James J. Germida

Distribution of microbial biomass and its activity in different soil aggregate size classes as affected by cultivation

Abstract Cultivation is known to influence the organic matter status and structural stability of soil. We investigated the effects of 69 yr of cultivation on the nature, distribution and activity of microbial biomass (MB) in different aggregate size classes of an Orthic Brown Chernozemic soil. Cultivation decreased MB content, its activity and enzyme activity in soil. Microaggregate (

Phosphate-solubilizing rhizobacteria enhance the growth and yield but not phosphorus uptake of canola (Brassica napus L.)

Abstract The ability of phosphate-solubilizing rhizobacteria to enhance the growth and phosphorus uptake of canola (Brassica napus L., cv. Legend) was studied in potted soil experiments in the growth chamber. One hundred and eleven bacteria isolated from the rhizosphere of field-grown plants, and a collection of nine bacteria known to be effective plant growth-promoting rhizobacteria (PGPR), were screened for P-solubilization in vitro. All rhizobacteria were identified using whole-cell fatty acids methyl ester (FAME) profiles. The best P-solubilizing isolates were two Bacillus brevis strains, B. megaterium, B. polymyxa, B. sphaericus, B. thuringiensis, and Xanthomonas maltophilia (PGPR strain R85). The P-solubilizers were tested for their effects on growth and P-uptake of canola plants in a P-deficient soil amended with rock phosphate. Although some of the P-solubilizing rhizobacteria significantly increased plant height or pod yield, none increased P-uptake. The most effective inoculant was a B. thuringiensis isolate which significantly increased the number and weight of pods and seed yield without rock phosphate. Xanthomonas maltophilia increased plant height, whereas the other bacilli increased the number on weight of pods. These results demonstrate the potential use of these P-solubilizing rhizobacteria as inoculants for canola, but indicate that P-solubilization was not the main mechanism responsible for positive growth response.

Changes in microbial community composition and function during a polyaromatic hydrocarbon phytoremediation field trial.

ABSTRACT The purpose of this study was to investigate the mechanism by which phytoremediation systems promote hydrocarbon degradation in soil. The composition and degradation capacity of the bulk soil microbial community during the phytoremediation of soil contaminated with aged hydrocarbons was assessed. In the bulk soil, the level of catabolic genes involved in hydrocarbon degradation (ndoB, alkB, and xylE) as well as the mineralization of hexadecane and phenanthrene was higher in planted treatment cells than in treatment cells with no plants. There was no detectable shift in the 16S ribosomal DNA (rDNA) composition of the bulk soil community between treatments, but there were plant-specific and -selective effects on specific catabolic gene prevalence. Tall Fescue (Festuca arundinacea) increased the prevalence of ndoB, alkB, and xylE as well as naphthalene mineralization in rhizosphere soil compared to that in bulk soil. In contrast, Rose Clover (Trifolium hirtum) decreased catabolic gene prevalence and naphthalene mineralization in rhizosphere soil. The results demonstrated that phytoremediation systems increase the catabolic potential of rhizosphere soil by altering the functional composition of the microbial community. This change in composition was not detectable by 16S rDNA but was linked to specific functional genotypes with relevance to petroleum hydrocarbon degradation.

Seasonal Changes in the Rhizosphere Microbial Communities Associated with Field-Grown Genetically Modified Canola (Brassica napus)

ABSTRACT The introduction of transgenic plants into agricultural ecosystems has raised the question of the ecological impact of these plants on nontarget organisms, such as soil bacteria. Although differences in both the genetic structure and the metabolic function of the microbial communities associated with some transgenic plant lines have been established, it remains to be seen whether these differences have an ecological impact on the soil microbial communities. We conducted a 2-year, multiple-site field study in which rhizosphere samples associated with a transgenic canola variety and a conventional canola variety were sampled at six times throughout the growing season. The objectives of this study were to identify differences between the rhizosphere microbial community associated with the transgenic plants and the rhizosphere microbial community associated with the conventional canola plants and to determine whether the differences were permanent or depended on the presence of the plant. Community-level physiological profiles, fatty acid methyl ester profiles, and terminal amplified ribosomal DNA restriction analysis profiles of rhizosphere microbial communities were compared to the profiles of the microbial community associated with an unplanted, fallow field plot. Principal-component analysis showed that there was variation in the microbial community associated with both canola variety and growth season. Importantly, while differences between the microbial communities associated with the transgenic plant variety were observed at several times throughout the growing season, all analyses indicated that when the microbial communities were assessed after winter, there were no differences between microbial communities from field plots that contained harvested transgenic canola plants and microbial communities from field plots that did not contain plants during the field season. Hence, the changes in the microbial community structure associated with genetically modified plants were temporary and did not persist into the next field season.

Growth promotion of winter wheat by fluorescent pseudomonads under field conditions

Abstract The ability of some pseudomonad strains to promote growth and yield of winter wheat was assessed at field sites during 1988 and 1989. The Kernen and Hagen sites were located on Dark Brown Chernozemic and Orthic Black Chernozemic soils, respectively. Plants were inoculated either by injecting a bacterial suspension into the rhizosphere of 250-day old plants in the spring (1988 study) or by soaking seeds in a bacterial suspension prior to fall planting (1989 study). Resistance to rifampicin and nalidixic acid (Rif r Nal r ) was used to differentiate introduced pseudomonads from indigenous soil bacteria. Pseudomonad inoculants injected into a rhizosphere produced winter wheat grain yields 1.05-2.08 times the control, but these increases were not significant due to variability between field plot replicates. The Rif r Nai r inoculant P. cepacia MR85 resulted in the highest number of tillers and increased dry weight of seeds by 1.53- and 2.08-fold at the 1988 Hagen and Kernen sites, respectively. When used as seed inoculants P, cepacia R85 and P. putida R105 stimulated ( P r Nal r inoculants, P. cepacia MR85 and P. putida MR111 significantly ( P P 4 –10 8 cfu g −1 of roots. Our results show that these pseudomonad inoculants colonized winter wheat roots and survived in the rhizosphere, even overwinter. Although the ability of these strains to promote winter wheat growth under field conditions varied from site-to-site during the 2 yr study, the consistent trend for some strains (e.g. R85 or MR85) to increase plant yields demonstrates the potential of these PGPR as field inoculants.

Taxonomic and functional diversity of pseudomonads isolated from the roots of field-grown canola

Among the most important rhizosphere bacteria are the pseudomonads, which are aggressive colonizers and utilize a wide range of substrates as carbon sources. The objective of this study was to determine if the taxonomic or metabolic diversity of pseudomonads differed among field-grown canola cultivars. Bacteria (n=2257) were isolated from the rhizosphere and root interior of six cultivars of field-grown canola, including three transgenic varieties. The bacteria were identified by fatty acid methyl ester (FAME) analysis, and about 35% were identified as Pseudomonas species. The most abundant species were Pseudomonas putida and Pseudomonas chlororaphis. Dendrograms based on FAME analysis revealed that many pseudomonad strains were found in all of the canola cultivars. Pseudomonads of the same strain were found in both the rhizosphere and the root interior of canola plants, suggesting that endophytic bacteria were a subset of the rhizosphere community. Because metabolic profiling provides more useful information than taxonomy, P. putida and P. chlororaphis isolates were characterized for their ability to utilize carbon substrates and produce several enzymes. Bacteria isolated from different plant cultivars had different carbon utilization profiles, but when only carbon substrates found in root exudates were analyzed, the cultivar effect was less pronounced. These characterizations also demonstrated that bacteria that were determined by FAME to be the same strain were metabolically different, suggesting functional redundancy among Pseudomonas isolates. The results of this study suggest that pseudomonads were functionally diverse. They differed in their metabolic potential among the canola cultivars from which they were isolated. Because bacteria capable of using many substrates can effectively adapt to new environments, these results have implications for the use of pseudomonads as biofertilizers, biological control agents and plant growth-promoting bacteria in canola.

Plant growth-promoting rhizobacteria alter rooting patterns and arbuscular mycorrhizal fungi colonization of field-grown spring wheat

The impact of plant growth-promoting rhizobacteria (PGPR) inoculants on the growth, yield and interactions of spring wheat with arbuscular mycorrhizal fungi (AMF) was assessed in field studies. The pseudomonad inoculants P. cepacia R55, R85, P. aeruginosa R80, P. fluorescens R92 and P. putida R104, which enhance growth and yield of winter wheat, were applied at a rate of ca. 107–108 cfu seed-1 and plots established on pea stubble or summer fallow at two different sites in Saskatchewan. Plant shoot and root biomass, yield and AMF colonization were determined at four intervals. Plant growth responses were variable and dependent on the inoculant strain, harvest date and growth parameter evaluated. Significant increases or decreases were measured at different intervals but these were usually transient and final seed yield was not significantly affected. Harvest index was consistently increased by all pseudomonad inoculants; responses to strain R55 and R104 were significant. Root biomass to 60 cm depth was not significantly affected by inoculants except strain R104, which significantly reduced root dry weight. However, root distribution, root length and AMF colonization of roots within the soil profile to 60 cm were significantly altered by inoculants. Most of these responses were reductions in the assessed parameter and occurred at depths below 15 cm; however, strains R85 and R92 significantly increased root dry weight in the 0- to 15-cm zone. These results indicate that some PGPR inoculants may adversely affect mutualistic associations between plants and indigenous soil microorganisms, and suggest a possible reason as to why spring wheat growth was not consistently enhanced by these pseudomonad PGPR.

Response of lentil under controlled conditions to co-inoculation with arbuscular mycorrhizal fungi and rhizobia varying in efficacy

This study assessed the co-inoculation response of lentil (Lens culinaris cv. Laird) to arbuscular mycorrhizal fungi (AMF) and effective and ineffective Rhizobium leguminosarum bv. viceae strains. Plants were inoculated with the AMF species Glomus clarum NT4 or G. mosseae NT6 and/or nine Rhizobium strains varying in efficacy, and grown for 110 d in soil containing indigenous AMF and rhizobia. The effectiveness of the Rhizobium strains on the N nutrition of 6-week-old lentil grown under gnotobiotic conditions was correlated (P<0.045; r=0.64) with the N nutrition of 110-d-old lentil grown in natural soil. The growth and yield responses of lentil to co-inoculation with AMF and Rhizobium strains depended on the particular AMF-Rhizobium strain combination. In some cases, the productivity of lentil inoculated with an effective Rhizobium strain was significantly (P<0.05) reduced by an apparently incompatible AMF species compared to the Rhizobium treatment. In contrast, the yield of lentil inoculated with some ineffective Rhizobium strains was significantly (P<0.05) enhanced by an apparently compatible AMF species compared to the Rhizobium treatment. However, maximum lentil productivity was achieved only in treatments with effective Rhizobium strains or co-inoculation treatments with effective Rhizobium strains and a compatible AMF species. Correlation analyses indicated that total shoot dry matter production was significantly (P<0.05) correlated with the total shoot N (P<0.0001; r=0.94) and P content (P<0.0001; r=0.96), indicating that this response was mediated by enhanced N and P nutrition. Furthermore, a (P<0.05) positive relationship between AMF colonization of roots and total shoot dry matter production (P<0.0187; r=0.43), N (P<0.0116; r=0.45) and P content (P<0.0183; r=0.43) of shoots was also noted. Our results suggest that synergistic interactions between AMF and Rhizobium strains can enhance lentil productivity.

Growth promotion of winter wheat by fluorescent pseudomonads under growth chamber conditions

Abstract The efficacy of Pseudomonas cepacia R85, P. putida R104 and R105, and P. fluorescens R111 and their rifampicin-nalidixic acid resistant (Rifr Nalr) counterparts to enhance the growth of winter wheat (Triticum aestivum L. var Norstar) was assessed in two soils under simulated fall conditions (at 5°C) in a growth chamber. Bacterial colonization and survival on wheat roots, and the effects of inoculation on plant yield, total-P, total-Fe and 15N-uptake from fertilizer were determined. Introduced Rifr Nalr pseudomonads colonized and survived on the plant roots throughout the 150-day study. Some wild-type and their Rifr Nalr mutants enhanced early plant biomass of winter wheat in a low-fertility Dark Brown Chernozemic soil, whereas grain yield was enhanced by 46–75% in a more fertile Ortho Black Chemozemic soil. Inoculation also affected the uptake of fertilizer N and soil Fe by winter wheat in both soils. Our results show that some fluorescent pseudomonads and their Rifr Nalr mutants stimulated growth and nutrient uptake of vernalized winter wheat, although the response to inoculation was dependent on soil characteristics. The use of Rifr Nalr marked bacteria allowed root colonization and population dynamics of inoculants in the rhizosphere of winter wheat to be studied, and may facilitate plant-inoculant studies under field conditions.

Phytoremediation of Organic Contaminants in Soil and Groundwater

Phytoremediation is an emerging technology for the clean-up of sites contaminated with hazardous chemicals. The term phytoremediation refers to a number of technologies that use photoautotrophic vascular plants for the remediation of sites contaminated with inorganic and organic contaminants. Phytoremediation of organic contaminants can be organized by considering 1) the green liver concept, which elucidates the metabolism of contaminants in planta versus that of contaminants ex planta (e.g. rhizosphere), 2) processes that lead to complete degradation (mineralization) of contaminants as opposed to those that only lead to partial degradation or transformation, and 3) active plant uptake versus passive processes (e.g. sorption). Understanding of these processes needs an interdisciplinary approach involving chemists, biologists, soil scientists, and environmentalists. This Review presents the basic concepts of phytoremediation of organic contaminants in soil and groundwater using selected contaminants as examples.