitive to plant effects, and phylogenetic analyses of root-colonizing Oxalobacteraceae revealed the presence of root-associated populations that were highly similar, regardless of treatment, and differed from the potting mix populations detected at the same sampling points. Conversely, Chryseobacterium community composition was found to be essentially invariant within treatments, but was strongly influenced by compost amendment. This persistence and stable nature of the Chryseobacterium community composition demonstrates that rhizosphere selection is not the exclusive factor involved in determining the composition of the cucumber spermosphere and rhizosphere communities.

Culturable leaf-associated bacteria on tomato plants and their potential as biological control agents

Culturable leaf-associated bacteria inhabiting a plant have been considered as promising biological control agent (BCA) candidates because they can survive on the plant. We investigated the relationship between bacterial groups of culturable leaf-associated bacteria on greenhouse- and field-grown tomato leaves and their antifungal activities against tomato diseases in vitro and in vivo. In addition, the isolated bacteria were analyzed for N-acyl-homoserine lactone (AHL) and indole-3-acetic acid (IAA) production, which have been reported to associate with bacterial colonization, and resistance to a tomato alkaloid (alpha-tomatine). Leaf washings and subsequent leaf macerates were used to estimate the population size of epiphytic and more internal bacteria. Bacterial population sizes on leaves at the same position increased as the leaves aged under both greenhouse and field conditions. Field-grown tomatoes had significantly larger population sizes than greenhouse-grown tomatoes. Analysis of 16S rRNA gene (rDNA) sequencing using 887 culturable leaf-associated bacteria revealed a predominance of the Bacillus and Pseudomonas culturable leaf-associated bacterial groups on greenhouse- and field-grown tomatoes, respectively. Curtobacterium and Sphingomonas were frequently recovered from both locations. From the 2138 bacterial strains tested, we selected several strains having in vitro antifungal activity against three fungal pathogens of tomato: Botrytis cinerea, Fulvia fulva, and Alternaria solani. Among bacterial strains with strong in vitro antifungal activities, Bacillus and Pantoea tended to show strong antifungal activities, whereas Curtobacterium and Sphingomonas were not effective. The results indicated the differences in antifungal activity among predominant bacterial groups. Analysis of alpha-tomatine resistance revealed that most bacterial strains in the dominant groups exhibited moderate or high resistance to alpha-tomatine in growth medium. Furthermore, some Sphingomonas and Pantoea strains showed AHL and IAA production activities. Strain 125NP12 (Pantoea ananatis) showed particular alpha-tomatine resistance, and AHL and IAA production had the highest protective value (91.7) against gray mold. Thus, the differences of these physiological properties among dominant bacteria may be associated with the disease suppression ability of BCAs on tomato plants.

Succession of bacterial communities during early plant development: transition from seed to root and effect of compost amendment

Compost amendments to soils and potting mixes are routinely applied to improve soil fertility and plant growth and health. These amendments, which contain high levels of organic matter and microbial cells, can influence microbial communities associated with plants grown in such soils. The purpose of this study was to follow the bacterial community compositions of seed and subsequent root surfaces in the presence and absence of compost in the potting mix. The bacterial community compositions of potting mixes, seed, and root surfaces sampled at three stages of plant growth were analyzed via general and newly developed Bacteroidetes-specific, PCR-denaturing gradient gel electrophoresis methodologies. These analyses revealed that seed surfaces were colonized primarily by populations detected in the initial potting mixes, many of which were not detected in subsequent root analyses. The most persistent bacterial populations detected in this study belonged to the genus Chryseobacterium (Bacteroidetes) and the family Oxalobacteraceae (Betaproteobacteria). The patterns of colonization by populations within these taxa differed significantly and may reflect differences in the physiology of these organisms. Overall, analyses of bacterial community composition revealed a surprising prevalence and diversity of Bacteroidetes in all treatments.

Defining the genetic differences between wild and domestic strains of Bacillus subtilis that affect poly-gamma-dl-glutamic acid production and biofilm formation

Biofilms are communities of microbial cells that are encased in a self-produced, polymeric matrix and are adherent to a surface. For several species of bacteria, an enhanced ability to form biofilms has been linked with an increased capability to produce exopolymers. To identify exopolymers of Bacillus subtilis that can contribute to biofilm formation, we transferred the genetic determinants that control exopolymer production from a wild, exopolymer-positive strain to a domesticated, exopolymer-negative strain. Mapping these genetic determinants led to the identification of gamma-poly-dl-glutamic acid (gamma-PGA) as an exopolymer that increases biofilm formation, possibly through enhancing cell-surface interactions. Production of gamma-PGA by Bacillus subtilis was known to be dependent on the two-component regulator ComPA; this study highlighted the additional dependence on the DegS-DegU, DegQ and SwrA regulator proteins. The inability of the domestic strain of B. subtilis to produce gamma-PGA was mapped to two base pairs; a single base pair change in the promoter region of degQ and a single base pair insertion in the coding region of swrA. Introduction of alleles of degQ and swrA from the wild strain into the domestic strain was sufficient to allow gamma-PGA production. In addition to controlling gamma-PGA production, ComPA and DegSU were also shown to activate biofilm formation through an as yet undefined pathway. The identification of these regulators as affecting gamma-PGA production and biofilm formation suggests that these processes are regulated by osmolarity, high cell density and phase variation.

Microbial diversity in soil: selection microbial populations by plant and soil type and implications for disease suppressiveness

An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats. The extent of the diversity of microorganisms in soil is seen to be critical to the maintenance of soil health and quality, as a wide range of microorganisms is involved in important soil functions. This review focuses on recent data relating how plant type, soil type, and soil management regime affect the microbial diversity of soil and the implication for the soil's disease suppressiveness. The two main drivers of soil microbial community structure, i.e., plant type and soil type, are thought to exert their function in a complex manner. We propose that the fact that in some situations the soil and in others the plant type is the key factor determining soil microbial diversity is related to the complexity of the microbial interactions in soil, including interactions between microorganisms and soil and microorganisms and plants. A conceptual framework, based on the relative strengths of the shaping forces exerted by plant and soil versus the ecological behavior of microorganisms, is proposed.

Microbial biodiversity: approaches to experimental design and hypothesis testing in primary scientific literature from 1975 to 1999

Research interest in microbial biodiversity over the past 25 years has increased markedly as microbiologists have become interested in the significance of biodiversity for ecological processes and as the industrial, medical, and agricultural applications of this diversity have evolved. One major challenge for studies of microbial habitats is how to account for the diversity of extremely large and heterogeneous populations with samples that represent only a very small fraction of these populations. This review presents an analysis of the way in which the field of microbial biodiversity has exploited sampling, experimental design, and the process of hypothesis testing to meet this challenge. This review is based on a systematic analysis of 753 publications randomly sampled from the primary scientific literature from 1975 to 1999 concerning the microbial biodiversity of eight habitats related to water, soil, plants, and food. These publications illustrate a dominant and growing interest in questions concerning the effect of specific environmental factors on microbial biodiversity, the spatial and temporal heterogeneity of this biodiversity, and quantitative measures of population structure for most of the habitats covered here. Nevertheless, our analysis reveals that descriptions of sampling strategies or other information concerning the representativeness of the sample are often missing from publications, that there is very limited use of statistical tests of hypotheses, and that only a very few publications report the results of multiple independent tests of hypotheses. Examples are cited of different approaches and constraints to experimental design and hypothesis testing in studies of microbial biodiversity. To prompt a more rigorous approach to unambiguous evaluation of the impact of microbial biodiversity on ecological processes, we present guidelines for reporting information about experimental design, sampling strategies, and analyses of results in publications concerning microbial biodiversity.

Genetically modified bacteria in agriculture

Certain bacteria isolated from soils possess properties that allow them to exert beneficial effects on plants either by enhancing crop nutrition or by reducing damages caused by pathogens or pests. Some of them, such as rhizobia, azospirilla, and agrobacteria, have been traditionally released in fields as seed inoculants and they often lead to increases in the yield of different crops while the application of others, such as pseudomonads, often fails to give the expected results. Bacteria genetically modified to be easily traceable and/or to be improved in their expression of beneficial traits have been constructed and released with plants in a number of experimental field plots. With these releases, it has been possible to monitor the modified inoculant bacteria after their introduction in field ecosystems and to assess their impact on the resident microflora. Local environmental factors appeared as playing a crucial role in the survival and persistence of bacteria once released in fields and in the expression of the beneficial traits whether improved or not. The spread of inoculant bacteria from their point of dissemination was limited. Transient shifts in favour of the released bacteria and in disfavour of some members of the bacterial and fungal populations present in the plant rhizosphere might occur with certain released bacteria. The changes observed were, however, less important than those observed under usual agricultural practices. Gene transfer from resident population to introduced bacteria was detected in one case. The transconjugants were found only transiently in the phytosphere of plants but not in soils. No differences between the survival, spread, persistence in field and ecological impacts of genetically modified bacteria and of the corresponding unmodified parent strain could be detected.

Potential for misidentification of a spore-forming Paenibacillus polymyxa isolate as an endophyte by using culture-based methods

While Paenibacillus polymyxa strain Pw-2 has been identified as an endophyte of lodgepole pine (M. Shishido, B. M. Loeb, and C. P. Chanway, Can. J. Microbiol. 41:707-713, 1995), P. polymyxa strain L6 has not, a distinction that could be explained by the differential abilities of these isolates to form spores, rather than the differential abilities to colonize the interior tissues of lodgepole pine. Chemical disinfection was used to destroy bacteria on the root exterior, but bacterial endospores are known for their ability to withstand chemical disinfection, and strain Pw-2 was found to produce 300 to 11,000 times more germinating endospores than strain L6 under the experimental conditions used by Shishido et al. (Can. J. Microbiol. 41:707-713, 1995). Attempts to identify strain Pw-2 within lodgepole pine root tissues by using confocal microscopy techniques failed. We discuss the possibility that spore-forming bacteria can be mistakenly identified as endophytes when culture-based methods alone are used.

Impact of 2,4-diacetylphloroglucinol-producing biocontrol strain Pseudomonas fluorescens F113 on intraspecific diversity of resident culturable fluorescent pseudomonads associated with the roots of field-grown sugar beet seedlings

The impact of the 2,4-diacetylphloroglucinol-producing biocontrol agent Pseudomonas fluorescens F113Rif on the diversity of the resident community of culturable fluorescent pseudomonads associated with the roots of field-grown sugar beet seedlings was evaluated. At 19 days after sowing, the seed inoculant F113Rif had replaced some of the resident culturable fluorescent pseudomonads at the rhizoplane but had no effect on the number of these bacteria in the rhizosphere. A total of 498 isolates of resident fluorescent pseudomonads were obtained and characterized by molecular means at the level of broad phylogenetic groups (by amplified ribosomal DNA restriction analysis) and at the strain level (with random amplified polymorphic DNA markers) as well as phenotypically (55 physiological tests). The introduced pseudomonad induced a major shift in the composition of the resident culturable fluorescent Pseudomonas community, as the percentage of rhizoplane isolates capable of growing on three carbon substrates (erythritol, adonitol, and L-tryptophan) not assimilated by the inoculant was increased from less than 10% to more than 40%. However, the pseudomonads selected did not display enhanced resistance to 2,4-diacetylphloroglucinol. The shift in the resident populations, which was spatially limited to the surface of the root (i.e., the rhizoplane), took place without affecting the relative proportions of phylogenetic groups or the high level of strain diversity of the resident culturable fluorescent Pseudomonas community. These results suggest that the root-associated Pseudomonas community of sugar beet seedlings is resilient to the perturbation that may be caused by a taxonomically related inoculant.

Impact of biocontrol Pseudomonas fluorescens CHA0 and a genetically modified derivative on the diversity of culturable fungi in the cucumber rhizosphere

Little is known about the effects of Pseudomonas biocontrol inoculants on nontarget rhizosphere fungi. This issue was addressed using the biocontrol agent Pseudomonas fluorescens CHA0-Rif, which produces the antimicrobial polyketides 2,4-diacetylphloroglucinol (Phl) and pyoluteorin (Plt) and protects cucumber from several fungal pathogens, including Pythium spp., as well as the genetically modified derivative CHA0-Rif(pME3424). Strain CHA0-Rif(pME3424) overproduces Phl and Plt and displays improved biocontrol efficacy compared with CHA0-Rif. Cucumber was grown repeatedly in the same soil, which was left uninoculated, was inoculated with CHA0-Rif or CHA0-Rif(pME3424), or was treated with the fungicide metalaxyl (Ridomil). Treatments were applied to soil at the start of each 32-day-long cucumber growth cycle, and their effects on the diversity of the rhizosphere populations of culturable fungi were assessed at the end of the first and fifth cycles. Over 11,000 colonies were studied and assigned to 105 fungal species (plus several sterile morphotypes). The most frequently isolated fungal species (mainly belonging to the genera Paecilomyces, Phialocephala, Fusarium, Gliocladium, Penicillium, Mortierella, Verticillium, Trichoderma, Staphylotrichum, Coniothyrium, Cylindrocarpon, Myrothecium, and Monocillium) were common in the four treatments, and no fungal species was totally suppressed or found exclusively following one particular treatment. However, in each of the two growth cycles studied, significant differences were found between treatments (e.g., between the control and the other treatments and/or between the two inoculation treatments) using discriminant analysis. Despite these differences in the composition and/or relative abundance of species in the fungal community, treatments had no effect on species diversity indices, and species abundance distributions fit the truncated lognormal function in most cases. In addition, the impact of treatments at the 32-day mark of either growth cycle was smaller than the effect of growing cucumber repeatedly in the same soil.

Structure and Colonization Dynamics of Epiphytic Bacterial Communities and of Selected Component Strains on Tomato (Lycopersicon esculentum) Leaves

The sizes and compositions of bacterial populations found on leaves of greenhouse and field grown tomato plants were studied by dilution plating, fatty acid methyl ester analysis (FAME), and BIOLOG plates of isolates in pure cultures. In the greenhouse, overhead-irrigated plants sustained higher microbial populations (up to 105 cfu g-1) than soil-irrigated plants (103 cfu g-1). Strains isolated from overhead-irrigated plants grown in a vegetable garden (n = 216) and from greenhouse-grown plants (n = 114) were subjected to FAME analysis. Similarly, strains from soil-irrigated field-grown plants (n = 83) were identified using BIOLOG plates. In each case, populations were dominated by a few genera. When concentrated phyllosphere washes (CPW) were sprayed on greenhouse-grown, soil-irrigated plants, leaf bacterial populations of more than 105 CFU g-1 were sustained for 4 days; sterile buffer-sprayed leaves sustained less than 104 CFU g-1. No significant enrichment of any strain isolated from the sprayed leaves could be detected by FAME identification of randomly selected colonies. However, when recurring leaf saprophytic species (both Gram-positive and Gram-negative) isolated from these experiments and from plants grown outdoors were tested for epiphytic colonization under stressful conditions, all could still be detected at various levels up to 4 days after inoculation, indicating differential epiphytic fitness. The non-epiphytic bacteria Escherichia coli and Azospirillum brasilense disappeared from the leaf surface within the same experimental period.