Colonization of the rhizosphere of crop plants by plant-beneficial pseudomonads

Profiling of antimicrobial metabolites of plant growth promoting Pseudomonas spp. isolated from different plant hosts

In this study, nine strains of Pseudomonas au rantiaca and P. chlororaphis, and two isolates of Pseudomonas sp.: At1RP4 and RS-1, were characterized for the in-vitro production of secondary metabolites in LB, DMB, and King's B media, and of the genes responsible for the production of antagonistic metabolites. Based on 16S rRNA gene sequence, isolates At1RP4 and RS-1 were identified as strains of P. aeruginosa and P. fluorescens. Five phenazine derivatives comprising phenazine, phenazine-1-carboxylic acid (PCA), 2-hydroxyphenazine-1-carboxylic acid (2-OH-Phz-1-COOH), phenazine-1,6-dicarboxylic acid (Phz-1,6-di-COOH), and 2-hydroxyphenazine (2-OH-Phz) were produced by all strains in all three culture media including DMB, King's B and LB. However, 2,8-dihydroxyphenazine, 6-methylphenazine-1-carboxylic acid, pyrrolnitrin, and the ortho-dialkyl-aromatic acids, were produced by the P. aurantiaca and P. chlororaphis strains. In addition, all strains produced 2-acetamidophenol, pyochelin, and diketopiperazine derivatives in variable amounts in all three culture media used. Highest levels of quorum-sensing signal molecules including PQS, 2-Octyl-3-hydroxy-4(1H)-quinolone, and hexahydro-quinoxaline-1,4-dioxide were recorded for P. aeruginosa At1RP4. Moreover, all strains produced volatile hydrogen cyanide (0.95-6.68 µg/L) and the phytohormone indole-3-acetic acid (0.42-13.9 µM). Production of extracellular lipase and protease was recorded in all pseudomonads, whereas, cellulase production and phosphate solubilization were variable. Genes for hydrogen cyanide and phenazine-1-carboxylic acid were detected in all eleven strains while the gene for pyrrolnitrin biosynthesis was amplified in P. aurantiaca and P. chlororaphis strains. Comparative metabolomic analysis provided detailed insights about the strain-specific metabolites in pseudomonads, and their pseudo-relative quantification in different bacterial growth media to be used as single-strain biofertilizer and biocontrol inoculums.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02585-8.

An alternative biocontrol agent of soil-borne phytopathogens: A new antifungal compound produced by a plant growth promoting bacterium isolated from North Algeria

Bacteria isolated from different environments can be exploited for biocontrol purposes by the identification of the molecules involved in the antifungal activity. The present study was aimed at investigating antifungal protein compounds purified from a previously identified plant growth promoting bacterium, Pseudomonas protegens N isolated from agricultural land in northern Algeria. Therefore, a novel protein was purified by chromatographic and ultrafiltration steps and its antifungal activity together with growth-inhibition mechanism was evaluated against different fungi by plate-based assays. In addition, stereomicroscopy and transmission electron microscopy (TEM) was performed to explore the inhibition activity of the compound on spore germination processes. The protein, showing a molecular mass of about 100 kDa under native conditions, was revealed to be in the surface-membrane fraction and displayed an efficient activity against a variety of phytopathogenic fungi, being Alternaria the best target towards which it exhibited a marked fungicidal action and inhibition of spore germination. Moreover, the compound was able to significantly decrease fungal infection on tomato fruits producing also morphological aberrations on conidia. The obtained results suggested that the isolated compound could represent a promising agent for eco-friendly management of plant pathogens in agriculture.

Antibacterial activity of antagonistic bacterium Bacillus subtilis DJM-51 against phytopathogenic Clavibacter michiganense subsp. michiganense ATCC 7429 in vitro

To investigate antibacterial activity against the tomato pathogen Clavibacter michiganense subsp. michiganense ATCC 7429 (Cmm ATCC 7429), Bacillus subtilis DJM-51 was isolated from rhizosphere soil. For isolation of bacteria, samples were taken from rhizosphere soil. The isolate, DJA-51, had strong antagonistic ability against Tomato pathogen Cmm ATCC 7429 on nutrient-broth yeast extract agar (NBYA) as indicated by inhibition zones around colonies. On the basis of the nucleotide sequence of a conserved segment of the 16S rRNA gene, the bacterium has been identified as B. subtilis DJM-51. The growth of Cmm ATCC 7429 on NBYA plates was inhibited by culture broth of B. subtilis DJM-51 including cells, by the supernatant of culture broth of B. subtilis DJM-51, and by the liquid material resulting from butanol extract of bacterial cultures. The OD value in co-culture mixture was lower than the control throughout the entire incubation period. Antibiotics obtained from B. subtilis DJM-51 inhibited the growth of Tomato pathogen Cmm ATCC 7429. These results provide potentially information about the protection of tomato from pathogen Cmm ATCC 7429 under greenhouse conditions in Quebec.

Characterizing the mode of action of Brevibacillus laterosporus B4 for control of bacterial brown strip of rice caused by A. avenae subsp. avenae RS-1

Biological control efficacy of Brevibacillus laterosporus B4 associated with rice rhizosphere was assessed against bacterial brown stripe of rice caused by Acidovorex avenae subsp. avenae. A biochemical bactericide (chitosan) was used as positive control in this experiment. Result of in vitro analysis indicated that B. laterosporus B4 and its culture filtrates (70%; v/v) exhibited low inhibitory effects than chitosan (5 mg/ml). However, culture suspension of B. laterosporus B4 prepared in 1% saline solution presented significant ability to control bacterial brown stripe in vivo. Bacterization of rice seeds for 24 h yielded a greater response (71.9%) for controlling brown stripe in vivo than chitosan (56%). Studies on mechanisms revealed that B. laterosporus B4 suppressed the biofilm formation and severely disrupted cell membrane integrity of A. avenae subsp. avenae, causing the leakage of intracellular substances. In addition, the expression level of virulence-related genes in pathogen recovered from biocontrol-agent-treated plants showed that the genes responsible for biofilm formation, motility, niche adaptation, membrane functionality and virulence of A. avenae subsp. avenae were down-regulated by B. laterosporus B4 treatment. The biocontrol activity of B. laterosporus B4 was attributed to a substance with protein nature. This protein nature was shown by using ammonium sulfate precipitation and subsequent treatment with protease. The results obtained from this study showed the potential effectiveness of B. laterosporus B4 as biocontrol agent in control of bacterial brown stripe of rice.

Screening of Rhizobacteria for Their Plant Growth Promotion Ability and Antagonism Against Damping off and Root Rot Diseases of Broad Bean (Vicia faba L.)

Development of microbial inoculants from rhizobacterial isolates with potential for plant growth promotion and root disease suppression require rigorous screening. Fifty-four (54) fluorescent pseudomonads, out of a large collection of rhizobacteria from broad bean fields of 20 different locations within Imphal valley of Manipur, were initially screened for antifungal activity against Macrophomina phaseolina and Rhizoctonia solani, of diseased roots of broad bean and also three other reference fungal pathogens of plant roots. Fifteen fluorescent pseudomonas isolates produced inhibition zone (8-29 mm) of the fungal growth in dual plate assay and IAA like substances (24.1-66.7 μg/ml) and soluble P (12.7-56.80 μg/ml) in broth culture. Among the isolates, RFP 36 caused a marked increase in seed germination, seedling biomass and control of the root borne pathogens of broad bean. PCR-RAPD analysis of these isolates along with five MTCC reference fluorescent pseudomonas strains indicated that the RFP-36 belonged to a distinct cluster and the PCR of its genomic DNA with antibiotic specific primers Phenazine-1-carboxylic acid and 2, 4-diacetyl phloroglucinol suggested possible occurrence of gene for the potent antibiotics. Overall, the result of the study indicated the potential of the isolate RFP 36 as a microbial inoculant with multiple functions for broad bean.

Bio-control and plant growth promotion potential of siderophore producing endophytic Streptomyces from Azadirachta indica A. Juss

Three endophytic actinomycetes strains recovered from surface sterilized root tissues of Azadirachta indica A. Juss. (Meliaceae), plants were selected through tests for their potential as bio-control and plant growth promoting agents. It was also observed that the seed treated with the spore suspension of three selected strains of Streptomyces, significantly promoted plant growth and antagonized the growth of Alternaria alternata, causal agent of early blight disease in tomato plant. It was observed that the three selected strains prolifically produce IAA and siderophores that play vital role in promotion of plant growth and in suppression of Alternaria alternata. Interestingly, Streptomyces strain AzR-051 produced the highest amount of IAA at 13.73 μmol ml(-1) , compared to strains AzR-049 and AzR-010 9.22 μmol ml(-1) and 10.43 μmol ml(-1) respectively. It also produces siderophores higher than the other two strains. Thus these endophytic isolates have the potential as plant growth promoters as well as a bio-control agent, which is a useful trait for crop production in nutrient deficient soils.

Evaluation of Seed and Soil Treatments with Novel Bacillus subtilis Strains for Control of Soybean Root Rot Caused by Fusarium oxysporum and F. graminearum

Fusarium root rot is an important disease of soybean in Ontario, Canada. This study is to select antagonistic bacterial agents as effective alternatives to chemical pesticides for the control of root rots caused by Fusarium oxysporum and F. graminearum. Twenty-two Bacillus subtilis strains from soybean and corn roots were tested in dual cultures for inhibition of mycelial growth of F. oxysporum and F. graminearum. All strains significantly reduced mycelial growth of F. oxysporum by approximately 17 to 48% and of F. graminearum by 10 to 32%. Ten B. subtilis strains selected based on their larger fungal inhibition zones were evaluated against macroconidial germination. These strains inhibited the spore germination of F. oxysporum by 20 to 48% and of F. graminearum by 14 to 32% in cell-free filtrates. Under greenhouse conditions, the efficacy of seed and soil treatments with B. subtilis strains against the two Fusarium root rot pathogens was evaluated based on root rot severity, seedling emergence, plant height, and root dry weight. Six B. subtilis strains (SB01, SB04, SB23, SB24, SB28, and SB33) from soybean roots and two strains (CB01 and CH22) from corn roots significantly reduced the severity of the two Fusarium root rots in seed or soil treatments. Strains SB01, SB04, SB23, and SB24 were the most effective treatments against both pathogens in either seed or soil treatment. When applied as seed treatments, these four strains reduced root rot severity by 43 to 63% and increased emergence by 13 to 17%, plant height by 9 to 18%, and root dry weight by 8.4 to 19%. When used as soil treatments, they reduced root rot severity by 68 to 74% and increased emergence by 14 to 18%, plant height by 11 to 23%, and root dry weight by 16 to 24%. These results suggest that the novel strains of B. subtilis identified in this research can be effective alternatives to fungicides in managing Fusarium root rots of soybean, and a greater level of efficacy may be achieved when they were used as soil treatments than seed treatments.

Rhizosphere Bacterial Signalling: A Love Parade Beneath Our Feet

Plant roots support the growth and activities of a wide variety of microorganisms that may have a profound effect on the growth and/or health of plants. Among these microorganisms, a high diversity of bacteria have been identified and categorized as deleterious, beneficial, or neutral with respect to the plant. The beneficial bacteria, termed plant growth-promoting rhizobacteria (PGPR), are widely studied by microbiologists and agronomists because of their potential in plant production. Azospirillum, a genus of versatile PGPR, is able to enhance the plant growth and yield of a wide range of economically important crops in different soils and climatic regions. Plant beneficial effects of Azospirillum have mainly been attributed to the production of phytohormones, nitrate reduction, and nitrogen fixation, which have been subject of extensive research throughout the years. These elaborate studies made Azospirillum one of the best-characterized genera of PGPR. However, the genetic and molecular determinants involved in the initial interaction between Azospirillum and plant roots are not yet fully understood. This review will mainly highlight the current knowledge on Azospirillum plant root interactions, in the context of preceding and ongoing research on the association between plants and plant growth-promoting rhizobacteria.

Behavior and fate of chlorpyrifos introduced into soil-crop systems by irrigation

The effect of chlorpyrifos added in irrigation water to a red soil from Central South China on the growth of wheat and oilseed rape seedlings, together with its uptake, was studied in a pot experiment. Addition of chlorpyrifos (1-10 microg g-1) in a single irrigation with distilled water resulted in absorption of chlorpyrifos by wheat (0.257-4.50 microg g-1) and also oilseed rape seedlings (0.249-2.02 microg g-1) during 20 d of plant growth. An initial concentration of chlorpyrifos in soil that is equivalent to or below 10 microg g-1 did not significantly influence the growth of wheat seedlings. Similarly, an initial concentration equivalent to or below 5 microg g-1 did not significantly influence the growth of oilseed rape seedlings. The degradation rate of chlorpyrifos was 1.4-4.2 times larger in oilseed rape rhizosphere soil than in unvegetated soil. The numbers of bacteria and fungi in oilseed rape rhizosphere soil were 3.18 times and 1.84 times larger, respectively, than those in unvegetated soil. This helps to explain the difference in degradation rates obtained.

Biocontrol of avocado dematophora root rot by antagonistic Pseudomonas fluorescens PCL1606 correlates with the production of 2-hexyl 5-propyl resorcinol

A collection of 905 bacterial isolates from the rhizospheres of healthy avocado trees was obtained and screened for antagonistic activity against Dematophora necatrix, the cause of avocado Dematophora root rot (also called white root rot). A set of eight strains was selected on the basis of growth inhibitory activity against D. necatrix and several other important soilborne phytopathogenic fungi. After typing of these strains, they were classified as belonging to Pseudomonas chlororaphis, Pseudomonas fluorescens, and Pseudomonas putida. The eight antagonistic Pseudomonas spp. were analyzed for their secretion of hydrogen cyanide, hydrolytic enzymes, and antifungal metabolites. P. chlororaphis strains produced the antibiotic phenazine-1-carboxylic acid and phenazine-1-carboxamide. Upon testing the biocontrol ability of these strains in a newly developed avocado-D. necatrix test system and in a tomato-F oxysporum test system, it became apparent that P. fluorescens PCL1606 exhibited the highest biocontrol ability. The major antifungal activity produced by strain P. fluorescens PCL1606 did not correspond to any of the major classes of antifungal antibiotics produced by Pseudomonas biocontrol strains. This compound was purified and subsequently identified as 2-hexyl 5-propyl resorcinol (HPR). To study the role of HPR in biocontrol activity, two Tn5 mutants of P. fluorescens PCL1606 impaired in antagonistic activity were selected. These mutants were shown to impair HRP production and showed a decrease in biocontrol activity. As far as we know, this is the first report of a Pseudomonas biocontrol strain that produces HPR in which the production of this compound correlates with its biocontrol activity.

Involvement of nitrate reductase and pyoverdine in competitiveness of Pseudomonas fluorescens strain C7R12 in soil

Involvement of nitrate reductase and pyoverdine in the competitiveness of the biocontrol strain Pseudomonas fluorescens C7R12 was determined, under gnotobiotic conditions, in two soil compartments (bulk and rhizosphere soil), with the soil being kept at two different values of matric potential (-1 and -10 kPa). Three mutants affected in the synthesis of either the nitrate reductase (Nar(-)), the pyoverdine (Pvd(-)), or both (Nar(-) Pvd(-)) were used. The Nar(-) and Nar(-) Pvd(-) mutants were obtained by site-directed mutagenesis of the wild-type strain and of the Pvd(-) mutant, respectively. The selective advantage given by nitrate reductase and pyoverdine to the wild-type strain was assessed by measuring the dynamic of each mutant-to-total-inoculant (wild-type strain plus mutant) ratio. All three mutants showed a lower competitiveness than the wild-type strain, indicating that both nitrate reductase and pyoverdine are involved in the fitness of P. fluorescens C7R12. The double mutant presented the lowest competitiveness. Overall, the competitive advantages given to C7R12 by nitrate reductase and pyoverdine were similar. However, the selective advantage given by nitrate reductase was more strongly expressed under conditions of lower aeration (-1 kPa). In contrast, the selective advantage given by nitrate reductase and pyoverdine did not differ in bulk and rhizosphere soil, indicating that these bacterial traits are not specifically involved in the rhizosphere competence but rather in the saprophytic ability of C7R12 in soil environments.

Growth interactions during bacterial colonization of seedling rootlets

Rootlet elongation and bacterial growth on rootlets were determined after inoculation of cucumber and spinach seedlings with Pseudomonas strains differing in production of siderophores and HCN. Siderophore producers grew more profusely than nonproducers on both species and promoted rootlet elongation on cucumber. Coinoculation of siderophore producers and nonproducers resulted in restricted growth of the latter. The total populations of nonproducers of HCN in the presence of HCN producers were not decreased, but the tenacity of their association with the rootlet surface was altered.

Microbial interactions and biocontrol in the rhizosphere

The loss of organic material from the roots provides the energy for the development of active microbial populations in the rhizosphere around the root. Generally, saproptrophs or biotrophs such as mycorrhizal fungi grow in the rhizosphere in response to this carbon loss, but plant pathogens may also develop and infect a susceptible host, resulting in disease. This review examines the microbial interactions that can take place in the rhizosphere and that are involved in biological disease control. The interactions of bacteria used as biocontrol agents of bacterial and fungal plant pathogens, and fungi used as biocontrol agents of protozoan, bacterial and fungal plant pathogens are considered. Whenever possible, modes of action involved in each type of interaction are assessed with particular emphasis on antibiosis, competition, parasitism, and induced resistance. The significance of plant growth promotion and rhizosphere competence in biocontrol is also considered. Multiple microbial interactions involving bacteria and fungi in the rhizosphere are shown to provide enhanced biocontrol in many cases in comparison with biocontrol agents used singly. The extreme complexity of interactions that can occur in the rhizosphere is highlighted and some potential areas for future research in this area are discussed briefly.

Fitness in soil and rhizosphere of Pseudomonas fluorescens C7R12 compared with a C7R12 mutant affected in pyoverdine synthesis and uptake

Fluorescent pseudomonads have evolved an efficient strategy of iron uptake based on the synthesis of the siderophore pyoverdine and its relevant outer membrane receptor. The possible implication of pyoverdine synthesis and uptake on the ecological competence of a model strain (Pseudomonas fluorescens C7R12) in soil habitats was evaluated using a pyoverdine minus mutant (PL1) obtained by random insertion of the transposon Tn5. The Tn5 flanking DNA was amplified by inverse PCR and sequenced. The nucleotide sequence was found to show a high level of identity with pvsB, a pyoverdine synthetase. As expected, the mutant PL1 was significantly more susceptible to iron starvation than the wild-type strain despite its ability to produce another unknown siderophore. As with the wild-type strain, the mutant PL1 was able to incorporate the wild-type pyoverdine and five pyoverdines of foreign origin, but at a significantly lower rate despite the similarity of the outer membrane protein patterns of the two strains. The survival kinetics of the wild-type and of the pyoverdine minus mutant, in bulk and rhizosphere soil, were compared under gnotobiotic and non-gnotobiotic conditions. In gnotobiotic model systems, both strains, when inoculated separately, showed a similar survival in soil and rhizosphere, suggesting that iron was not a limiting factor. In contrast, when inoculated together, the bacterial competition was favorable to the pyoverdine producer C7R12. The efficient fitness of PL1 in the presence of the indigenous microflora, even when coinoculated with C7R12, is assumed to be related to its ability to uptake heterologous pyoverdines. Altogether, these results suggest that pyoverdine-mediated iron uptake is involved in the ecological competence of the strain P. fluorescens C7R12.

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.

Effect of field inoculation with Sinorhizobium meliloti L33 on the composition of bacterial communities in rhizospheres of a target plant (Medicago sativa) and a non-target plant (Chenopodium album)-linking of 16S rRNA gene-based single-strand conformation polymorphism community profiles to the diversity of cultivated bacteria

Fourteen weeks after field release of luciferase gene-tagged Sinorhizobium meliloti L33 in field plots seeded with Medicago sativa, we found that the inoculant also occurred in bulk soil from noninoculated control plots. In rhizospheres of M. sativa plants, S. meliloti L33 could be detected in noninoculated plots 12 weeks after inoculation, indicating that growth in the rhizosphere preceded spread into bulk soil. To determine whether inoculation affected bacterial diversity, 1,119 bacteria were isolated from the rhizospheres of M. sativa and Chenopodium album, which was the dominant weed in the field plots. Amplified ribosomal DNA restriction analysis (ARDRA) revealed plant-specific fragment size frequencies. Dominant ARDRA groups were identified by 16S rRNA gene nucleotide sequencing. Database comparisons indicated that the rhizospheres contained members of the Proteobacteria (alpha, beta, and gamma subgroups), members of the Cytophaga-Flavobacterium group, and gram-positive bacteria with high G+C DNA contents. The levels of many groups were affected by the plant species and, in the case of M. sativa, by inoculation. The most abundant isolates were related to Variovorax sp., Arthrobacter ramosus, and Acinetobacter calcoaceticus. In the rhizosphere of M. sativa, inoculation reduced the numbers of cells of A. calcoaceticus and members of the genus Pseudomonas and increased the number of rhizobia. Cultivation-independent PCR-single-strand conformation polymorphism (SSCP) profiles of a 16S rRNA gene region confirmed the existence of plant-specific rhizosphere communities and the effect of the inoculant. All dominant ARDRA groups except Variovorax species could be detected. On the other hand, the SSCP profiles revealed products which could not be assigned to the dominant cultured isolates, indicating that the bacterial diversity was greater than the diversity suggested by cultivation.

The establishment of an introduced community of fluorescent pseudomonads in the soil and in the rhizosphere is affected by the soil type

Indigenous populations of fluorescent pseudomonads were previously shown to vary in two different soils (Châteaurenard and Dijon) and in the rhizosphere of a plant species (Linum usitatissimum L.) cultivated in these two soils. These differences could be related to the soil type and to their crop history. In the present study, the influence of the soil type on the diversity of fluorescent pseudomonads in bulk and rhizospheric soils was evaluated. The soils of Châteaurenard and Dijon were sterilized before being inoculated with the same community of fluorescent pseudomonads. Bacterial isolates from bulk and rhizospheric soils were characterized on the basis of their repetitive extragenic palindromic-PCR patterns allowing the comparison of the distributions of the introduced populations. The influence of the soil type on the establishment of the introduced bacterial community was recorded in the two bulk soils. Indeed, the density and the structure of the community differed significantly between the two soils. The rhizosphere effect was also affected by the soil type. This effect was expressed in the Châteaurenard soil but not in the Dijon soil. Hence, the structure of the bacterial community associated with the roots of the same plant species cultivated in the two soils differed significantly.

Green fluorescent protein-marked Pseudomonas fluorescens: localization, viability, and activity in the natural barley rhizosphere

The gfp-tagged Pseudomonas fluorescens biocontrol strain DR54-BN14 was introduced into the barley rhizosphere. Confocal laser scanning microscopy revealed that the rhizoplane populations of DR54-BN14 on 3- to 14-day-old roots were able to form microcolonies closely associated with the indigenous bacteria and that a majority of DR54-BN14 cells appeared small and almost coccoid. Information on the viability of the inoculant was provided by a microcolony assay, while measurements of cell volume, the intensity of green fluorescent protein fluorescence, and the ratio of dividing cells to total cells were used as indicators of cellular activity. At a soil moisture close to the water-holding capacity of the soil, the activity parameters suggested that the majority of DR54-BN14 cells were starving in the rhizosphere. Nevertheless, approximately 80% of the population was either culturable or viable but nonculturable during the 3-week incubation period. No impact of root decay on viability was observed, and differences in viability or activity among DR54-BN14 cells located in different regions of the root were not apparent. In dry soil, however, the nonviable state of DR54-BN14 was predominant, suggesting that desiccation is an important abiotic regulator of cell viability.

Phylogeny, ribosomal RNA gene typing and relative abundance of new Pseudomonas species (sensu stricto) isolated from two pinyon-juniper woodland soils of the arid southwest U.S

Rhizosphere-inhabiting Pseudomonas species interact with plant roots and may be important for plant performance under stressful environmental conditions. A comparison was conducted of culturable Pseudomonas isolates associated with pinyon rhizosphere and between-tree interspace areas in a hot, dry, volcanic cinder field and an adjacent sandy loam soil, in order to identify Pseudomonas species which may be involved in pinyon pine survival under stressful conditions. From a collection of 800 isolates, eleven isolates exhibiting different colony morphology were selected for 16S ribosomal RNA gene sequencing. Phylogenetic analysis of rDNA sequences from the eleven field isolates, forty-six described Pseudomonas species, and thirty-four previously characterized environmental isolates indicated that the isolates from the cinders and sandy loam soil clustered into three groups. The field isolates were distinct from any of the named species or other environmental isolates. Oligonucleotide primer pairs that differentiated three field isolate groups were designed from the 16S rDNA sequences, and eight hundred Pseudomonas field isolates cultured from pinyon rhizospheres and interspaces in the cinders and sandy loam soils were typed into the three groups using PCR assays. The composition of Pseudomonas populations in four environments was significantly different. The relative abundance of the three rDNA-based groups appeared to be affected by both the soil type and the pinyon rhizosphere.

The composition of fluorescent pseudomonad populations associated with roots is influenced by plant and soil type

Populations of fluorescent pseudomonads isolated from an uncultivated soil and from the roots of two plant species were previously shown to differ (P. Lemanceau, T. Corberand, L. Gardan, X. Latour, G. Laguerre, J.-M. Boeufgras, and C. Alabouvette, Appl. Environ. Microbiol. 61:1004-1012, 1995). The diversities of fluorescent pseudomonads, from two uncultivated soils and from the roots of two plant species cultivated in these two soils, were compared. The phenotypic diversity of the bacterial isolates was characterized on the basis of biochemical and physiological tests and on the basis of their ability to utilize 147 different organic compounds. The genotypic diversity of the isolates was characterized on the basis of the types of 16S genes coding for rRNA (rDNA), their repetitive extragenic palindromic patterns by PCR, and plasmid profiles. Taxonomic identification of the isolates was achieved with both biochemical and physiological tests and by comparing their 16S rDNA types to those of reference and type strains of fluorescent Pseudomonas spp. Numerical analysis of phenotypic characteristics allowed the clustering of isolates that showed high levels of similarity. This analysis indicated that both soil type and host plant had an effect on the diversity of fluorescent pseudomonads. However, of the two factors studied, the soil was clearly the dominating one. Indeed, the populations associated with the roots of each plant species varied from one soil to the other. This variation could possibly be ascribed to the differences recorded between the phenotypically diverse populations of fluorescent pseudomonads from the two uncultivated soils. The plant selection was, at least partly, plant specific. It was not related to bacterial species and biovars or to the presence of plasmid DNA. The phenotypic clustering of isolates was well correlated with genotypic characterization by repetitive extragenic palindrome-PCR fingerprinting.