Soil mycoflora in tomato fields

Density and species richness of fungal communities in soils ofFusarium infested and non-infested tomato-growing localities were studied by comparison of rhizoplanes, rhizospheres, and root-free soils. The rhizosphere soils harbored the highest counts of fungi, followed by root-free soil and rhizoplanes in both localities. Species richness was high in the rhizosphere and root-free soil but distinctly low in the rhizoplane. The population density of the zhizosphere and the rhizoplane showed a significant difference between infested and non-infested localities.     

Biodegradation of wheat stubbles by soil micro-organisms and role of the products on soil fertility

Summary Soil microorganisms caused considerable degradation of wheat stubbles under laboratory conditions. Mixtures of different organisms proved to be more efficient than individual organisms in degrading lignin, holocellulose and nitrogenous substances which constitute the major components in stubble. Lignin and holocellulose content in fresh stubble was about 25% and 60% of dry weight respectively. Degradation of these compounds caused an increase in simpler components like soluble carbohydrates. Degradation of nitrogenous substances (represented by 0.7% total nitrogen in fresh stubbes) caused accretion in the soluble nitrogen of the degraded product. In most cases, these products proved to be important in improving fertility of the soil thereby causing significant promotion of growth of crops like maize and rice.     

Biodegradation of propoxur by Pseudomonas species

A bacterium capable of degrading propoxur (2-isopropoxyphenyl-N-methylcarbamate) was isolated from soil by enrichment cultures and was identified as a Pseudomonas species. The organism grew on propoxur at 2 g/l as sole source of carbon and nitrogen, and accumulated 2-isopropoxyphenol as metabolite in the culture medium. The cell free extract of Pseudomonas sp. grown on propoxur contained the activity of propoxur hydrolase. The results suggest that the organism degraded propoxur by hydrolysis to yield 2-isopropoxyphenol and methylamine, which was further utilized as carbon source.     

Biodegradation of 4-chlorobiphenyl by Micrococcus species

A Micrococcus sp., isolated by enrichment culture, grew on 4-chlorobiphenyl at 2 g/l as sole carbon source and produced 4-chlorobenzoic acid in the culture medium as a dead-end metabolite. The organism degraded 4-chlorobiphenyl by 2,3-dihydroxylation followed by meta-ring cleavage to yield 4-chlorobenzoate and carbon fragments for cell growth.     

Biodegradation of Swainsonine by Acinetobacter calcoaceticus strain YLZZ-1 and its isolation and identification

Eight swainsonine (SW)-degrading bacteria were isolated from the soil where locoweed was buried for 6 months and one of the strains (YLZZ-1) was selected for further study. Based on morphology, physiologic tests, 16S rRNA gene sequence, and phylogenetic characteristics, the strain showed the greatest similarity to members of the order Acinetobacters and within the order to members of the Acinetobacter calcoaceticus group. The ability of the strain for degrading SW, as sole carbon source, was investigated under different culture conditions. The preferential temperature and initial pH for the strain were 25–35°C and 6–9, respectively. The optimal temperature for the strain was 30°C and the optimal pH was 7.0. There was a positive correlation between degradation rate and inoculation amount. The concentration of SW affected the degradation ability. When the concentration of SW was lower than 100 mg/l, SW decreased immediately after incubation, and when the concentration of SW was 200 mg/l, there was an inhibiting effect for bacteria growth and SW degradation. The strain could degrade SW completely within 14 h when the concentration of SW was 50 mg/l. These results highlight the potential of this bacterium to be used in detoxifying of SW in livestock consuming locoweed.     

Relationship between growth rate of Helminthosporium oryzae isolates on calluses of rice cultivars and their disease reaction on rice plants

Rice cultivars showed differential reaction to various isolates of Helminthosporium oryzae, the brown spot pathogen. The calluses obtained from those cultivars behaved in a similar manner to the mycelial growth of pathogenic isolates on them. However, amount of inoculum, size of the callus and period of incubation influenced the reaction of the callus to the fungal isolates.     

Biodegradation of Ethametsulfuron-Methyl by <Emphasis Type="Italic">Pseudomonas</Emphasis> sp. SW4 Isolated from Contaminated Soil

A soil bacterium SW4, capable of degrading the sulfonylurea herbicide ethametsulfuron-methyl (ESM), was isolated from the bottom soil of a herbicide factory. Based on physiological characteristics, biochemical tests and phylogenetic analysis of the 16S rRNA gene sequence, the strain was identified as a Pseudomonas sp. The total degradation of ESM in the medium containing glucose was up to 84.6% after 6 days of inoculation with SW4 strain. The inoculation of strain SW4 to soil treated with ESM resulted in a higher degradation rate than in noninoculated soil regardless of the soil sterilized or nonsterilized. Five metabolites of ESM degradation were analyzed by liquid chromatography/mass spectrometry. Based on the identified products, strain SW4 seemed to degrade ESM after two separate and different pathways: one leads to the cleavage of the sulfonylurea bridge, whereas the other to the dealkylation and opening of the triazine ring of ESM.     

Biological control of rice bacterial blight by Lysobacter antibioticus strain 13-1

Bacterial leaf blight (BB) is a worldwide destructive rice disease caused by pathogen Xanthomonas oryzae pv. oryzae (Xoo). A novel strain of Lysobacter antibioticus, which was isolated from the rhizosphere of rice in Yunnan Province of China, can significantly inhibit the growth of various phytopathogenic bacteria and fungi, especially BB pathogen Xoo. In greenhouse experiments, whole bacterial broth culture (WBC) of strain 13-1 was more effective in reducing BB than other components of the culture, with disease suppression efficiency up to 69.7%. However, bacterial cells re-suspended in water, cell-free culture extracts, and heated cultures also significantly reduced BB severity. Suppression efficiencies ranged from 79.0% to 61.8% for undiluted to 100-fold dilution treatments and from 57.6% to 31.7% when the WBC of strain 13-1 (10⁸ CFU/mL) was applied at 3 days and 7 days prior to pathogen inoculation, respectively. In three field trials, strain 13-1 reduced BB incidence by 73.5%, 78.3%, and 59.1%, respectively. Disease suppression by strain 13-1 varied significantly among different rice cultivars, although efficacy was not directly related to the susceptibility level of the cultivars. Efficacy of biocontrol was also affected by different pathogen isolates, with some isolates of Xoo being more sensitive to 13-1 suppression than others. These results suggest that antibiotics and density of colonization on leaves may be involved for biological control of rice BB by strain 13-1. To our knowledge, this is the first report of L. antibioticus being a potential biocontrol agent for rice bacterial blight.     

Availability of phosphorus in a calcareous soil treated with rock phosphate or superphosphate as affected by phosphate-dissolving fungi

A study was undertaken to isolate some fungi exhibiting phosphate-dissolution ability, and to test whether these fungi are capable of increasing the amount of available P in a calcareous soil treated with rock phosphate (RP) or with triple superphosphate (TSP) and its subsequent uptake by sorghum (Sorghum bicolor L. Moench).Penicillium sp. and twoAspergillus foetidus (Naka) isolates significantly increased the availability of P in soil treated with RP or TSP during the growing season.Penicillium sp. isolate was more effective in increasing available P in the soil treated with RP or TSP than were Aspergillus isolates. However, the dry matter and P uptake responses to inoculation with these fungi were better in the soil treated with RP than in soil treated with TSP. In the TSP treated soil, the fungi achieved their maximum P releasing capacity two weeks earlier than in soil treated with RP. Positive and significant correlation coefficients among available P, P uptake and dry matter production at different periods of the growing season were observed following inoculation. However, none of these variables were found to be significantly correlated with the fungal populations.     

Rapid biodegradation of metsulfuron-methyl by a soil fungus in pure cultures and soil

Summary Four strains of bacteria, 9 strains of fungi and 20 strains of actinomycetes capable of utilizing metsulfuron-methyl as sole carbon and energy source were isolated from a metsulfuron-methyl-treated soil by the enrichment culture method. A fungus named DS11F was selected as the most highly effective one according to the maximum tolerance concentration of 1,200 mg l⁻¹ and metsulfuron-methyl-degrading rate of 0.0716 g g⁻¹ cells h⁻¹, and was identified as an unknown strain of Penicillium sp. on the basis of colony growth, morphology and biochemical characteristics.␣Through liquid pure culture, the optimal metsulfuron-methyl-degrading conditions of DS11F were determined to be metsulfuron-methyl concentration 22.6 mg l⁻¹, inoculum concentration 12.25 mg l⁻¹, pH 7.0 and temperature 30°C. As additional C sources, supernatant of soaked compost could increase metsulfuron-methyl degradation by 8%, but glucose was ineffective. DS11F inoculation was found to significantly enhance the degradation of metsulfuron-methyl in soil, with the reduction of the concentration reaching 50% in 6 days. Admixture of compost could promote metsulfuron-methyl degradation to some extent. The growth of the inocula in the soils remained dominant and degradation resumed immediately when metsulfuron-methyl was applied again. The results show that addition of the isolated Penicillium sp. enhances the degradation of metsulfuron-methyl in water and soil.     

Decomposition of 14C-labelled lignin and phenols by a Nocardia sp.

A Gram-positive bacterium which was isolated from a Finnish soil and identified as a Nocardia sp., was able to decompose lignin and to assimilate lignin degradation products as a carbon source. It could release ¹⁴CO₂ from ¹⁴C-labelled methoxyl groups, side chains or ring carbons of coniferyl alcohol dehydropolymers (DHP) and from specifically ¹⁴C-labelled lignin of plant material. Furthermore, it could release ¹⁴CO₂ from phenolcarboxylic and cinnamic acids and alcohols labelled in the OCH₃, COOH groups, side chain or aromatic ring carbons.Non-Common Abbreviations Used DHP dehydropolymers of coniferyl alcohol     

Biodegradation of diphenyl ethers by a copper-resistant mutant ofErwinia sp.

Summary A bacterium tentatively identified as anErwinia sp. was isolated from sewage by enrichment on methanol and lignin. Several mutants developed from this strain were studied for their ability to degrade aromatic ethers. Different concentrations of the chemicals were incubated with the organisms and the degradation was estimated by high-performance liquid chromatography (HPLC). Among these mutants, one isolate,Erwinia sp. strain CU3614, showed resistance to copper ions (>20 mM CuSO₄) and the ability to degrade 4-hydroxydiphenyl ether (4-HDPE), 4-chlorodiphenyl ether (4-CDPE), 4-nitrodiphenyl ether (4-NDPE) and 2,7-dichlorodibenzo-p-dioxin (2,7-DCDD) in the presence of copper ions. Increased concentrations of copper in the medium resulted in higher degradation of 4-HDPE. Further studies with copper-sensitive mutants obtained fromErwinia sp. CU3614 by Tn5 transposon-induced mutagenesis showed a corresponding decrease in the ability to degrade 4-HDPE. These results suggest the presence of a copper-associated activity in the biotransformation of aromatic ethers.     

Biodegradation of p-nitrophenol by microalgae

A study was made on the use of a mixed microalgal consortium to degrade p-nitrophenol. The consortium was obtained from a microbial community in a waste container fed with the remains and by-products of medium culture containing substituted aromatic pollutants (nitrophenols, chlorophenols, fluorobenzene). After selective enrichment with p-nitrophenol (p-NP), followed by an antibiotic treatment, an axenic microalgal consortium was recovered, which was able to degrade p-nitrophenol. At a concentration of 50 mg L^–1, total degradation occurred within 5 days. Two species, Chlorella vulgaris var. vulgaris f. minuscula and Coenochloris pyrenoidosa, were isolated from the microalgal consortium. The species were able to accomplish p-NP biodegradation when cultured separately, although Coenochloris pyrenoidosa was more efficient, achieving the same degradation rate as the original axenic microalgal consortium. When Coenochloris pyrenoidosa was associated with Chlorella vulgaris in a 3:1 ratio, complete removal of the nitro-aromatic compound occurred within three days. This is apparently the first report on the degradation of a nitro-aromatic compound by microalgae.     

Control of blast and sheath blight diseases of rice using antifungal metabolites produced by Streptomyces sp. PM5

Two antifungal aliphatic compounds, SPM5C-1 and SPM5C-2 with a lactone and ketone carbonyl unit, respectively obtained from Streptomyces sp. PM5 were evaluated under in vitro and in vivo conditions against major rice pathogens, Pyricularia oryzae and Rhizoctonia solani. These compounds were dissolved in distilled water/medium to get the required concentrations. The well diffusion bioassay indicated that the of SPM5C-1 remarkably inhibited the mycelial growth of P. oryzae and R. solani in comparison to SPM5C-2. Though SPM5C-2 showed low antifungal activity against P. oryzae, it was not active against R. solani. Further, SPM5C-1 completely inhibited the growth of P. oryzae and R. solani at concentrations of 25, 50, 75 and 100 μg/ml. Greenhouse experiments revealed that spraying of SPM5C-1 at 500 μg/ml on rice significantly decreased blast and sheath blight development by 76.1% and 82.3%, respectively, as compared to the control with a corresponding increase in rice grain yield.     

Requirement for particular seed-borne fungi for seed germination and seedling growth of <Emphasis Type="Italic">Xyris complanata</Emphasis>, a pioneer monocot in topsoil-lost tropical peatland in Central Kalimantan,Indonesia

Hawaii yellow-eyed grass (Xyris complanata: Xyridaceae) inhabits infertile, acidic peat soil in the rainy tropical zone in Southeast Asia. This monocot plant produces a large number of dormant seeds in order to make a large deposit to seed bank in the soil. Under laboratory conditions, surface-sterilized X. complanata seeds are rarely able to germinate on sterilized peat moss bed; they require inoculation with either seed epiphytic or soil fungi to facilitate active seed germination. In the present study, three different genera of seed epiphytic fungi were isolated, and two common fungal genera, Fusarium sp. (strain R-1) and Penicillium sp. (strain Y-1), were found to promote seed germination of X. complanata. In sterile peat moss beds, the germination-stimulating fungi also showed growth-promoting effects on X. complanata seedlings. These results suggest that the seed germination-promoting fungi likely function as genuine partners for X. complanata in tropical open peat lands.     

Colonization and degradation of oxidized bituminous and lignite coals by fungi

Summary APenicillium sp. previously shown to grow on lignite coals degraded an air-oxidized bituminous coal (Illinois #6) to a material that was more than 80% soluble in 0.5 N NaOH. Scanning electron microscopy of the oxidized Illinois #6 revealed colonization of the surface by thePenicillium sp., production of conidia, and erosion of the coal surface. The average molecular weight (MW) of Illinois #6 degraded by the fungus and base-solubilized was approximately 1000 Da. The average MW for base-solubilized Illinois #6 that was not exposed to the fungus was 6000 Da, suggesting solubilizing mechanisms other than base catalysis. A spectrophotometric assay to quantify the microbial conversion of biosolubilized coal was developed. Standard curves were constructed based on the absorbance at 450 nm of different quantities of microbe-solubilized coal. An acid precipitation step was necessary to remove medium and/or microbial metabolites from solubilized coal to prevent overestimation of the extent of coal biosolubilization. Furthermore, the absorption spectra for different coal products varied, necessitating construction of standard curves for individual coals.     

Biodegradation of organochlorine pesticide, endosulfan, by a fungal soil isolate, Aspergillus niger

Endosulfan is a chlorinated pesticide widely used in India for the protection of cotton, tea, sugarcane and vegetables. The persistence of endosulfan in environment and toxic effects on biota necessitate its removal. The role of soil fungi in recycling organic matter prompted us to attempt biodegradation of endosulfan using fungi. This study aims at enrichment, isolation and screening of fungi capable of metabolizing endosulfan. In all, 16 fungal isolates were obtained by enrichment of soil samples that had seems exposed to endosulfan before. Isolates were screened by a gradient plate assay, and results were confirmed by broth assay. On the basis of tolerance to endosulfan, an isolate, identified as Aspergillus niger was selected for further studies. The culture could tolerate 400 mg ml⁻¹ of technical grade endosulfan. Complete disappearance of endosulfan was seen on 12 days of incubation. Evolution of carbon dioxide during endosulfan metabolism has indicated the complete mineralization of endosulfan. Change in pH of culture broth to acidic range supported the biological transformation. Thin layer chromography (TLC) analyses revealed the formation of various intermediates of endosulfan metabolism including endosulfan diol, endosulfan sulfate, and an unidentified metabolite. The toxic intermediate, endosulfan sulfate, was also metabolized, further resulting in complete mineralization of endosulfan. Direct desulfurization of endosulfan sulfate or a novel pathway could be the mechanism of endosulfan and endosulfan sulfate degradation in Aspergillus niger. The fungal strain isolated by us could prove valuable for bioremediation of endosulfan contaminated soils and waters.     

Identification of a YAC clone carrying the Xa-1 allele, a bacterial blight resistance gene in rice

Map-based cloning methods have been applied for isolation of Xa-1, one of the bacterial blight resistance genes in rice.Xa-1 was previously mapped on chromosome 4 using molecular markers. For positional cloning of Xa-1, a high-resolution genetic map was made for theXa-1 region using an F₂ population of 402 plants and additional molecular markers. Three restriction fragment length polymorphism (RFLP) markers, XNpb235, XNpb264 and C600 were found to be linked tightly to Xa-1, with no recombinants, and U08 ₇₅₀ was mapped 1.5 cM from Xa-1. The screening of a yeast artificial chromosome (YAC) library using theseXa-1-linked RFLP markers resulted in the identification of ten contiguous YAC clones. Among these, one YAC clone, designated Y5212, with an insert of 340 kb, hybridized with all three tightly linked markers. This YAC was confirmed to possess the Xa-1 allele by mapping the Xa-1 gene between both end clones of this YAC (Y5212R and Y5212L).     

Biodegradation of 1,4-dioxane and transformation of related cyclic compounds by a newly isolated Mycobacterium sp. PH-06

A new bacterial strain PH-06 was isolated using enrichment culture technique from river sediment contaminated with 1,4-dioxane, and identified as belonging to the genus Mycobacterium based on 16S rRNA sequencing (Accession No. EU239889). The isolated strain effectively utilized 1,4-dioxane as a sole carbon and energy source and was able to degrade 900 mg/l 1,4-dioxane in minimal salts medium within 15 days. The key degradation products identified were 1,4-dioxane-2-ol and ethylene glycol, produced by monooxygenation. Degradation of 1,4-dioxane and concomitant formation of metabolites were demonstrated by GC/MS analysis using deuterium labeled 1,4-dioxane (1,4-dioxane-d8). In addition to 1,4-dioxane, this bacterium could also transform structural analogues such as 1,3-dioxane, cyclohexane and tetrahydrofuran when pre-grown with 1,4-dioxane as the sole growth substrate. Our results suggest that PH-06 can maintain sustained growth on 1,4-dioxane without any other carbon sources.     

Nitrogen fixation by Spirillum sp. from rice roots

Nitrogen fixation by Spirillum sp. obtained from the roots of rice plants grown at different levels of combined nitrogen was studied. The roots of rice plants exposed to low levels of combined nitrogen (20–40 kg N/ha) harboured Spirillum sp. possessing higher nitrogen-fixing efficiency as compared to the cultures from plants receiving 60–100 kg N/ha. More-over, the nitrogen-fixing efficiency of these Spirillum spp. varied with age of the plant, irrespective of the dosage of combined nitrogen.