Distribution of Legionella longbeachae serogroup 1 and other legionellae in potting soils in Australia.

Legionella longbeachae serogroup 1 and other Legionella spp. were isolated from 73% of 45 potting soils made in Australia by 13 manufacturers but were not detected in 19 potting soils made in Greece, Switzerland, and the United Kingdom examined between March 1989 and May 1990. Several Legionella species were isolated from a small number of samples of uncomposted pine sawdusts, but it is not known whether sawdust was the source of some of the legionellae found in potting soils. Legionella spp. persisted for periods ranging from 3 to 10 months in a potting soil held at temperatures between -20 and 35 degrees C. Isolates of L. longbeachae serogroup 1 from soil did not grow at 43 degrees C, a temperature which was also lethal for this species in soil. Most Legionella spp. isolated from potting and natural soils belonged to one distinct group according to analysis of ubiquinones and were serologically related to several known species in this group. A small number of potting soils contained L. pneumophila and L. micdadei.     

Distribution of Legionella longbeachae serogroup 1 and other legionellae in potting soils in Australia

Legionella longbeachae serogroup 1 and other Legionella spp. were isolated from 73% of 45 potting soils made in Australia by 13 manufacturers but were not detected in 19 potting soils made in Greece, Switzerland, and the United Kingdom examined between March 1989 and May 1990. Several Legionella species were isolated from a small number of samples of uncomposted pine sawdusts, but it is not known whether sawdust was the source of some of the legionellae found in potting soils. Legionella spp. persisted for periods ranging from 3 to 10 months in a potting soil held at temperatures between -20 and 35 degrees C. Isolates of L. longbeachae serogroup 1 from soil did not grow at 43 degrees C, a temperature which was also lethal for this species in soil. Most Legionella spp. isolated from potting and natural soils belonged to one distinct group according to analysis of ubiquinones and were serologically related to several known species in this group. A small number of potting soils contained L. pneumophila and L. micdadei.     

Pectolytic Clostridium spp. in soils and rhizospheres of carrot and other arable crops in east Scotland

Carrot root tissue discs rotted rapidly in anaerobic conditions after inoculation with soil from 40 different carrot fields and from ten fields of a mixed arable farm. Significant differences occurred in rotting potential between the soils and pectolytic Clostridium spp. were isolated from the rotted discs. Direct counts of pectolytic clostridia on selective pectate plates detected populations of 44–23.5 × 10³ viable propagules/g dry soil in field soils. Significant increases in viable propagules were found in the rhizosphere soils of most carrot crops and in a range of other arable crops examined. The ratios of populations in the rhizospheres and surrounding soils varied between 1.8 and 8.2. Irrigating to excess and inter-row cultivation of carrot crops did not consistently affect populations in soil or on roots.     

Decomposition of cellulose in soils

1. Cellulose decomposition in forest and orchard soils was investigated by studying the breakdown of boiled and washed cellophane in the soils and in vitro. Decomposition occurred from quick to slow in the order: orchard on clay soil, forest on clay soil, forest on sandy loam, and in the latter in the order: calcareous mull, acid mull and mor. 2. In the different forest soils which were investigated the rate of decomposition was parallel to their water capacity. It slowed down considerably when the water content of the soil decreased, especially after the wilting point was reached. 3. Of the fungi isolated from these soils, those from orchard soil — 5% to 50%Fusarium spp. — were among the fastest decomposers of cellulose. This agrees with, and may explain the high rate of decomposition in orchard soil. 4. Decomposition in pure culture is quicker than in soil. As filtersterilized soil extract checked the decomposition in pure culture, but heat-sterilized soil extract did not, an extractable but heat-sensitive substance may be one retarding factor.     

Differential isolatoion of Pythium species from soil by means of selective media,temperature, and pH.

Pythium aphanidermatum, with an optimum temperature for growth at 35C, grew welland was readily isolated from soil on pimaricin-vancomycin medium (MPVM) when incubated for 24h at 38-40C. The pH of the medium affected recovery; maximum numbers developed above pH 6.0. Other Pythium spp. were recovered on MPVM at 20-25C, but were excluded by incubation at 38-40C. These Pythium spp. included P. ultimun, P. paroecandrum, P. irregular, P. mamillatum, and an unidentified Pythium sp. These species grew well and were readily siolated from soil on gallic acid medium (GAM) when incubated for 24-8h at 20 C.P. aphanidermatum and P. myriotylum grew from mycelium on GAM, but their oospores did not germinate nor could they be isolated from soilon this medium. P. myriotylum grew well on MPVM, but was only rarely isolated, evenfrom soils with known high potential for disease caused by P. myriotylum. Propagules of Pythium were enumerated by a plate-dilution frequency method or by a smearplateethod is valuable for studies on the ecology, survival, and inoculum potential in soils with mixed populations of P. aphanidermatum and other Pythium spp.     

Aromatic hydrocarbon-degrading bacteria from soil near Scott Base, Antarctica

Hydrocarbons persist in Antarctic soils when fuel oils such as JP8 jet fuel are spilled. For clean-up of hydrocarbon-contaminated soils in Antarctica, bioremediation has been proposed using hydrocarbon-degrading microbes indigenous to Antarctic soils. A number of alkane-degrading bacteria have been isolated previously from Antarctic soils. In this paper we describe the direct isolation of aromatic hydrocarbon-degrading bacteria from oil-contaminated Antarctic soil. Isolates that grew on JP8 jet fuel were characterised for their ability to degrade aromatic and aliphatic hydrocarbons and for growth at a range of temperatures. All isolates were gram-negative, oxidase-positive, rod-shaped bacteria. Representative strains were identified using 16S rDNA sequence analysis as either Sphingomonas spp. or Pseudomonas spp. Aromatic-degrading bacteria from Antarctic soils were psychrotolerant and appear similar to those found worldwide. Accepted: 27 September 1999     

Microbial mineralization of organic phosphate in soil

Summary Phosphate-dissolving microorganisms were isolated from non-rhizosphere and rhizosphere of plants. These isolates included bacteria, fungi and actinomycetes. In broth cultures, Gram-negative short rod,Bacillus andStreptomyces species were found to be more active in solubilizing phosphate thanAspergillus, Penicillium, Proteus, Serratia, Pseudomonas andMicrococcus spp. The sterile soils mixed with isolated pure culture showed slower mineralization of organic phosphate than that of non-sterile soil samples at all incubation periods. Maximum amount of phosphate mineralization by isolated microorganisms were obtained at the 60th and the 75th day of incubation in sterile and non-sterile soils respectively. The mixed cultures were most effective in mineralizing organic phosphate and individuallyBacillus sp. could be ranked next to mixed cultures. Species ofPseudomonas andMicrococcus were almost the same as that of the control under both sterile and non-sterile conditions.     

Ecology of Hymexazol-Insensitive Pythium Species in Field Soils

Soils from 100 irrigated fields (95 under vegetables, 5 under citrus) in different geographical locations in the West Bank (Palestinian Autonomous Territory) were surveyed for hymexazol-insensitive (HIS) Pythium species using the surface soil dilution plate (SSDP) method with the VP3 medium amended with 50 mg/L hymexazol (HMI) (VP3H50), over a period of 12 months. HIS Pythium species were isolated from 37% of the soils surveyed, with mean population levels ranging from 4.3-1422 CFU g(-1) dry weight. Eight HIS Pythium taxa were recovered on the VP3H50 medium, the most abundant of which was P. vexans (found in 29% of field soils surveyed). Seasonal variations in population levels of HIS Pythium species were studied in four fields over a period of 12 months. Significant seasonal variations in HIS population levels were detected in the four fields, with the highest population levels of HIS Pythium spp. encountered in spring and the lowest population levels in winter in three of the fields surveyed. Effects of HMI on linear growth and colony morphology of 149 Pythium ssp. isolates were examined on CMA amended with HMI at five concentrations. Pythium vexans isolates responded differently from those of the other Pythium species. Isolates of this important pathogen were more insensitive to HMI at high concentrations than the other main species tested. A large proportion of the P. ultimum isolates was either insensitive or weakly sensitive to HMI. Furthermore, a few isolates of other Pythium species were insensitive to the fungicide at various concentrations. The colony morphology of P. vexans isolates was not affected by HMI, whereas colonies of the other species showed sparse growth on the HMI amended medium relative to the control. The pathogenicity of P. vexans and P. ultimum isolates to cucumber seedlings was examined in growth chambers. Insensitive isolates of both species were found to be more virulent damping-off pathogens than the sensitive isolates. The present study demonstrates that HMI can not be used effectively in controlling Pythium spp. in soil inhabited with high densities of HIS Pythium spp. pathogens.     

Crude oil utilization by fungi.

Sixty fungal isolates, 34 obtained by a static enrichment technique from soils of northern Canadian oil-producing areas and 26 from culture collections, were screened for their ability to grow on n-tetradecane, toluene, naphthalene, and seven crude oils of varying composition. Forty cultures, including 28 soil isolates, were capable of growth on one or more crude oils. The genera most frequently isolated from soils were those producing abundant small condida, e.g. Penicillium and Verticillium spp. Oil-degrading strains of Beauveria bassiana, Mortieriella sp., Phoma sp., Scolecobasidium obovatum, and Tolypocladium inflatum were also isolated. Qualitative and quantitative differences were noted among the capacities of different crude oils to sustain the growth of individual fungal isolates. Data are presented which show that ability to grow on a pure n-alkane is not a good indicator of ability to grow on crude oil. Degradation of Rainbow Lake crude oil by individual isolates was demonstrated by gravimetric and gas-chromatographic techniques. The problems involved in determining the response and the potential of fungi to degrade oil spilled in the environment are discussed.     

Distribution and phylogeny of hexachlorocyclohexane-degrading bacteria in soils from Spain

Hexachlorocyclohexane (HCH)-degrading bacteria are believed to mediate natural attenuation of HCH contamination and have potential for active bioremediation processes. This study addressed the very limited understanding of the distribution, diversity and substrate specificity of such bacteria from 13 soil samples, varying in levels of HCH contamination, from four sites in Spain. Hexachlorocyclohexane removal occurred in 16 of 36 enrichment cultures. Hexachlorocyclohexane-degrading populations were clearly associated with HCH-contaminated soils, and populations growing on the delta-HCH isomer were only found in soil contaminated with delta-HCH. beta-Hexachlorocyclohexane was persistent in enrichment cultures, and there was no evidence for populations growing on beta-HCH. From alpha- and gamma-HCH enrichment cultures, nine HCH-degrading isolates were obtained, which were all Sphingomonas spp. Attempts to isolate organisms from delta-HCH enrichment cultures failed. None of the isolates grew on HCH as a sole organic substrate in pure culture. All isolates degraded alpha- and gamma-HCH, and most degraded beta-HCH. delta-Hexachlorocyclohexane inhibited growth of most isolates, but could be degraded by cell suspensions of at least four strains. Denaturing gradient gel electrophoresis indicated that the isolates represented predominant populations in the enrichment cultures, but additional predominant populations, including some Pseudomonas spp., could not be isolated.     

Chlorobenzoate-Degrading Bacteria in Similar Pristine Soils Exhibit Different Community Structures and Population Dynamics in Response to Anthropogenic 2-, 3-, and 4-Chlorobenzoate Levels

A study was conducted to determine the diversity of 2-, 3-, and 4-chlorobenzoate (CB) degraders in two pristine soils with similar physical and chemical characteristics. Surface soils were collected from forested sites and amended with 500 g of 2-, 3-, or 4-CB g^–1 soil. The CB levels and degrader numbers were monitored throughout the study. Degraders were isolated, grouped by DNA fingerprints, identified via 16S rDNA sequences, and screened for plasmids. The CB genes in selected degraders were isolated and/or sequenced. In the Madera soil, 2-CB and 4-CB degraded within 11 and 42 d, respectively, but 3-CB did not degrade. In contrast, 3-CB and 4-CB degraded in the Oversite soil within 14 and 28 d, respectively, while 2-CB did not degrade. Approximately 10⁷ CFU g^–1 of degraders were detected in the Madera soil with 2-CB, and the Oversite soil with 3- and 4-CB. No degraders were detected in the Madera soil with 4-CB even though the 4-CB degraded. Nearly all of the 2-CB degraders isolated from the Madera soil were identified as a Burkholderia sp. containing chromosomally encoded degradative genes. In contrast, several different 3- and 4-CB degraders were isolated from the Oversite soil, and their populations changed as CB degradation progressed. Most of these 3-CB degraders were identified as Burkholderia spp. while the majority of 4-CB degraders were identified as Bradyrhizobium spp. Several of the 3-CB degraders contained the degradative genes on large plasmids, and there was variation between the plasmids in different isolates. When a fresh sample of Madera soil was amended with 50, 100, or 200 g 3-CB g^–1, 3-CB degradation occurred, suggesting that 500 g 3-CB g^–1 was toxic to the degraders. Also, different 3-CB degraders were isolated from the Madera soil at each of the three lower levels of 3-CB. No 2-CB degradation was detected in the Oversite soil even at lower 2-CB levels. These results indicate that the development of 2-, 3-, and 4-CB degrader populations is site-specific and that 2-, 3-, and 4-CB are degraded by different bacterial populations in pristine soils. These results also imply that the microbial ecology of two soils that develop under similar biotic and abiotic environments can be quite different.     

Distribution of bacteria and fungi in the earthworm Libyodrillus violaceous (Annelida: Oligochaeta), a native earthworm from Nigeria

Earthworms are soil invertebrates that play a key role in recycling organic matter in soils. In Nigeria, earthworms include Libyodrillus violaceous. Aerobic and anaerobic bacterial counts, as well as fungal counts of viable microorganisms in soils and gut sections, were made on twenty L. violaceous collected from different sites on the campus of the University of Agriculture, Abeokuta, Nigeria. The samples were collected between April and November, 2002. Numbers of microorganisms were higher in castings and gut sections than in un-ingested soil samples. The guts and their contents also had higher moisture and total nitrogen contents than the un-ingested soils. Bacteria and fungi isolated from the samples were identified by standard microbiological procedures on the bases of their morphological and biochemical characteristics. Isolated bacteria were identified as Staphylococcus, Bacillus spp., Pseudomonas aeruginosa, Streptococcus mutans, Clostridium, Spirocheata spp., Azotobacter spp., Micrococcus lylae, Acinetobacter spp., Halobacterium for bacteria. Yeast isolates were identified as Candida spp., Zygosaccharomyces spp., Pichia spp., and Saccharomyces spp while molds were identified as, Aspergillus spp., Pytium spp., Penicillium spp., Fusarium spp and Rhizopus spp. Of the five locations examined, the refuse dump area had the highest numbers of both aerobic and anaerobic organisms, followed by the arboretum while the cultivated land area recorded the lowest counts. The higher numbers of microorganisms observed in the gut sections and casts of the earthworms examined in this work reinforce the general concept that the gut and casts of earthworms show higher microbial diversity and activity than the surrounding soil.     

Growth and nitrogen fixation ofAzolla pinnata andAzolla caroliniana as affected by urea fertilizer and their influence on rice yield

Soils from avocado (Persea americana Mill.) orchards in Israel (IS) and California (CA), both sites with a Mediterranean climate, were sampled and analyzed for the species and quantities of vesicular-arbuscular mycorrhizal fungus (VAMF) spores in them, and for soil physical and chemical characteristics.Numbers of spores were similar in soil from IS and CA but the dominant VAMF species were very different. In IS the most common fungi were Sclerocystis sinuosa and Glomus macrocarpum. In CA, Gl. constrictum was present in every orchard examined and Gl. fasciculatum was nearly as widespread. Acaulospora spp. and other Glomus spp. also were found, including A. elegans which has never before been reported from CA.The differences in VAMF populations and species constituents found on two continents but in areas with similar climates and soil types may be due to host or edaphic factors. Different avocado rootstocks are used in the two countries and lower pH and higher soil fertility levels were present in CA soils.The total VAMF spore populations in each orchard was about 275 per 100 mL soil. The population level was not correlated with any of the soil physical or chemical characteristics examined nor with avocado cultivar or age. In IS no fungus spores were found in three orchards; available P, Ca, Mg and Cu levels were high in these soils.     

High abundance and role of antifungal bacteria in compost-treated soils in a wildfire area

Compost has been widely used in order to promote vegetation growth in post-harvested and burned soils. The effects on soil microorganisms were scarcely known, so we performed the microbial analyses in a wildfire area of the Taebaek Mountains, Korea, during field surveys from May to September 2007. Using culture-dependent and -independent methods, we found that compost used in burned soils influenced a greater impact on soil fungi than bacteria. Compost-treated soils contained higher levels of antifungal strains in the genera Bacillus and Burkholderia than non-treated soils. When the antifungal activity of Burkholderia sp. strain O1a_RA002, which had been isolated from a compost-treated soil, was tested for the growth inhibition of bacteria and fungi isolated from burned soils, the membrane-filtered culture supernatant inhibited 19/37 fungal strains including soil fungi, Eupenicillium spp. and Devriesia americana; plant pathogens, Polyschema larviformis and Massaria platani; an animal pathogen, Mortierella verticillata; and an unidentified Ascomycota. However, this organism only inhibited 11/151 bacterial strains tested. These patterns were compatible with the culture-independent DGGE results, suggesting that the compost used in burned soils had a greater impact on soil fungi than bacteria through the promotion of the growth of antifungal bacteria. Our findings indicate that compost used in burned soils is effective in restoring soil conditions to a state closer to those of nearby unburned forest soils at the early stage of secondary succession.     

Distribution and characterisation of entomopathogenic fungi from Korean soils

We investigated the occurrence of entomopathogenic fungi in 1080 soil samples representing multiple locations and conditions in Korea. Entomopathogenic fungi were isolated from soils using a selective medium containing dodine and antibiotics. Following an initial identification based on morphology, the fungal isolates were more precisely identified by the sequence of their nuclear ribosomal RNA (rRNA) internal transcribed spacer (ITS) regions. As a result, entomopathogenic fungi were found to occur in 32% (342 isolates) of the soil samples studied. The most abundant species were Beauveria spp. (125 isolates) and Metarhizium spp. (82 isolates). Entomopathogenic fungi were more often recovered from natural mountain and riparian soils than from agricultural habitats. The pathogenicity of isolated fungi was evaluated by using wax moth Galleria mellonella L. (Lepidoptera: Pyralidae) larvae. It was determined that 60% (207 isolates) of the isolates were pathogenic using this model. These entomopathogenic fungi may, therefore, have potential use against a variety of agricultural pests. This is the first study of the isolation and distribution of entomopathogenic fungi in representative sampling locations throughout Korea.     

Soil mycoflora from trufflè native areas of Saudi Arabia

Soil fungi of areas in the North-Eastern region of Saudi Arabia where truffles are native were surveyed. Forty-three species of fungi belonging to twenty genera were isolated. Most were recovered from soils underneath or around truffle ascocarps: thirty species from soil under the surface of Tirmania nivea ascocarps, twenty-four from Terfezia boudieri soil and twenty species each from Tirmania pinoyi and Terfezia claveryi soils. Rhizosphere soil of Helianthemum lippi, on the other hand, yielded twenty-four fungal species while only fourteen fungal species were found in soil without vegetation. The total counts of fungi/g soil were highest in soils from the under surface of truffles, followed by rhizosphere soil, with the lowest in soils without vegetation.     

Evidence for biological nature of the grape replant problem in California

A bioassay was developed to investigate causes of grape replant problems under controlled conditions. Soils were collected from methyl bromide-fumigated and non-fumigated plots at a site cleared from a 65-year-old grape vineyard (Vitis vinifera cv. Thompson seedless) at Parlier, CA. Subsamples of the non-fumigated soil were either left non-treated, subjected to autoclaving (twice 45 min), or heating at 40, 50, 60, 70, 80 or 90 °C for 30 min. Subsequently, the samples were placed in 120-mL pots, planted with rooted hardwood grape cuttings (V. vinifera, cv. Carignane) and placed in a greenhouse or growth chamber. Three months after transplanting, vines from non-treated or 40 °C-treated soil had lower shoot weights and densities of healthy lateral roots than vines from the other treatments. Pythium spp. were isolated from 45 to 55% of the plated root segments from vines grown in non-treated, or soil that had been heated at 40 or 50 °C but were not detected in roots from soil given other treatments. Egg masses of root-knot nematode, Meloidogyne spp., were produced on roots from non-treated or heated at 40 °C soil, but no egg masses were detected on roots of the other treatments. In another test with the same soils, remnant roots from non-fumigated or pre-plant methyl bromide-fumigated soil were extracted and amended to non-fumigated soil, soil from fumigated field plots, soil fumigated in a small container, or autoclaved potting mix. The transfer of old vine roots from non-fumigated field soil resulted in incidence of Pythium spp. on grape assay roots, but there was no measurable effect of the transfer on growth and health of the bioassay plant roots. The results of the bioassays indicate that grape replant problem at the California site had biological causes. The bioassay approach may aid in future determinations of the etiology of grape replant problems.     

Natural suppression of take-all disease of wheat in Montana soils

This research was initiated to determine whether soils suppressive to take-all of wheat caused by Gaeumannomyces graminis var. tritici (Ggt) occur in Montana, and to identify the organisms most likely involved in this suppression. From an initial screening of eight soils collected from different wheat growing areas of Montana, two were highly suppressive to take-all. Microbial characterization of these soils indicated that different mechanisms were involved in the suppression. In Larslan soil, mycoparasitism appeared to be the main mechanism. Two different fungi with exceptional ability to reduce the severity of take-all were isolated from this soil. One of these fungi could parasitize the hyphae of Ggt. Field tests with these fungi in Ggt infested soil showed increases of over 100% in both harvestble tillers and grain yield as compared to treatments without these two fungi. In tests with 48 different bacteria and 10 actinomycetes from Larslan soil, none were able to consistently reduce severity of take-all alone, or in mixtures. In Toston soil, antibiosis by actinomycetes and perhaps the involvement of Pseudomonas spp. in production of antibiotics and/or siderophores appeared to be the most likely mechanisms involved in take-all suppression. Increases in shoot dry weight over that in the Ggt infested control using mixtures of pseudomonads and actinomycetes ranged from 25% to 87%. Actinomycetes added individually or in mixtures to soil infested with Ggt consistently reduced the severity of the disease to a greater extent than did mixtures of Pseudomonas spp.     

Culturable populations of Sporomusa spp. and Desulfovibrio spp. in the anoxic bulk soil of flooded rice microcosms.

Most-probable-number (MPN) counts were made of homoacetogenic and other bacteria present in the anoxic flooded bulk soil of laboratory microcosms containing 90- to 95-day-old rice plants. MPN counts with substrates known to be useful for the selective enrichment or the cultivation of homoacetogenic bacteria (betaine, ethylene glycol, 2, 3-butanediol, and 3,4,5-trimethoxybenzoate) gave counts of 2.3 x 10(3) to 2.8 x 10(5) cells per g of dry soil. Homoacetogens isolated from the terminal positive steps of these dilution cultures belonged to the genus Sporomusa. Counts with succinate, ethanol, and lactate gave much higher MPNs of 5.9 x 10(5) to 3.4 x 10(7) cells per g of dry soil and led to the isolation of Desulfovibrio spp. Counting experiments on lactate and ethanol which included Methanospirillum hungatei in the medium gave MPNs of 2.3 x 10(6) to 7.5 x 10(8) cells per g of dry soil and led to the isolation of Sporomusa spp. The latter strains could grow with betaine, ethylene glycol, 2, 3-butanediol, and/or 3,4,5-trimethoxybenzoate, but apparently most cells of Sporomusa spp. did not initiate growth in counting experiments with those substrates. Spores apparently accounted for 2. 2% or less of the culturable bacteria. It appears that culturable Desulfovibrio spp. and Sporomusa spp. were present in approximately equal numbers in the bulk soil. Multiple, phylogenetically-distinct, phenotypically-different, strains of each genus were found in the same soil system.