Crenarchaeota affiliated with group 1.1b are prevalent in coastal mineral soils of the Ross Sea region of Antarctica.

The objective of this study was to examine the presence and diversity of Archaea within mineral and ornithogenic soils from 12 locations across the Ross Sea region. Archaea were not abundant but DNA sufficient for producing 16S rRNA gene clone libraries was extracted from 18 of 51 soil samples, from four locations. A total of 1452 clones were analysed by restriction fragment length polymorphism and assigned to 43 operational taxonomic units from which representatives were sequenced. Archaea were primarily restricted to coastal mineral soils which showed a predominance of Crenarchaeota belonging to group 1.1b (> 99% of clones). These clones were assigned to six clusters (A through F), based on shared identity to sequences in the GenBank database. Ordination indicated that soil chemistry and water content determined archaeal community structure. This is the first comprehensive study of the archaeal community in Antarctic soils and as such provides a reference point for further investigation of microbial function in this environment.

Culturable microbes in shallow groundwater underlying ornithogenic soil of Cape Hallett, Antarctica.

The objective of this study was to investigate the culturable psychrotolerant microbial community in groundwater from Seabee Hook, Antarctica. Shallow groundwater can be present in coastal regions at higher latitudes during the Antarctic summer. Perched groundwater atop ice-cemented permafrost occurs on Seabee Hook, Cape Hallett, at depths from 5 to 80 cm below the soil surface. Compared with terrestrial water from other sites in Antarctica, the groundwater was high in salt and nutrients, reflecting proximity to the sea and ornithogenic soil. Microbial communities in groundwater samples from Seabee Hook exhibited aerobic metabolism of 14C-acetate at 5 degrees C. Numbers of culturable aerobic heterotrophs in the samples ranged from <10 to ca. 1 x 106 colony-forming units.mL-1, and similar numbers of microaerophiles and nitrate reducers were detected. In contrast, numbers of nitrifiers, sulfate reducers, and iron reducers were up to 1000-fold lower. All cultures were incubated at 5 degrees C. Aerobic heterotrophic bacteria isolated from the groundwater were assigned to Actinobacteria, Proteobacteria, or Bacteroidetes. The isolates were most similar to cultured bacteria from Antarctic soil or sediment and were cold, salt, and alkaline pH tolerant, indicating they are adapted to in situ conditions.

Bacterial diversity associated with ornithogenic soil of the Ross Sea region, Antarctica.

In the Ross Sea region of Antarctica, ornithogenic soils form on land under Adélie Penguin rookeries. Compared with mineral soils of the Ross Sea region, ornithogenic soils are generally high in microbial biomass, organic carbon, and total nitrogen and phosphorus, with high electrical conductivity and large variations in pH. The objective of this study was to assess the bacterial composition of ornithogenic soils from Cape Hallett and Cape Bird in the Ross Sea region using culture-independent methods. Soil clone libraries were constructed and those clones that occurred > or = 3 times were sequenced. The bacterial diversity of the soils was dependent on the presence of penguins. Firmicutes most closely related to the endospore-formers (e.g., Oceanobacillus profundus and Clostridium acidurici) and (or) Gammaproteobacteria belonging to the genus Psychrobacter dominated soils currently occupied with penguins. In contrast, Gammaproteobacteria, closely related to cultured members of the genera Rhodanobacter, Psychrobacter, Dokdonella, and Lysobacter, dominated the soils previously colonized by penguins. Results of this study indicate that despite relatively high nutrient levels and microbial biomass, bacterial communities of ornithogenic soils were not more diverse than those of mineral soils of the Ross Sea region of Antarctica.

Verification of cleaning efficiency and its possible role in programmed hygiene inspections of food businesses undertaken by local authority officers.

AIM: The aim of this study was to determine whether or not the assessment of surface cleanliness could make a contribution to visual inspections of food premises. METHODS AND RESULTS: Forty-five premises were studied with both rapid (ATP) and traditional microbiological swabbing being used to test surfaces that either come into direct contact with prepared foods or were likely to be touched by hands during food preparation. A significant link was found between aerobic colony counts and ATP measurements. In most cases, the visual appearance of surfaces could not be used to accurately predict either microbial or ATP results. CONCLUSION: This study suggests that ATP testing is a useful indicator of surface cleanliness and could be helpful to local authority officers as part of risk assessment inspections. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provides further evidence that visual inspection alone may not always be adequate to assess surface cleanliness. In high-risk premises, ATP could, if appropriately targeted, help identify potential problem areas. The results are available at the time of the inspection and can be used as an on-the-spot teaching aid.

Two separate outbreaks of Salmonella enteritidis phage type 14b food poisoning linked to the consumption of the same type of frozen food.

OBJECTIVES: To ascertain, using a combination of epidemiological, environmental and microbiological methods of investigation, a possible link between two outbreaks of salmonella food poisoning. METHODS: Case-control studies were carried out on the known at-risk populations. Environmental investigations took place in the food preparation areas used for the social functions and microbiological examinations were carried out on faecal specimens obtained from cases, environmental swabs, and food specimens when these were available. RESULTS: In both outbreaks, illness was associated with the consumption of sesame prawn toast (outbreak one P<0.004; outbreak two P<0.0001). Salmonella enteritidis phage type 14b was cultured from the faecal specimens of cases in both outbreaks and from a packet of sesame prawn toast used for the second outbreak function. Molecular typing methods indicated that the salmonella cultures obtained in both outbreaks were indistinguishable from each other and from cultures obtained from imported Spanish eggs in a previous survey. Imported Spanish eggs were used in the manufacture of the sesame prawn toast. CONCLUSIONS: Adequate cooking must take place of raw food products, which should be clearly labelled as such. Manufacturers should consider, when possible, the use of pasteurized egg in the preparation of food products.

Culturable bacteria in subglacial sediments and ice from two Southern Hemisphere glaciers.

Viable prokaryotes have been detected in basal sediments beneath the few Northern Hemisphere glaciers that have been sampled for microbial communities. However, parallel studies have not previously been conducted in the Southern Hemisphere, and subglacial environments in general are a new and underexplored niche for microbes. Unfrozen subglacial sediments and overlying glacier ice samples collected aseptically from the Fox Glacier and Franz Josef Glacier in the Southern Alps of New Zealand now have been shown to harbor viable microbial populations. Total direct counts of 2-7 x 10(6) cells g(-1) dry weight sediment were observed, whereas culturable aerobic heterotrophs ranged from 6-9 x 10(5) colony-forming units g(-1) dry weight. Viable counts in the glacier ice typically were 3-4 orders of magnitude smaller than in sediment. Nitrate-reducing and ferric iron-reducing bacteria were detected in sediment samples from both glaciers, but were few or below detection limits in the ice samples. Nitrogen-fixing bacteria were detected only in the Fox Glacier sediment. Restriction fragment analysis of 16S rDNA amplified from 37 pure cultures of aerobic heterotrophs capable of growth at 4 degrees C yielded 23 distinct groups, of which 11 were identified as beta-Proteobacteria. 16S rDNA sequences from representatives of these 11 groups were analyzed phylogenetically and shown to cluster with bacteria such as Polaromonas vacuolata and Rhodoferax antarcticus, or with clones obtained from permanently cold environments. Chemical analysis of sediment and ice samples revealed a dilute environment for microbial life. Nevertheless, both the sediment samples and one ice sample demonstrated substantial aerobic mineralization of 14C-acetate at 8 degrees C, indicating that sufficient nutrients and viable psychrotolerant microbes were present to support metabolism. Unfrozen subglacial sediments may represent a significant global reservoir of biological activity with the potential to influence glacier meltwater chemistry.

Characterization of Sphingomonas sp. Ant 17, an aromatic hydrocarbon-degrading bacterium isolated from Antarctic soil.

Sphingomonas sp. strain Ant 17 was isolated from fuel-contaminated soil collected at Scott Base, Ross Island, Antarctica. We anticipated that Ant 17 would be a good model organism for studying cold climate bioremediation, and therefore determined its biodegradation capabilities and tolerance of potentially growth-limiting environmental conditions. Sphingomonas sp. Ant 17 degrades the aromatic fraction of several different crude oils, jet fuel, and diesel fuel at low temperatures and without nutrient amendment. It utilizes or transforms a broad range of pure aromatic substrates, including hydrocarbons, heterocycles, and aromatic acids and alcohols. Ant 17 grows at temperatures of 1 degree C to 35 degrees C and mineralizes radiolabeled phenanthrene over a range of more than 24 degrees C. This psychrotolerant isolate appears to utilize hydrocarbons more efficiently at low temperatures than would be predicted by mesophilic enzyme kinetics. The optimum pH for growth was 6.4 at 22 degrees C, with extended lag phases observed in more alkaline media. However, there was less effect of pH on lag phase at lower temperatures. Ant 17 displayed greater tolerance to UV irradiation and freeze-thaw cycles than the hydrocarbon-degrading isolate Sphingomonas sp. WPO-1, which may reflect adaptation to its Antarctic soil environment. However, it was more sensitive than expected to desiccation and to low concentrations of NaCl and CaCl(2). Ant 17 was phenotypically stable and lacked detectable plasmids, suggesting a chromosomal location for genes encoding aromatic degradation enzymes. Its broad aromatic substrate range and tolerance of low and fluctuating temperature and low nutrients make Sphingomonas sp. Ant 17 a valuable microbe for examining fuel spill bioremediation in cold soils.

Viral and chemical tracer movement through contrasting soils.

Land treatment of animal or human waste can result in chemical and microbial contamination of shallow ground water and/or water-ways. We investigated the fate of a host-specific Salmonella bacteriophage and a nonreactive chemical (Br-) tracer when applied to large intact lysimeter soil cores (500 mm diam. by 700 mm high). The soils included a poorly drained Gley Soil and well-drained Pumice, Allophanic, and Recent Soils. A depth of 30 mm of water containing the bacteriophage and Br- was applied to the soil at a rate of 5 mm h(-1) followed by up to about 1.8 pore volumes of simulated rainfall. Resulting leachates, collected continuously over at least one pore volume were analyzed for the bacteriophage and bromide (Br-) tracers. Bromide moved uniformly through the Pumice and Allophanic Soils with peak concentrations at about 1 pore volume, while the bacteriophage was detected only at trace levels or not at all. In contrast, both Br- and bacteriophage tracers moved rapidly through Gley and Recent Soils, appearing early in the leachate and then tailing off. Such flow patterns in the Gley and Recent Soils are indicative of bypass flow. Coarse soil structure in the Gley Soil, and finger-flow due to water repellency in the sandy Recent Soil are considered responsible for the observed bypass flow in these two soils. Allophanic and Pumice Soils have finer, more porous soil structure leading to a predominance of matrix flow over bypass flow. This study suggests vertical movement of viruses varies significantly with soil type.

Isolation of Terrabacter sp. strain DDE-1, which metabolizes 1, 1-dichloro-2,2-bis(4-chlorophenyl)ethylene when induced with biphenyl.

Terrabacter sp. strain DDE-1, able to metabolize 1,1-dichloro-2, 2-bis(4-chlorophenyl)ethylene (DDE) in pure culture when induced with biphenyl, was enriched from a 1-1-1-trichloro-2, 2-bis(4-chlorophenyl)ethane residue-contaminated agricultural soil. Gas chromatography-mass spectrometry analysis of culture extracts revealed a number of DDE catabolites, including 2-(4'-chlorophenyl)-3,3-dichloropropenoic acid, 2-(4'-chlorophenyl)-2-hydroxy acetic acid, 2-(4'-chlorophenyl) acetic acid, and 4-chlorobenzoic acid.

Polycyclic aromatic hydrocarbons in fuel-oil contaminated soils, Antarctica.

Where fuel oil spills have occurred on Antarctic soils polycyclic aromatic hydrocarbons (PAH) may accumulate. Surface and subsurface soil samples were collected from fuel spill sites up to 30 years old, and from nearby control sites, and analysed for the 16 PAHs on the USEPA priority pollutants list, as well as for two methyl substituted naphthalenes, 1-methylnaphthalene and 2-methylnaphthalene. PAH levels ranged from 41-8105 ng g-1 of dried soil in the samples from contaminated sites and were below detection limits in control site samples. PAH were detected in surface soils and had migrated to lower depths in the contaminated soil. The predominant PAH detected were naphthalene and its methyl derivatives.

Isolation and description of carbazole-degrading bacteria.

Carbazole is a nitrogen heterocyclic compound associated with fossil fuels and their products. Enrichment cultures were established to isolate bacteria able to degrade carbazole and a plate assay was developed to select carbazole-degrading microorganisms from the enrichments. Three different bacterial isolates capable of mineralizing carbazole were obtained. No intermediates of carbazole degradation were detected. The bacteria had a limited substrate specificity; all used benzoate for growth but were unable to utilize the analogues of carbazole, fluorene, or dibenzothiophene.

Description of bacteria able to degrade isoquinoline in pure culture.

Isoquinoline is a nitrogen heterocyclic compound that is associated with coal- and oil-derived wastes. Four strains of bacteria able to degrade isoquinoline in pure culture were isolated from sites known to be contaminated with oil. Isoquinoline was used as the sole source of carbon and nitrogen by these isolates. Isoquinoline was initially transformed to 1-hydroxyisoquinoline, which accumulated in the broth culture, and then disappeared. The four strains isolated were Gram negative, aerobic, rod-shaped bacteria with polar flagella. The strains have been presumptively identified as members of the family Comamonadaceae.

Construction of a DNA probe to detect isoquinoline-degrading bacteria.

To facilitate the cloning of DNA encoding isoquinoline degradation an assay was developed that allowed the rapid visual scoring of the isoquinoline degradation phenotype of single colonies. Transposon mutagenesis of one of the isolates. Comamonas acidovorans IQ3, was performed using Tn5, and nine Isq-mutants deficient in the ability to utilise isoquinoline as the sole nitrogen source were isolated. These mutants were also incapable of utilising the first metabolite of the isoquinoline degradation pathway, 1-hydroxyisoquinoline, as the sole carbon source. For each Isq-mutant, the EcoRI fragment containing the Tn5 insertion was cloned into pBR322. Restriction and Southern analyses of the cloned DNA revealed that of the nine Isq-mutants, six contained Tn5 insertions in a common 8.9-kb EcoRI fragment derived from the wild type, C. acidovorans IQ3. The cloned DNA thought to be involved in the degradation of isoquinoline proved to be specific when used as a probe in colony hybridization to some bacteria possessing the ability to degrade isoquinoline.

Polycyclic aromatic hydrocarbons in nearshore marine sediments of Australia.

The occurrence and fate of polycyclic aromatic hydrocarbons (PAH) in nearshore marine sediments of Australia is discussed. Available information indicates that PAH are accumulating in the sediments and organisms of estuaries and harbours with both highly urbanized/industrialized and non-urban catchments. PAH levels in polluted sediments are similar to those of grossly polluted areas of Japan, North America and Europe, however PAH sources cannot be identified from the information available. PAH appear to persist in reducing environments, while in relatively pristine environments that have been previously exposed to PAH, conditions are probably favourable for the aerobic degradation of PAH by microorganisms.

Microbial degradation of quinoline and methylquinolines.

Several bacterial cultures were isolated that are able to degrade quinoline and to transform or to degrade methylquinolines. The degradation of quinoline by strains of Pseudomonas aeruginosa QP and P. putida QP produced hydroxyquinolines, a transient pink compound, and other undetermined products. The quinoline-degrading strains of P. aeruginosa QP and P. putida QP hydroxylated a limited number of methylquinolines but could not degrade them, nor could they transform 2-methylquinoline, isoquinoline, or pyridine. Another pseudomonad, Pseudomonas sp. strain MQP, was isolated that could degrade 2-methylquinoline. P. aeruginosa QP was able to degrade or to transform quinoline and a few methylquinolines in a complex heterocyclic nitrogen-containing fraction of a shale oil. All of the quinoline- and methylquinoline-degrading strains have multiple plasmids including a common 250-kilobase plasmid. The 225-, 250-, and 320-kilobase plasmids of the P. aeruginosa QP strain all contained genes involved in quinoline metabolism.

Isolation of microorganisms capable of degrading isoquinoline under aerobic conditions.

Isoquinoline-degrading microbial cultures were isolated from oil- and creosote-contaminated soils. The establishment of initial enrichment cultures required the use of emulsified isoquinoline. Once growth on isoquinoline was established, isoquinoline emulsification was no longer required for utilization of isoquinoline as the sole source of carbon and nitrogen by these cultures. An isoquinoline-degrading Acinetobacter strain was isolated from one of the enrichment cultures. The degradation of isoquinoline was accompanied by the accumulation of a red cell-associated pigment and of 1-hydroxyisoquinoline, which was further degraded to unknown intermediary ring-cleavage products and carbon dioxide.

Biodegradation of nitriles in shale oil.

Enrichment cultures were obtained, after prolonged incubation on a shale oil as the sole source of nitrogen, that selectively degraded nitriles. Capillary gas chromatographic analyses showed that the mixed microbial populations in the enrichments degraded the homologous series of aliphatic nitriles but not the aliphatic hydrocarbons, aromatic hydrocarbons, or heterocyclic-nitrogen compounds found in this oil. Time course studies showed that lighter nitriles were removed more rapidly than higher-molecular-weight nitriles. A Pseudomonas fluorescens strain isolated from an enrichment, which was able to completely utilize the individual nitriles undecyl cyanide and undecanenitrile as sole sources of carbon and nitrogen, was unable to attack stearonitrile when provided alone as the growth substrate. A P. aeruginosa strain, also isolated from one of the enrichments, used nitriles but not aliphatic or aromatic hydrocarbons when the oil was used as a sole nitrogen source. However, when the shale oil was used as the sole source of carbon, aliphatic hydrocarbons in addition to nitriles were degraded but aromatic hydrocarbons were still not attacked by this P. aeruginosa strain.