Influence of soil pH on the nitrate-reducing microbial populations and their potential to reduce nitrate to NO and N2O

Abstract After the introduction of Rhizobium leguminosarum biovar trifolii into natural loamy sand and silt loam, bacterial numbers increased only directly after inoculation. Thereafter, bacterial numbers decreased until an equilibrium was reached. This decrease was exponential on a log scale and could be described by the function Y = A + B − R ', where Y is the log number of rhizobial cells at time: T ; A represents the lgo of the final population size; B is the difference between the log (initial number of bacteria) and A ; R is the daily reduction factor of Y−A and t is time in days after inoculation. The final population sizes increased with increasing inoculum densities (10⁴−10⁸ bacteria/g soil). In sterilized soil, however, the populations increased up to an equilibrium, which was not affected by the inoculum density.
The final population sizes were higher in silt loam than in loamy sand in natural, as well as in sterilized soil. The final population size was reached earlier in natural silt loam than in loamy sand. Also the growth rate in sterilized soil was higher in silt loam than in loamy sand. The growth rate of low inoculum densities in silt loam was exponential and approximately the same as in yeast extract mannitol broth. The growth rate in loamy sand could be improved by incresing the bulk density of the soil from 1.0 to 1.4 g/cm³.     

Transport of bacterial inoculants through intact cores of two different soils as affected by water percolation and the presence of wheat plants

Abstract Water flow-innduced transport of Burkholderia cepacia strain P2 and Pseudomonas fluorescens strain R2f cells through intact cores of loamy sand and silt loam field soils was measured for two percolation regimes, 0.9 and 4.4 mm h⁻¹, applied daily during 1 hour. For each strain, transport was generally similar between the two water regimes. Translocation of B. cepacia , with 4.4 mm h⁻¹, did occur initially in both soils. In the loamy sand soil, no change in the bacterial distribution occurred during the experiment (51 days). In the silt loam, B. cepacia cell numbers in the lower soil layers were significantly reduced, to levels at or below the limit of detection. Transport of P. fluorescens in both soils also occurred initially and was comparable to that of B. cepacia . Later in the experiment, P. fluorescens was not detectable in the lower soil layers of the loamy sand cores, due to a large decrease in surviving cell numbers. In the silt loam, the inoculant cell distribution did not change with time. Pre-incubation of the inoculated cores before starting percolation reduced B. cepacia inoculant transport in the loamy sand soil measured after 5 days, but not that determined after 54 days. Delayed percolation in the silt loam soil affected bacterial transport only after 54 days. The presence of growing wheat plants overall enhanced bacterial translocation as compared to that in unplanted soil cores, but only with percolating water. Percolation water from silt loam cores appeared the day after the onset of percolation and often contained inoculant bacteria. With loamy sand, percolation water appeared only 5 days after the start of percolation, and no inoculant bacteria were found. The results presented aid in predicting the fate of genetically manipulated bacteria in a field experiment.     

An Ecological Study of Marked Rhizobium trifolii Strains on the Host Plant Trifolium repens var. Huai in an Acidic Peat and a Neutral Mineral Soil

An ecological study of the nodulation of Trifolium repens var. grassland Huai by genetically marked Rhizobium trifolii was carried out in two Irish soils, a neutral mineral and an acidic peat. An indigenous population of 2 x 10⁴ R. trifolii /g was found in the mineral soil. In the peat soil, 4 x 10¹ R. trifolii /g was found in the uninoculated peat. This number increased to 4.5 x 10⁵ R. trifolii /g, however, eight weeks after the peat soil was neutralized, supplemented with nutrients and sown with uninoculated clover seed. Indigenous R. trifolii strains from the mineral soil were effective whereas strains from the peat soil were ineffective on the host plant T. repens under plant room conditions. The introduced strains were inoculated on to clover seed at the rate of 1 x 10⁵ R. trifolii /seed. In the mineral soil, the introduced inoculum failed to establish at any period during the growing season. In the peat soil, the percentage establishment of the introduced inoculum varied from 40-50% of nodules selected eight weeks after sowing to 70-90% of nodules selected at the end of the growing season.     

Application of subtraction hybridization for the development of a Rhizobium leguminosarum biovar phaseoli and Rhizobium tropici group-specific DNA probe

Abstract A combined subtraction hybridization and polymerase chain reaction/amplification technique was used to develop a DNA probe which was specific for the Rhizobium leguminosarum biovar phaseoli and the Rhizobium tropici group. Total genomic DNA preparations from Rhizobium leguminosarum biovar viciae, Rhizobium leguminosarum biovar trifolii, Rhizobium sp., Agrobacterium tumefaciens, Rhizobium fredii, Bradyrhizobium japonicum, Bradyrhizobium ssp. and Rhizobium meliloti were pooled and used as subtracter DNA against total genomic DNA from the Rhizobium leguminosarum biovar phaseolo strain KIM5s. Only one round of subtraction hybridization at 65°C was necessary to remove all cross-hybridizing sequences. Dot blot hybridizations with total genomic DNA of the eight subtracter organisms and 29 bacteria of different groups confirmed the high specificity of the isolated DNA sequences. Dot blot hybridizations and total genomic DNA from ten different R. Leguminosarum biovar phaseoli and R. tropici strains resulted in strong hybridization signals for all strains tested. The DNA probe for the R. tropici and R. leguminosarum biovar phaseoli group was used for dot blot hybridization with DNA extracts from three tropical and one boreal soil. When correlated with data from Most Probable Number analyses the probe was capable of detecting as low as 3 × 10⁴ homologous indigenous rhizobia per g soil. The technique offers great benefits for the development of DNA probes for monitoring bacterial populations in environmental samples.     

The construction, detection and use of bioluminescent Rhizobium leguminosarum biovar trifolii strains

A. CRESSWELL, L. SKØT AND A.R. COOKSON. 1994. The gene encoding the firefly luciferase enzyme ( luc ) was introduced to Rhizobium leguminosarum biovar trifolii strains with a view to using the resulting bioluminescent strains to study the survival of genetically-engineered rhizobia in soil microcosms. The genetically-engineered micro-organisms (GEMs) behaved similarly to their parent strains with respect to growth rate in laboratory media and in their symbiotic performance with their host plants. No gene transfer could be detected in laboratory mating experiments. When inoculated onto a non-sterile soil the population of the GEM declined sharply from an initial cell density of 2 times 107⁷ g^-1 soil to approach a stable cell density of approximately 3 times 10² g^-1 after 150 d. Direct photography of bioluminescent rhizobia enabled the detection of colonies as small as 0.1 mm in diameter without the need for transferring colonies onto filter paper. When a Rhizobium strain carrying the luc marker on a plasmid was used as inoculant it was possible to visualize differences in colonization of the rhizosphere of white clover and ryegrass by contact print and colour transparency films. The photographic detection methods described here demonstrate the possibilities of using bioluminescent rhizobia for assessing their survival in soil, and for looking at rhizosphere populations which may be an important site for potential gene transfer.     

Rhizobial siderophore as an iron source for clover

Iron uptake by clover plants ( Trifoliuin pratense L. cv. Hruszowska) was studied using radioactive ferric iron (⁵⁵FeCl₂). As shown by autoradiography of non-infected plants, purified rhizobial siderophore isolated from Rhizobium leguminosarum by, trifolii , stimulated the uptake and shoot transport of iron. Addition of rhizobial siderophore into the growth medium of nodulated clover did not affect the iron transport to the shoots. In the absence of the rhizobial siderophore, clover infected by either nitrogen-fixing (Nod⁻ Fix⁺) or nonfixing (Nod⁺ Fix⁻) R. L. trifolii strains took up and transported into the shoots more iron than the non-infected control plants. Nodulated clover reduced Fe(III) more efficiently than the non-infected control plants.     

AUTOMATED 35S-LABELLED PROTEIN ELECTROPHORESIS FOR IDENTIFICATION OF STRAINS OF RHIZOBIUM LEGUMINOSARUM bv. TRIFOLII

A technique for strain-level identification within a Rhizobium biovar is described, based on automated sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) of ³⁵S-labelled proteins, offering substantial improvements on existing SDS-PAGE methods particularly in the areas of standardization of electrophoresis conditions and rapidity of positive identification. Gels were analysed with a β-scanner, the beta particle emission data being directly relayed to an IBM PC/AT computer for subsequent manipulation. Analysis of the total protein profiles obtained by this method revealed regions of variability between strains of R. leguminosarum bv. trifolii. Automated comparison of these regions enabled identification of strains. The method was successfully used for identifying root nodule isolates obtained from competition studies between known pairs of R. leguminosarum bv. trifolii strains inoculated onto Trifolium repens.     

Phosphoenolpyruvate carboxylase in Corynebacterium glutamicum is dispensable for growth and lysine production

Abstract The symbiotic plasmid pRHc1J and the helper plasmid pJB3JI were transferred from Rhizobium "hedysari" strain RJ77 to Agrobacterium tumefaciens strain GMI9023. Transconjugants harboured recombinant plasmids (R-prime plasmids) consisting of pJB3JI carrying DNA fragments, of different sizes, surrounding the Tn 5 mob insert in pRHc1J. Two of these R-prime plasmids (pR1 and pR2) carried nod genes and were able to restore the Nod⁺ phenotype of pSym⁻ derivatives of R. "hedysari" . The R. "hedysari" nod genes harboured by both R-primes were expressed in R. leguminosarum biovar trifolii wild-type but not in a pSym⁻ derivative.     

Identification of Rhizobium leguminosarum and Rhizobium sp. (Cicer) strains using a custom Fatty Acid Methyl Ester (FAME) profile library

The potential of using fatty acid methyl ester (FAME) profiles of Rhizobium leguminosarum bv. viceae , phaseoli and trifolii , and Rhizobium sp. ( Cicer ) strains, for the identification of unknown isolates was assessed. This was achieved by developing a Rhizobium FAME library using 16 different Rhizobium strains of Rh. leguminosarum bv. viceae ( n  ₌ 5), Rh. leguminosarum bv. phaseoli ( n  ₌ 5), Rh. leguminosarum bv. trifolii ( n  ₌ 1) and Rhizobium sp. ( Cicer ) ( n  ₌ 5). Although there were considerable differences between Rh. leguminosarum biovars and strains and Rhizobium sp. ( Cicer ) strains, the variation within a particular biovar of Rh. leguminosarum was not high. Nevertheless, the feature FAME profiles of the various groups in the library allowed 75 putative rhizobia obtained from surface-sterilized nodules of field-grown lentil and pea plants to be identified.     

A determination of protective microhabitats for bacteria introduced into soil

Abstract Survival studies with rhizobia introduced into loamy sand showed that a kaolinite amendment of the soil improved the survival of Rhizobium , and that bentonite had a very strong positive effect on rhizobial survival. The survival level was significantly higher in soil amended with 10% than with 5% bentonite. The amount of water present in the bentonite amended soil had a significant influence on rhizobial survival; in drier soil, survival levels were highest. For the loamy sand, the loamy sand amended with 5 and 10% bentonite or with 10% kaolinite, the number of rhizobial cells surviving on day 57 after introducing 2.5–5.0×10⁷ cells g⁻¹ dry soil could be described using the distribution of pores from three size classes in a mathematical relationship. Pores with necks < 3 μm and between 3 and 6 μm positively affected the survival of introduced rhizobia whereas pores with necks > 6 μm had a negative effect.     

Viable but non-culturable salmonellas in soil

P.E. TURPIN, K.A. MAYCROFT, C.L. ROWLANDS AND E.M.H. WELLINGTON. 1993. An enzyme-linked immunosorbent assay (ELISA) and a microwell fluorescent antibody (FA) direct count method have been developed for the monitoring of salmonellas in soil. Both methods have a minimum detection level of ca 10⁶ cells per gram of soil. The FA direct count method gave a linear recovery for the inoculum range 10⁶–10⁹ cells per gram of soil. When monitored by plate counts the survival of salmonellas was greater in a sterile than in a non-sterile soil. Evidence was found for the production of viable but non-culturable salmonellas in non-sterile soil; plate counts dropped rapidly with time, but FA direct counts and ELISA remained level. The salmonella cells became progressively smaller and rounder with time. Dead salmonella cells introduced into soil rapidly disappeared.     

Consumption of NO by methanotrophic bacteria in pure culture and in soil

Abstract The methanotrophs Methylomonas angile (type I) and Methylosinus trichosporium (type II) produced nitrite, nitrate and N₂O during growth on methane, apparently by heterotrophic nitrification of ammonium. The methanotrophs were also able to consume NO but did not produce it. After incubation of soil from a drained paddy field in the presence of CH₄ the numbers of methanotrophs increased from 10⁵ to 10⁷ per gram dry weigth. The thus enriched soil showed increased rates of NO consumption while rates of NO production did not change.     

Role of Microniches in Protecting Introduced Rhizobium leguminosarum biovar trifolii against Competition and Predation in Soil

The importance of microniches for the survival of introduced Rhizobium leguminosarum biovar trifolii cells was studied in sterilized and recolonized sterilized loamy sand and silt loam. The recolonized soils contained several species of soil microorganisms but were free of protozoa. Part of these soil samples was inoculated with the flagellate Bodo saltans, precultured on rhizobial cells. The introduced organisms were enumerated in different soil fractions by washing the soil, using a standardized washing procedure. With this method, free organisms and organisms associated with soil particles or aggregates >50 μm were separated. The total number of rhizobia was influenced slightly (silt loam) or not at all (loamy sand) by the recolonization with microorganisms or by the addition of flagellates alone. However, when both flagellates and microorganisms were present, numbers of rhizobia decreased drastically. This decrease was more than the sum of both effects separately. Nevertheless, populations of rhizobia were still higher than in natural soil. In the presence of flagellates, higher percentages of rhizobia and other microorganisms were associated with soil particles or aggregates >50 μm than in the absence of flagellates. In recolonized soils, however, the percentages of particle-associated rhizobia were lower than in soils not recolonized previous to inoculation. Thus, the presence of other microorganisms hindered rhizobial colonization of sites where they are normally associated with soil particles or aggregates.     

Transfer of plasmid RP4 between pseudomonads after introduction into soil; influence of spatial and temporal aspects of inoculation

Abstract Transfer of plasmid RP4 between introduced strains of Pseudomonas fluorescens was studied in 2 soils, Ede loamy sand and Guelph loam, in non-rhizosphere and rhizosphere soil using soil chambers and microcosm systems. Short-term organism survival was generally at high levels (> 10⁶/g dry soil), in both soils, whereas long-term survival was poorer, particularly in the loamy sand. Amendment of this soil with bentonite clay improved bacterial survival. Plasmid transfer between donor and recipient strains freshly introduced into separate portions of Ede loamy sand, which were subsequently mixed, was only detected in the vicinity of growing wheat roots, suggesting roots stimulate bacterial migration and/or growth. However, no transfer was detected between resident donor and recipient cell populations (introduced 48 days previously), due to poor organism survival. Plasmid transfer was detected in the rhizosphere between established, resident donor cell populations, and newly-introduced recipients, and vice-versa, in both soils. These data suggested that plant roots enhance the frequency of bacterial matings not only between organisms present in the same niches, but also between organisms from different niches, or in different conditions of stress, probably by stimulating bacterial migration and/or growth, or by providing additional surfaces for cell-to-cell contact.     

Soil types with different texture affects development of Rhizoctonia root rot of wheat seedlings

The effect of different soil textures, sandy (97.5% sand, 1.6% silt, 0.9% clay), loamy sand (77% sand, 11% silt, 12% clay) and a sandy clay loam (69% sand, 7% silt, 24% clay), on root rot of wheat caused by Rhizoctonia solani Kühn Anastomosis Group (AG) 8 was studied under glasshouse conditions. The reduction in root and shoot biomass following inoculation with AG-8 was greater in sand than in loamy sand or sandy clay loam. Dry root weight of wheat in the sand, loamy sand and sandy clay loam soils infested with AG-8 was 91%, 55% and 28% less than in control uninfested soils. There was greater moisture retention in the loamy sand and sandy clay loam soils as compared to the sand in the upper 10–20 cm. Root penetration resistance was greater in loamy sand and sandy clay loam than in sand. Root growth in the uninfested soil column was faster in the sand than in the loamy sand and sandy clay loam soils, the roots in the sandy soil being thinner than in the other two soils. Radial spread of the pathogen in these soils in seedling trays was twice as fast in the sand in comparison to the loamy sand which in turn was more than twice that in the sandy clay loam soil. There was no evidence that differences among soils in pathogenicity or soil spread of the pathogen was related to their nutrient status. This behaviour may be related to the severity of the disease in fields with sandy soils as compared to those with loam or clay soils. This revised version was published online in June 2006 with corrections to the Cover Date.     

The effect of moisture potential on growth and survival of root nodule bacteria in peat culture and on seed

Peat from three sources was dried, milled and packed separately in polyethylene bags and sterilized by irradiation. The carrier was impregnated with broth cultures of either Rhizobium leguminosarum bv. trifolii strain WU95, Bradyrhizobium japonicum strain CB1809 or B. lupini strain WU425 and sterile water to provide five moisture potentials in the range > - 1 × 10⁴ - 1 × 10⁶ Pa. The packets were stored at 26°C under conditions which restricted moisture loss. Numbers of root nodule bacteria were counted at intervals up to 12 weeks. No single moisture potential was optimum for all strains in all carriers because of a significant ( P < 0.05) interaction between moisture potential × strain × carrier × time. Where direct comparisons could be made, all strains survived best at - 1 × 10⁴ and/or −3.2 × 10⁴ Pa. Seeds of Trifolium subterraneum and polypropylene beads (used to avoid seed coat toxicity), were inoculated with WU95 prepared in two sources of peat and at each of the above moisture potentials and stored at 15°C. Seed coat toxicity significantly effected the log death rate ( k ) of WU95 on subterraneum clover seed for the period 0–0.25 d ( k 1.796) compared with k - 0.399 for polypropylene beads. In the first 24 h moisture did not affect survival but by 28 d rhizobia grown in Badenoch peat survived best at −3.2 × 10⁴ Pa. In Millicent peat, survival was equally as good at −3.2 × 10⁴ and −1 × 10⁴ Pa.     

A PCR-MPN BASED QUANTITATIVE APPROACH TO ENUMERATE NITRIFYING BACTERIA IN ZEOPONIC SUBSTRATES

Self-sustaining, regenerative life-support systems are required for long duration missions to the Moon and Mars. Improved activity of nitrifying bacteria to convert NH₄⁺ to NO₃^- has been shown to promote plant growth in zeoponic substrates. Due to physiological characteristics, such as slow growth and low yield, nitrifying bacteria are not easily enumerated by traditional microbiological techniques. A method for rapid detection and enumeration of a commercial inoculum of nitrifying bacteria in a zeoponic substrate was developed using a polymerase chain reaction (PCR)-most probable number (MPN) approach. Samples from four-week laboratory incubation studies were processed to extract their total microbial community DNA and the sequences specific to 16s rRNA of Nitrobacter spp. were PCR amplified. The detection limit of the methodology was 2,000 Nitrobacter cells per assay. The quantitative assay demonstrated that the zeoponic substrate was capable of supporting 10⁵ to 10⁶ MPN Nitrobacter cells per gram of substrate. The PCR-MPN method can be an effective and rapid approach to enumerate nitrifying bacteria in zeoponic substrates.     

Effect of soil type on infectivity and persistence of the entomopathogenic nematodes Steinernema scarabaei, Steinernema glaseri, Heterorhabditis zealandica, and Heterorhabditis bacteriophora

We tested the effect of soil type on the performance of the entomopathogenic pathogenic nematodes Steinernema scarabaei, Steinernema glaseri, Heterorhabditis zealandica, and Heterorhabditis bacteriophora. Soil types used were loamy sand, sandy loam, loam, silt loam, clay loam, acidic sand, and a highly organic potting mix. Infectivity was tested by exposing third-instar Anomala orientalis or Popillia japonica to nematodes in laboratory and greenhouse experiments and determining nematode establishment in the larvae and larval mortality. Infectivity of H. bacteriophora and H. zealandica was the highest in potting mix, did not differ among loamy sand and the loams, and was the lowest in acidic sand. Infectivity of S. glaseri was significantly lower in acidic sand than in loamy sand in a laboratory experiment but not in a greenhouse experiment, and did not differ among the other soils. Infectivity of S. scarabaei was lower in silt loam and clay loam than in loamy sand in a greenhouse experiment but not in a laboratory experiment, but was the lowest in acidic sand and potting mix. Persistence was determined in laboratory experiments by baiting nematode-inoculated soil with Galleria mellonella larvae. Persistence of both Heterorhabditis spp. and S. glaseri was the shortest in potting mix and showed no clear differences among the other substrates. Persistence of S. scarabaei was high in all substrates and its recovery declined significantly over time only in clay loam. In conclusion, generalizations on nematode performance in different soil types have to be done carefully as the effect of soil parameters including soil texture, pH, and organic matter may vary with nematode species.     

Survival of κ-carrageenan-encapsulated and unencapsulated Pseudomonas aeruginosa UG2Lr cells in forest soil monitored by polymerase chain reaction and spread plating

Abstract A method was developed for direct extraction, purification and amplification of DNA from forest soil. Eighty-two % of the DNA in Pseudomonas aeruginosa UG2Lr introduced into soil was recovered. The detection limit for the strain was approximately 800 cfu g⁻¹ of dry soil based on the polymerase chain reaction (PCR). Survival of κ-carrageenan-encapsulated and unencapsulated UG2Lr was monitored by antibiotic selective and bioluminescence-based nonselective plating and PCR-amplification of a tnsA fragment. After freeze-thaw treatment of soil samples, the unencapsulated UG2Lr declined from an initial population density of 1 × 10⁹ cfu g⁻¹ of dry soil to below the detection threshold of both selective (14 cfu g⁻¹ of dry soil) and nonselective (1 × 10³ cfu g⁻¹ of dry soil) plating. However, presence of nonculturable UG2Lr cells in the soil was revealed by PCR and resuscitation of the bacteria. Population density of the encapsulated UG2Lr increased from 2.7 × 10⁶ to 2.9 × 10⁸ cfu g⁻¹ of dry soil after a 3-week incubation at 22°C and declined to 6.3 × 10⁶ cfu g⁻¹ of dry soil after the freeze-thaw treatment.     

Phosphatases and the utilization of organic phosphorus by Rhizobium leguminosarum biovar viceae

Rhizobium leguminosarum biovar viceae strain TAL 1236 growing on different organic phosphorus compounds as sources of phosphate exhibited phosphatase activities. The strain was able to produce both acid and alkaline phosphatases. However, its ability to produce alkaline phosphatase was much higher. When cellular phosphate fell to 0.115% of cell protein, cellular and extracellular phosphatase activities were promoted. Mg²⁺, Co²⁺ and Ca²⁺ enhanced slightly the activity of alkaline phosphatase more than acid phosphatase. However, Mn²⁺ and Fe²⁺ activated acid phosphatase rather than alkaline phosphatase. It may be concluded that Rh. leguminosarum plays an important role in the release of phosphorus from its organic compounds through the action of phosphatases which can be slightly activated by a range of cations.