Diversity of pseudomonads isolated from three different plant rhizospheres

Genome Analysis of Pseudomonas fluorescens PCL1751: A Rhizobacterium that Controls Root Diseases and Alleviates Salt Stress for Its Plant Host

Pseudomonas fluorescens PCL1751 is a rod-shaped Gram-negative bacterium isolated from the rhizosphere of a greenhouse-grown tomato plant in Uzbekistan. It controls several plant root diseases caused by Fusarium fungi through the mechanism of competition for nutrients and niches (CNN). This mechanism does not rely on the production of antibiotics, so it avoids the concerns of resistance development and is environmentally safe. Additionally, this bacterium promotes plant growth by alleviating salt stress for its plant host. To investigate the genetic mechanisms that may explain these observations, we determined the complete genome sequence of this bacterium, examined its gene content, and performed comparative genomics analysis with other Pseudomonas strains. The genome of P. fluorescens PCL1751 consisted of one circular chromosome that is 6,143,950 base-pairs (bp) in size; no plasmid was found. The annotation included 19 rRNA, 70 tRNA, and 5,534 protein-coding genes. The gene content analysis identified a large number of genes involved in chemotaxis and motility, colonization of the rhizosphere, siderophore biosynthesis, and osmoprotectant production. In contrast, the pathways involved in the biosynthesis of phytohormones or antibiotics were not found. Comparison with other Pseudomonas genomes revealed extensive variations in their genome size and gene content. The presence and absence of secretion system genes were highly variable. As expected, the synteny conservation among strains decreased as a function of phylogenetic divergence. The integration of prophages appeared to be an important driver for genome rearrangements. The whole-genome gene content analysis of this plant growth-promoting rhizobacterium (PGPR) provided some genetic explanations to its phenotypic characteristics. The extensive and versatile substrate utilization pathways, together with the presence of many genes involved in competitive root colonization, provided further support for the finding that this strain achieves biological control of pathogens through effective competition for nutrients and niches.

Changes in the soil bacterial communities in a cedar plantation invaded by moso bamboo

Moso bamboo is fast-growing and negatively allelopathic to neighboring plants. However, there is little information on the effects of its establishment and expansion to adjacent forest soil communities. To better understand the impacts of bamboo invasion on soil communities, the phylogenetic structure and diversity of the soil bacterial communities in moso bamboo forest, adjacent Japanese cedar plantation, and bamboo-invaded transition zone were examined using a combination of 16S rRNA gene clone libraries and bar-coded pyrosequencing techniques. Based on the number of operational taxonomic units (OTUs), Shannon diversity index, Chao1 estimator, and rarefaction analysis of both techniques, the bamboo soil bacterial community was the most diverse, followed by the transition zone, with the cedar plantation possessing the lowest diversity. The results from both techniques revealed that the Acidobacteria and Proteobacteria predominated in the three communities, though the relative abundance was different. The 250 most abundant OTUs represented about 70% of the total sequences found by pyrosequencing. Most of these OTUs were found in all three soil communities, demonstrating the overall similarity among the bacterial communities. Nonmetric multidimensional scaling analysis showed further that the bamboo and transition soil communities were more similar with each other than the cedar soils. These results suggest that bamboo invasion to the adjacent cedar plantation gradually increased the bacterial diversity and changed the soil community. In addition, while the 10 most abundant OTUs were distributed worldwide, related sequences were not abundant in soils from outside the forest studied here. This result may be an indication of the uniqueness of this region.

Genetic and functional heterogeneities among fluorescent Pseudomonas isolated from environmental samples

Fluorescent Pseudomonas from diverse environmental samples including wastes were identified and screened for the solubilization of tricalcium phosphate, indole-3-acetic acid (IAA), production and inhibition of extracellular N-acylhomoserine lactone (AHLs) and characterized for their siderophores. Genotypic analysis by amplified rDNA restriction analysis (ARDRA) and BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) typing resulted respectively in 14 ARDRA types and 24 different BOX-types with diverse incidence among the analyzed strains. Based on 16S rRNA sequence analysis the isolates were assigned to P. aeruginosa, P. otitidis, P. plecoglossicida, P. mosselii, P. monteilii, P. koreensis, P. taiwanenesis, P. frederiksbergensis and P. graminis. Of the 66 isolates, 56 (84.85%) isolates solubilized tri-calcium phosphate (TCP), 53 (80.30%) isolates produced plant growth hormone IAA, 62 (94%) produced bacteriocin and 34 (52%) isolates produced extracellular N-acylhomoserine lactone while 30 (45%) isolates were able to interfere with N-acylhomoserine lactone. Isolates were clustered into 17 siderotypes and (59)Fe cross-incorporation experiments permitted assignment of all siderotypes but two into well-defined siderovars.

Culturable bacterial community analysis in the root domains of two varieties of tree peony (Paeonia ostii)

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.

Genetic and functional diversity among the antagonistic potential fluorescent pseudomonads isolated from tea rhizosphere

Twenty-five fluorescent pseudomonads from rhizospheric soil of six tea gardens in four district of Upper Assam, India were isolated and screened for antagonistic activity against fungal pathogens such as Fusarium oxysporum f. sp. raphani (For), Fusarium oxysporum f. sp. ciceri (Foc), Fusarium semitectum (Fs), and Rhizoctonia solani (Rs); and bacterial pathogens-Staphylococcus aureus (Sa), Escherichia coli (Ec), and Klebsiella pneumoniae (Kp). Most of the isolates exhibited strong antagonistic activity against the fungal pathogens and gram-positive bacterium i.e. Staphylococcus aureus. Productions of siderophore, salicylic acid (SA), hydrogen cyanide (HCN), and cell wall-degrading enzyme (chitinase) were studied to observe the possible mechanisms of antagonistic activity of the isolates. Correlation between the antagonistic potentiality of some isolates and their levels of production of siderophore, salicylic acid, and hydrogen cyanide was observed. Out of the 25 isolates, antibiotic-coding genes, 2,4-diacetylphloroglucinol (DAPG) and pyoluteorin (PLT) were detected in the isolates, Pf12 and Pf373, respectively. Genetic diversity of these fluorescent pseudomonads were analyzed with reference to four strains of Pseudomonas fluorescens NICM 2099(T), P. aeruginosa MTCC 2582(T), P. aureofaciens NICM 2026(T), and P. syringae MTCC 673(T). 16S rDNA-RFLP analysis of these isolates using three tetra cutter restriction enzymes (HaeIII, AluI and MspI) revealed two distinct clusters. Cluster A comprised only two isolates Pf141 and 24-PfM3, and cluster B comprised 23 isolates along with four reference strains.

Effects of methamidophos on the community structure, antagonism towards Rhizoctonia solani, and phlD diversity of soil Pseudomonas

A microcosm incubation study using an aquic brown soil from northeast China (a Cambisol in the UN Food and Agriculture Organization FAO Soil Taxonomy) was conducted to examine the effects of different concentrations (0, 50, 150, and 250 mg kg(-1)) of methamidophos (O,S-dimethyl phosphoramidothioato) on Pseudomonas, one of the most important gram-negative bacteria in soil. Amplified ribosomal DNA restriction analysis (ARDRA) was performed to study the Pseudomonas community structure, an in vitro assay was made to test the antagonistic activity of isolated Pseudomonas strains against soil-borne Rhizoctonia solani, a major member of the pathogens highly related to soil-borne plant diseases, and special primer amplification and sequencing were performed to investigate the diversity of phlD, an essential gene in the biosynthesis of 2, 4-diacetylphloroglucinol (2, 4-DAPG), which has biocontrol activity in phlD(+)isolates. With exposure to increasing methamidophos concentrations, the total number of soil Pseudomonas ARDRA patterns decreased significantly, but with less change in the same treatments over 1, 3, and 5 weeks of incubation. The number of isolated Pseudomonas strains with antagonistic activity against R. solani as well as the diversity and appearance frequency of the strains' phlD gene also decreased with increasing concentrations of methamidophos, especially at high methamidophos concentrations. Applying methamidophos could increase the risk of soil-borne plant diseases by decreasing the diversity of the soil Pseudomonas community and the amount of R. solani antagonists, particularly those with the phlD gene.

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.

Stress tolerance and genetic variability of phosphate-solubilizing fluorescent Pseudomonas from the cold deserts of the trans-Himalayas

Nineteen efficient phosphate-solubilizing fluorescent Pseudomonas from the cold deserts of the trans-Himalayas were screened for stress tolerance against temperature, alkalinity, salinity, calcium salts, and desiccation. Phylogenetic analysis based on 16S rRNA gene sequencing placed these bacteria under three groups with fourteen strains in Group I including Pseudomonas trivialis and P. poae, two strains in Group II together with Pseudomonas kilonensis and P. corrugata, and three strains in Group III along with Pseudomonas jessenii and P. moraviensis. Genetic diversity assessed by ERIC and BOX-PCR revealed variability among strains belonging to the same phylogenetic groups. Cluster analysis based on the growth characteristics under regimes of different stress levels placed the strains into three distinct clusters displaying no correlation to their phylogenetic groups. Stress-tolerant strains differed in the level of decline in phosphate solubilization under increasing intensity of various stress parameters. The highest decrease occurred with 5% CaCO(3,) followed by 2.5% CaCO(3), pH 11, 5% NaCl, temperature of 37 degrees C, 40% PEG, 5% CaSO(4), 2.5% NaCl, 2.5% CaSO(4), pH 9 and temperature of 15 degrees C. Two strains belonging to Phylogenetic Group I exhibited higher phosphate solubilization at lower temperature. The results revealed that stress-tolerance ability was not limited to any particular phylogenetic group. Knowledge about the genetic variants of phosphate-solubilizing fluorescent Pseudomonas with potential for tolerance to desiccation, alkalinity, temperature, and salinity could be useful in understanding their ecological role under stressful environments of low phosphate availability.

Biodiversity of phosphate solubilizing bacteria in rhizosphere of chickpea, mustard and wheat grown in different regions of Haryana

The native population of phosphate solubilizing bacteria (PSB) was studied in the rhizosphere of chickpea, mustard and wheat grown in different regions of Haryana. A total of 193 PSB were isolated from 245 rhizospheric samples collected from south-west and north-east zones. The PSB count showed large variations (3-67 × 10(5)cfu/g) and biodiversity within the crop and place of sampling. Using biochemical analysis, the isolates were tentatively identified as belonging to four genera, Pseudomonas, Aeromonas, Klebsiella and Enterobacter. Phosphate solubilization of these isolates varied from 5.9 to 123.8% and 2.2 to 227.2 μg/ml in solid and liquid Pikovskaya's medium, respectively. Based on their morphological traits, all the isolates were placed into 20 groups, majority of them falling in the group having white, round and gummy colonies, irrespective of the crop or the region. The intrinsic antibiotic resistance pattern showed large variations among the isolates and most of the isolates were resistant to streptomycin, ampicillin and penicillin. The highest PSB number and greatest variability were found in the rhizosphere of chickpea, followed by wheat and then mustard.

Diversity and differentiation among fluorescent pseudomonads in crop rhizospheres with whole-cell protein profiles

Fluorescent pseudomonads from rhizospheres of four different crops, grown under similar soil and climatic conditions were phenotypically characterized to differentiate them into biovars. In protein electrophenogram studies of relationships among fluorescent pseudomonads by UPGMA cluster analysis based on DICE similarity index, the isolates were mainly discerned into three major clusters representing four different biovars. The biovars generally matched the delineated phenotypic clusters with the exception of a strain belonging to biovar II. However, the isolates representing similar rhizospheres and geographic locations were generally distributed into different phenotypic clusters as influenced by factors yet to be determined. The studies reinstated the importance of whole-cell protein analyses in characterizing pseudomonads and assessing their diversity.

Influence of soil reaction on diversity and antifungal activity of fluorescent pseudomonads in crop rhizospheres

The diversity and antifungal activity of fluorescent pseudomonads isolated from rhizospheres of tea, gladiolus, carnation and black gram grown in acidic soils with similar texture and climatic conditions were studied. Biochemical characterisation including antibiotic resistance assay, RAPD and PCR-RFLP studies revealed a largely homogenous population. At soil pH (5.2), the isolates exhibited growth with varying levels of siderophore production, irrespective of crop rhizospheres. Two isolates with maximum chitinase production showed antagonism. The bacterial populations in general lacked the ability to produce deleterious traits such as cellulase, pectinase and hydrogen cyanide. However, increased pH levels beyond 5.2 caused reduction in metabolite production with reduced antifungal activity. The homogeneity of the bacterial population irrespective of crop rhizospheres together with decreased secondary metabolite production at higher pH levels reinstated the importance of soil over host plant in influencing rhizosphere populations. The studies also yielded acid tolerant chitinase producing antagonistic fluorescent pseudomonads.

Selection for biocontrol bacteria antagonistic toward Rosellinia necatrix by enrichment of competitive avocado root tip colonizers

Biological control of soil-borne pathogens is frequently based on the application of antagonistic microorganisms selected solely for their ability to produce in vitro antifungal factors. The aim of this work was to select bacteria that efficiently colonize the roots of avocado plants and display antagonism towards Rosellinia necatrix, the causal agent of avocado white root rot. A high frequency of antagonistic strains (ten isolates, 24.4%) was obtained using a novel procedure based on the selection of competitive avocado root tip colonizers. Amplification and sequencing of the 16S rRNA gene, in combination with biochemical characterization, showed that eight and two of the selected isolates belonged to the genera Pseudomonas and Stenotrophomonas, respectively. Characterization of antifungal compounds produced by the antagonistic strains showed variable production of exoenzymes and HCN. Only one of these strains, Pseudomonas sp. AVO94, produced a compound that could be related to antifungal antibiotics. All of the ten selected strains showed twitching motility, a cell movement involved in competitive colonization of root tips. Production of N-acyl-homoserine lactones and indole-3-acetic acid was also reported for some of these isolates. Resistance to several bacterial antibiotics was tested, and three strains showing resistance to only one of them were selected for biocontrol assays. The three selected strains persisted in the rhizosphere of avocado plants at levels considered crucial for efficient biocontrol, 10(5)-10(6) colony forming units/g of root; two of them, Pseudomonas putida AVO102 and Pseudomonas pseudoalcaligenes AVO110, demonstrated significant protection of avocado plants against white root rot.

Identification and specific detection of a novel pseudomonadaceae cluster associated with soils from winter wheat plots of a long-term agricultural field experiment

The genus Pseudomonas (sensu stricto) represents a group of microorganisms directly involved in functions conferring plant health. We performed a study in the DOK long-term agricultural field experiment on the basis of previously published Pseudomonas-selective PCR primers in order to investigate the community structure of the microbial groups defined by the target range of these primers. Three different agricultural management systems, i.e., conventional, biodynamic, and bio-organic, along with mineral and unfertilized controls were investigated, with each system planted with either winter wheat or a grass-clover ley. Amplified small-subunit rRNA gene fragments were analyzed using the genetic profiling techniques restriction fragment length polymorphism (RFLP) and denaturing gradient gel electrophoresis (DGGE), revealing distinct differences between soils planted with winter wheat and grass clover but only minor differences between the management systems. Phylogenetic analyses of 59 clone sequences retrieved from bio-organic and unfertilized systems identified sequences related to Pseudomonas fluorescens and a novel cluster termed Cellvibrio-related Pseudomonadaceae (CRP). The CRP clones were exclusively isolated from winter wheat soil samples and were responsible for the crop-specific differences observed in RFLP and DGGE profiles. New primers were designed for the amplification of CRP targets directly from soil DNA, yielding strong signals exclusively for winter wheat soils. We concluded that crop-associated CRP exist in agricultural soils and that genetic profiling followed by specific probe design represents a valuable approach for identification as well as sensitive and rapid monitoring of novel microbial groups in the environment.

Phylogenetic diversity of fluorescent pseudomonads in agricultural soils from Korea

AIMS

To identify and compare the relative diversity and distribution of genotypes of culturable fluorescent pseudomonads from soils.

METHODS AND RESULTS

Analysis of 160 isolates from seven soil samples using randomly amplified polymorphism DNA methods revealed 53 genotypes, which were subsequently identified by their 16S ribosomal DNA sequences. Phylogenetic analyses of the 53 genotypes along with 43 fluorescent pseudomonad type strains separated the genotypes into 10 distinct clusters that included two phylogenetic groups that were not represented by previously described type strains.

CONCLUSIONS

The diversity of genotypes that was obtained from the soil samples was highly variable among the different soils and appeared to be associated with different soil management practices that also influence plant yields.

SIGNIFICANCE AND IMPACT OF THE STUDY

The identification and phylogenetic analysis of these genotypes offers opportunities for study of phenotypic traits that may be associated within taxonomically related groups of fluorescent pseudomonad species and how these groups vary in relation to soil management practices.