Antimicrobial and Antibiofilm Activities of the Fungal Metabolites Isolated from the Marine Endophytes Epicoccum nigrum M13 and Alternaria alternata 13A

Epicotripeptin (1), a new cyclic tripeptide along with four known cyclic dipeptides (2-5) and one acetamide derivative (6) were isolated from seagrass-associated endophytic fungus Epicoccum nigrum M13 recovered from the Red Sea. Additionally, two new compounds, cyclodidepsipeptide phragamide A (7) and trioxobutanamide derivative phragamide B (8), together with eight known compounds (9-16), were isolated from plant-derived endophyte Alternaria alternata 13A collected from a saline lake of Wadi El Natrun depression in the Sahara Desert. The structures of the isolated compounds were determined based on the 1D and 2D NMR spectroscopic data, HRESIMS data, and a comparison with the reported literature. The absolute configurations of 1 and 7 were established by advanced Marfey's and Mosher's ester analyses. The antimicrobial screening indicated that seven of the tested compounds exhibited considerable (MIC range of 2.5-5 µg/mL) to moderate (10-20 µg/mL) antibacterial effect against the tested Gram-positive strains and moderate to weak (10-30 µg/mL) antibacterial effect against Gram-negative strains. Most of the compounds exhibited weak or no activity against the tested Gram-negative strains. On the other hand, four of the tested compounds showed considerable antibiofilm effects against biofilm forming Gram-positive and Gram-negative strains.

A Crispy Diet: Grazers of Achromatium oxaliferum in Lake Stechlin Sediments

Achromatium is the largest freshwater bacterium known to date and easily recognised by conspicuous calcite bodies filling the cell volume. Members of this genus are highly abundant in diverse aquatic sediments and may account for up to 90% of the bacterial biovolume in the oxic-anoxic interfaces. The high abundance implies that Achromatium is either rapidly growing or hardly prone to predation. As Achromatium is still uncultivated and does not appear to grow fast, one could assume that the cells might escape predation by their unusual shape and composition. However, we observed various members of the meiofauna grazing or parasitizing on Achromatium. By microphotography, we documented amoebae, ciliates, oligochetes and plathelminthes having Achromatium cells ingested. Some Achromatium cells harboured structures resembling sporangia of parasitic fungi (chytrids) that could be stained with the chitin-specific dye Calcofluor White. Many Achromatia carried prokaryotic epibionts in the slime layer surrounding the cells. Their regular distribution over the cell might indicate that they are commensalistic rather than harming their hosts. In conclusion, we report on various interactions of Achromatium with the sediment community and show that although Achromatium cells are a crispy diet, full of calcite bodies, predators do not spare them.

Analysis of the Anti-Cancer Effects of Cincau Extract (Premna oblongifolia Merr) and Other Types of Non-Digestible Fibre Using Faecal Fermentation Supernatants and Caco-2 Cells as a Model of the Human Colon

Green cincau (Premna oblongifolia Merr) is an Indonesian food plant with a high dietary fibre content. Research has shown that dietary fibre mixtures may be more beneficial for colorectal cancer prevention than a single dietary fibre type. The aim of this study was to investigate the effects of green cincau extract on short chain fatty acid (SCFA) production in anaerobic batch cultures inoculated with human faecal slurries and to compare these to results obtained using different dietary fibre types (pectin, inulin, and cellulose), singly and in combination. Furthermore, fermentation supernatants (FSs) were evaluated in Caco-2 cells for their effect on cell viability, differentiation, and apoptosis. Cincau increased total SCFA concentration by increasing acetate and propionate, but not butyrate concentration. FSs from all dietary fibre sources, including cincau, reduced Caco-2 cell viability. However, the effects of all FSs on cell viability, cell differentiation, and apoptosis were not simply explainable by their butyrate content. In conclusion, products of fermentation of cincau extracts induced cell death, but further work is required to understand the mechanism of action. This study demonstrates for the first time that this Indonesian traditional source of dietary fibre may be protective against colorectal cancer.

Effect of edible coatings with essential oils on the quality of red raspberries over shelf-life

BACKGROUND

The objective of the present work was to develop strategies for increasing the shelf-life of red raspberries (Rubus idaeus L.), by preventing microorganism growth.

RESULTS

Fruits coated with alginate plus lemon essential oil (0.2%) or orange essential oil (0.1%) after 15 days of storage had less red skin than the remaining samples. The less red color verified in these samples was also coincident with the lower concentration of anthocyanins at the end of the experiment as well as the lower capacity for scavenging ABTS free radicals or quenching singlet oxygen. Cyanidin and pelargonidin glucosides were found in raspberries fruits. The edible coatings supplemented with the essential oil of orange either at 0.1% or 0.2% were very efficient for controlling yeast and mold growth after 15 days of storage. To control the development of aerobic mesophilic bacteria the use of essential oil of lemon 0.2% and essential oil of orange 0.1% were the most efficient.

CONCLUSION

The application of the film improved post-harvest quality of raspberry, since the addition of essential oils of citrus films promoted to the inhibitory effect of fungi and bacteria growth after 15 days of storage, without changing quality parameters. © 2016 Society of Chemical Industry.

High Occurrence Rate and Contamination Level of Bacillus cereus in Organic Vegetables on Sale in Retail Markets

Organic foods have risen in popularity recently. However, the increased risk of bacterial contamination of organic foods has not been fully evaluated. In this study, 100 samples each of organic and conventional fresh vegetables (55 lettuce samples and 45 sprout samples) sold in South Korea were analyzed for aerobic bacteria, coliforms, Escherichia coli, and Bacillus cereus. Although the aerobic bacteria and coliform counts were not significantly different between the two farming types (p > 0.05), the occurrence rate of B. cereus was higher in organically cultivated vegetables compared with those grown conventionally (70% vs. 30%, respectively). The mean contamination level of B. cereus-positive organic samples was also significantly higher (1.86 log colony-forming unit [CFU]/g vs. 0.69 log CFU/g, respectively) (p < 0.05). In addition, six samples of organic vegetables were found to be contaminated with B. cereus at over 4 log CFU/g categorized as unsatisfactory according to Health Protection Agency guideline. The relatively higher occurrence rate of B. cereus in organic vegetables emphasizes the importance of implementing control measures in organic vegetable production and postharvest processing to reduce the risk of food poisoning.

Quantification and identification of microorganisms found on shell and kernel of fresh edible chestnuts in Michigan

BACKGROUND

Chestnut is a relatively new cultivated crop for Michigan, and postharvest loss due to decay has been problematic as production has increased each year. In 2007, more than 25% of chestnuts were lost to postharvest decay, equivalent to approximately 5300 kg of fresh product. To determine the organisms responsible for decay, a microbiological survey was performed in 2006 and 2007 to identify microorganisms involved in postharvest shell (external surface) mold and internal kernel (edible portion) decay of chestnuts.

RESULTS

Filamentous fungi including Penicillium expansum, Penicillium griseofulvum, Penicillium chrysogenum, Coniophora puteana, Acrospeira mirabilis, Botryosphaeria ribis, Sclerotinia sclerotiorum, Botryotinia fuckeliana (anamorph Botrytis cinerea) and Gibberella sp. (anamorph Fusarium sp.) were the predominant microorganisms that negatively impacted fresh chestnuts. Populations of microorganisms varied between farms, harvesting methods and chestnut parts.

CONCLUSION

Chestnuts harvested from the orchard floor were significantly (P < 0.05) more contaminated than chestnuts harvested directly from the tree, by more than 2 log colony-forming units (CFU) g(-1) . In addition, a significant difference (P < 0.05) in the microbial population was seen between chestnuts submitted by different growers, with average count ranges of fungi, mesophilic aerobic bacteria (MAB) and yeasts equal to 4.75, 4.59 and 4.75 log CFU g(-1) respectively. © 2016 Society of Chemical Industry.

Biological activities and DNA interactions of Amanita ovoidea

CONTEXT

Amanita ovoidea (Bull.) Link (Amanitaceae) is a well-known species due to its pleasant aroma and flavor since ancient times in the worldwide. This species is also known in Turkey and people consume it extensively.

OBJECTIVE

To evaluate medicinal importance of A. ovoidea for human health, to explain the effect of mushroom extracts on bacterial DNA, and to find preventive role on bacterial disease.

MATERIALS AND METHODS

Chloroform, acetone, and methanol extracts of A. ovoidea were tested for the antimicrobial activities against four Gram-positive bacteria, five Gram-negative bacteria, and yeast using a micro-dilution method. In addition, DNA binding, DNA cleavage activity, and restriction enzyme digestion of the methanol extract of A. ovoidea were examined at different concentrations (40.000-78.125 µg/mL).

RESULTS

The highest minimum inhibitory concentration (MIC) value observed against the test micro-organisms was with the chloroform extract (MIC 19.5 µg/mL concentration) against Candida albicans. Other highest antimicrobial effects observed against the test micro-organisms were with the methanol extracts against Bacillus subtilis, Staphylococcus aureus, Listeria monocytogenes, Streptococcus pyogenes, Candida albicans, Klebsiella pneumoniae, Proteus vulgaris, and Salmonella enteritidis (MICs, 78 µg/mL concentrations). All concentrations reduced the mobility of plasmid DNA. BamHI and HindIII targeted specially to supercoils and cut them. Amanita ovoidea extract prevented cutting with HindIII by binding especially to the AA region in open circular DNA.

DISCUSSION AND CONCLUSION

Present results demonstrated that A. ovoidea has excellent antimicrobial and antifungal activities by its DNA interaction activity on pBR322.

Application of response surface methodology to optimise microbial inactivation of shrimp and conch by supercritical carbon dioxide

BACKGROUND

Supercritical carbon dioxide (SC-CO2 ) has been shown to have a good pasteurising effect on food. However, very few research papers have investigated the possibility to exploit this treatment for solid foods, particularly for seafood. Considering the microbial safety of raw seafood consumption, the study aimed to explore the feasibility of microbial inactivation of shrimp (Metapenaeus ensis) and conch (Rapana venosa) by SC-CO2 treatment.

RESULTS

Response surface methodology (RSM) models were established to predict and analyse the SC-CO2 process. A 3.69-log reduction in the total aerobic plate count (TPC) of shrimp was observed by SC-CO2 treatment at 53°C, 15 MPa for 40 min, and the logarithmic reduction in TPC of conch was 3.31 at 55°C, 14 MPa for 42 min. Sensory scores of the products achieved approximately 8 (desirable). The optimal parameters for microbial inactivation of shrimp and conch by SC-CO2 might be 55°C, 15 MPa and 40 min.

CONCLUSION

SC-CO2 exerted a strong bactericidal effect on the TPC of shrimp and conch, and the products maintained good organoleptic properties. This study verified the feasibility of microbial inactivation of shrimp and conch by SC-CO2 treatment.

[Antimicrobial activity of bacteriocin S760 produced by Enterococcus faecium strain LWP760]

Antimicrobial activity of bacteriocin S760 (enterocin) produced by Enterococcusfaecium strain LWP760 was studied. Bacteriocin S760 is a cationic, hydrophobic, and heat stable peptide with the molecular weight of 5.5 kDa and pl of 9.8. Enterocin S760 is shown to inhibit in vitro the growth both of sensitive and resistant to antibacterials gramnegative and grampositive bacteria of 25 species. MICs of the bacteriocin S760 vary between 0.05-1.6 mg/l for Escherichia coli 0157:H117, Salmonella typhimurium, Salmonella enteritidis, Campylobacter jejuni, Yersinia enterocolitica, Yersinia pseudotuberculosis, Listeria monocytogenes and Clostridium perfringens, that are main food-borne pathogens, and from 0.4-1.6 mg/l for Streptococcus pyogenes, Streptococcus pneumoniae and Corynebacterium diphteriae. It is also active against antibioticresistant strains of Staphylococcus aureus, Enterobacter cloacae, Acinetobacter baumannii (with MICs of 0.05-3 mg/l), Klebsiella pneumoniae (with MICs of 6 mg/l), Pseudomonas aeruginosa (with MICs of 0.4-25 mg/1), as well against fungi belonging to species of Candida albicans, Candida krusei and Aspergillus niger (with MICs of 0.1-0.2 mg/l). Enterocin S760 is a novel antimicrobial agents useful in medicine, veterinary and food industry.

[Symbiotic microflora in fishes of different ecological groups]

Published data on the taxonomic composition of the intestinal bacterial flora in fishes living under different conditions (marine and freshwater fishes) and differing in the type of feeding are reviewed. The results confirm the conclusion that the composition of intestinal microflora differs depending on fish ecology. A limited number of bacterial taxa found in the intestines of some fish species may be evidence not only for a low diversity of these bacteria but also for insufficient knowledge about them. Considerable differences in the composition of intestinal microflora in marine and freshwater fishes are described.

Presumed pseudobacteremia outbreak resulting from contamination of proportional disinfectant dispenser

Reported here are the microbiological and epidemiological details of a presumed outbreak of aerobic gram-negative bacilli infections affecting 19 hematological patients, which was traced to contaminated disinfectant. Over a 5-month period, the following organisms were isolated from the blood cultures of 19 neutropenic patients: Pseudomonas fluorescens (n = 13), Achromobacter xylosoxidans (n = 12), Comamonas testosteroni (n = 2) or Stenotrophomonas maltophilia (n = 1). The affected patients were all treated with an expensive regimen of broad-spectrum antibiotic therapy. The same bacteria were recovered from environmental samples as well as from the water pipes of an apparatus for dispensing disinfectant (didecyldimethylammonium chloride). Genotyping results indicated that many of the clinical strains were identical to strains isolated from the apparatus. It was eventually discovered that the night staff was in the habit of disinfecting the blood-culture bottles before use, thereby contaminating the bottles with bacteria contained in the disinfectant. Contamination of the apparatus resulted from faulty maintenance.

Purification and biochemical characterization of a protease secreted by the Salinivibrio sp. strain AF-2004 and its behavior in organic solvents

A metalloprotease secreted by the moderately halophilic bacterium Salinivibrio sp. strain AF-2004 when the culture reached the stationary growth phase. This enzyme was purified to homogeneity by acetone precipitation and subsequent Q-Sepharose anion exchange and Sephacryl S-200 gel filtration chromatography. The apparent molecular mass of the protease was 31 kDa by SDS-PAGE, whereas it was estimated as approximately 29 kDa by Sephacryl S-200 gel filtration. The purified protease had a specific activity of 116.8 mumol of tyrosine/min per mg protein on casein. The optimum temperature and salinity of the enzyme were at 55 degrees C and 0-0.5 M NaCl, although at salinities up to 4 M NaCl activity still remained. The protease was stable and had a broad pH profile (5.0-10.0) with an optimum of 8.5 for casein hydrolysis. The enzyme was strongly inhibited by phenylmethyl sulfonylfluoride (PMSF), Pefabloc SC, chymostatin and also EDTA, indicating that it belongs to the class of serine metalloproteases. The protease in solutions containing water-soluble organic solvents or alcohols was more stable than that in the absence of organic solvents. These characteristics make it an ideal choice for applications in industrial processes containing organic solvents and/or salts.

Antagonistic activity against pathogenic bacteria by human vaginal lactobacilli

This study attempted to isolate lactobacilli strains from healthy vaginal ecosystem to search for a new effective antibacterial probiotic strain. The strains were identified and characterized for their probiotic properties including bile salt and acid tolerance, growth at acidic pH, their ability to utilize protein, starch, and lipid, the production of hydrogen peroxide and bacteriocin as well as their antibiotic resistance patterns. The antibacterial activity of the culture supernatant of these strains were tested against a wide range of Gram-positive and Gram-negative pathogenic bacteria including Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae. Salmonella typhi, and Salmonella typhimurium. None of the strains inhibited the growth of Gram-negative bacteria. Contrastly, the culture supernatant of strain L 22, identified as Lactobacillus reuteri, significantly inhibited all of the clinical isolates of methicillin-resistant S. aureus (MRSA). The antibacterial effect of the selected strain L 22 was further investigated. In the presence of L 22, the bacterial growth was assessed in vitro by viable bacterial counting. The numbers of viable cells were significantly lower in L 22-containing broth than those in the control by 6h. This finding clearly demonstrates that strain L 22 can produce an anti-MRSA effect. The antibacterial ability of the strain L 22 was fundamentally attributed to their bacteriocin production which can cause both cell inhibition and cell death.

Adaptation of sympatric Achromatium spp. to different redox conditions as a mechanism for coexistence of functionally similar sulphur bacteria

Changes in the abundance of sympatric Achromatium spp. in response to the artificial manipulation of redox conditions in sediment microcosms was determined by fluorescence in situ hybridization (FISH). Adaptation to different redox conditions was shown to be one mechanism that supported the coexistence of functionally similar Achromatium spp. In sediment microcosms, in which the overlying water was oxygenated, Achromatium community size and composition remained unchanged over time. However, imposition of anoxic conditions induced changes in community structure. Anoxia caused a reduction in the relative abundance of Achromatium sp. RY8 (72 +/- 4% to 49 +/- 2%) and an increase in Achromatium sp. RY5 (19 +/- 5% to 32 +/- 3%) and a newly identified Achromatium sp., RYKS (14 +/- 4% to 27 +/- 2%). In anoxic microcosms supplemented with a single addition of nitrate at different initial concentrations the relative decline in Achromatium sp. RY8 was dependent on the initial nitrate concentration. In these experiments nitrate was rapidly removed. In contrast, when high levels of nitrate were maintained by periodic replacement of the overlying water with nitrate supplemented anoxic water, the composition of the Achromatium community remained stable over time. This suggested that all of the coexisting Achromatium spp. are obligate or facultative anaerobes, but, Achromatium sp. RY8 was more sensitive to sediment redox conditions than the other Achromatium species. Given the heterogeneous nature of sedimentary environments, redox-related niche differentiation may promote coexistence of sympatric Achromatium spp.

Influence of growth environment on coaggregation between freshwater biofilm bacteria

AIM

To characterize the expression of coaggregation between Blastomonas natatoria 2.1 and Micrococcus luteus 2.13 following growth in liquid culture, on agar and in an artificial biofilm matrix composed of poloxamer hydrogel.

METHODS AND RESULTS

The ability of B. natatoria 2.1 and M. luteus 2.13 to coaggregate with one another was assessed following growth in liquid culture as colonies on agar or within a poloxamer hydrogel matrix. In all these environments a cycle of gain and loss of coaggregation occurred when the two cell types were aged simultaneously, with optimum expression occurring in early stationary phase. Blastomonas natatoria 2.1 cells only coaggregated maximally after entry into stationary phase. Conversely, M. luteus 2.13 cells only coaggregated in exponential phase and early stationary phase and coaggregation ability was lost in late stationary phase. Maximal coaggregation therefore only occurred between the two strains if both were in early stationary phase, when the surface properties of the two cell types were optimal for coaggregation.

CONCLUSION

In addition to occurring between cells grown in liquid culture, coaggregation between aquatic bacteria occurs after growth as a biofilm on agar and in an artificial biofilm matrix in poloxamer. Under all conditions, the B. natatoria 2.1 coaggregation adhesin and complementary receptor on M. luteus 2.13 were only expressed simultaneously during early stationary phase.

[Features of solid materials' colonization by pure and mixed cultures of methanotrophs]

The process of colonization of hydrophilic (glass) and hydrophobic (polysterene) carriers by pure cultures of methanotrophs Methylocystis parvus UCM B-3490T, Methylococcus capsulatus UCM B-3030, as well as by their cultures mixed with Bacillus megaterium UCM B 5723T and Pseudomonas putida VKPM B-4188 under the conditions efficient for methanotrophic bacteria. M. parvus demonstrated the highest intensity of this process on the above carriers owing to high hydrophobic cell surface. Both methanotrophs colonized the glass surface more quickly with formation of microcolonies on carriers after 6 days of incubation in pure and mixed cultures with B. megaterium. The number of bacilli on these carriers quickly decreased. In the mixed cultures with P. putida the glass and polysterene colonization intensity decreased, while the amount of pseudomonas on carriers increased.

Production of free and organic iodine byRoseovariusspp

Two strains of iodine-producing bacteria were isolated from marine samples. 16S rRNA gene sequences indicated the strains were most closely related to Roseovarius tolerans, and phylogenetic analysis indicated both belong to the same genus. 5 mM iodide inhibited the growth of strain 2S5-2 almost completely, and of strain S6V slightly. Both strains produced free iodine and organic iodine from iodide. CH2I2, CHI3 and CH2ClI were the main organic iodines produced by strain 2S5-2, and CHI3 and CH2I2 by strain S6V. Experiments using cells and spent media suggested that the organic iodines were produced from the compounds released or contained in the media and cells were necessary for the considerable production of CH2I2 and CH2ClI, though CHI3 was produced by spent media with H2O2 or free iodine.

Synthetic dihydropacidamycin antibiotics: a modified spectrum of activity for the pacidamycin class

Dihydropacidamycins having an antibacterial spectrum modified from that of the natural product pacidamycins and mureidomycins have been synthesized. Synthetic dihydropacidamycins with noteworthy antibacterial activity against wild-type and resistant Escherichia coli have been identified (MIC=4-8 microg/mL). Some dihydropacidamycins are shown to have activity against multi-resistant clinical strains of Mycobacterium tuberculosis. Compounds of this class are inhibitors of the cell wall biosynthetic enzyme, MraY.

[Leptospirillum-like bacteria and their role in pyrite oxidation]

Two strains of Leptospirillum-like bacteria isolated from dumps of Alaverdi and Akhtala sulfide ore deposits in Armenia were studied. The optimum and maximum temperatures for the growth of both strains were 37 and 40 degrees C, respectively. The pH optimum was 2.0-2.3. Bacterial growth and ferrous iron oxidation were inhibited by yeast extract. The pyrite-leaching activity of the Leptospirillum-like bacteria under mesophilic conditions was close to that of Acidithiobacillus ferroxidans and exceeded by 2.0-2.7 times the activity of these moderately thermophilic bacteria at 37 degrees C. The leaching of pyrite by Leptospirillum-like bacteria increased in the presence of sulfur-oxidizing bacteria, particularly, in their association with a thermotolerant sulfur-oxidizing bacterium.

[Effect of gas mixture component composition on the process of hard materials colonization by methanotrophic bacteria]

A device has been proposed which allows decreasing a possibility to contaminate the inoculum of methane-using bacteria (methanotrophs) under its growing. The gas mixture composition has been investigated for the intensity of grass and polysterene colonization by two species of methanotrophs: Methylococcus capsulatus UCM B-3030, possessing hydrophilic surface and hydrophobic Methylocystis parvus UKM B-3490T. It has been shown that immobilized methanotrophic bacteria can colonize the above materials in the wide range of methane and oxygen concentrations in gas mixture. The process of hard materials colonization was most intensive when the mixture contained 17-28% of methane and 5-28% of oxygen. No essential differences have been registered under colonization of hydrophilic (glass) and hydrophobic (polysterene) materials by the both cultures.

Microbial growth on dichlorobiphenyls chlorinated on both rings as a sole carbon and energy source

We have isolated bacterial strains capable of aerobic growth on ortho-substituted dichlorobiphenyls as sole carbon and energy sources. During growth on 2,2'-dichlorobiphenyl and 2,4'-dichlorobiphenyl strain SK-4 produced stoichiometric amounts of 2-chlorobenzoate and 4-chlorobenzoate, respectively. Chlorobenzoates were not produced when strain SK-3 was grown on 2,4'-dichlorobiphenyl.

A novel protein-deamidating enzyme from Chryseobacterium proteolyticum sp. nov., a newly isolated bacterium from soil

A novel protein-deamidating enzyme, which has potential for industrial applications, was purified from the culture supernatant of Chryseobacterium proteolyticum strain 9670(T) isolated from rice field soil in Tsukuba, Japan. The deamidating activities on carboxybenzoxy (Cbz)-Gln-Gly and caseins and protease activity were produced synchronously by the isolate. Both deamidating activities were eluted as identical peaks separated from several proteases by phenyl-Sepharose chromatography of the culture supernatant. The enzyme catalyzed the deamidation of native caseins with no protease and transglutaminase activities. Phenotypic characterization and DNA analyses of the isolate were performed to determine its taxonomy. Physiological and biochemical characteristics, 16S rRNA gene sequence analysis, and DNA-DNA relatedness data indicated that the isolate should be placed as a new species belonging to the genus Chryseobacterium. The isolate showed no growth on MacConkey agar and produced acid from sucrose. The levels of DNA-DNA relatedness between the isolate and other related strains were less than 17%. The name Chryseobacterium proteolyticum is proposed for the new species; strain 9670 is the type strain (=FERM P-17664).

Anaerobic-aerobic process for microbial degradation of tetrabromobisphenol A

Tetrabromobisphenol A (TBBPA) is a flame retardant that is used as an additive during manufacturing of plastic polymers and electronic circuit boards. Little is known about the fate of this compound in the environment. In the current study we investigated biodegradation of TBBPA, as well as 2,4,6-tribromophenol (TBP), in slurry of anaerobic sediment from a wet ephemeral desert stream bed contaminated with chemical industry waste. Anaerobic incubation of the sediment with TBBPA and peptone-tryptone-glucose-yeast extract medium resulted in a 80% decrease in the TBBPA concentration and accumulation of a single metabolite. This metabolite was identified by gas chromatography-mass spectrometry (GC-MS) as nonbrominated bisphenol A (BPA). On the other hand, TBP was reductively dehalogenated to phenol, which was further metabolized under anaerobic conditions. BPA persisted in the anaerobic slurry but was degraded aerobically. A gram-negative bacterium (strain WH1) was isolated from the contaminated soil, and under aerobic conditions this organism could use BPA as a sole carbon and energy source. During degradation of BPA two metabolites were detected in the culture medium, and these metabolites were identified by GC-MS and high-performance liquid chromatography as 4-hydroxybenzoic acid and 4-hydroxyacetophenone. Both of those compounds were utilized by WH1 as carbon and energy sources. Our findings demonstrate that it may be possible to use a sequential anaerobic-aerobic process to completely degrade TBBPA in contaminated soils.

Ecological study of a bioaugmentation failure

A nitrifying sequencing batch reactor was inoculated twice with the aerobic denitrifying bacterium Microvirgula aerodenitrificans and fed with acetate. No improvement was obtained on nitrogen removal. The second more massive inoculation was even followed by a nitrification breakdown, while at the same time, nitrification remained stable in a second reactor operated under the same conditions without bioaugmentation. Fluorescent in situ hybridization with rRNA-targeted probes revealed that the added bacteria almost disappeared from the reactor within 2 days, and that digestive vacuoles of protozoa gave strong hybridization signals with the M. aerodenitrificans-specific probe. An overgrowth of protozoa, coincident with the disappearance of free-living bacteria, was monitored by radioactive dot-blot hybridization only in the bioaugmented reactor. Population dynamics were analysed with a newly developed in situ quantification procedure of the probe-targeted bacteria. The nitrifying groups of bacteria decreased in a similar way in the bioaugmented and non-bioaugmented reactors. Other bacterial groups evolved differently. The involvement of different ecological parameters are discussed separately for each reactor. These results underline the importance of predator-prey interaction and illustrate the undesirable effects of massive bioaugmentation.

Coaggregation between aquatic bacteria is mediated by specific-growth-phase-dependent lectin-saccharide interactions

Coaggregating strains of aquatic bacteria were identified by partial 16S rRNA gene sequencing. The coaggregation abilities of four strains of Blastomonas natatoria and one strain of Micrococcus luteus varied with culture age but were always maximum in the stationary phase of growth. Each member of a coaggregating pair carried either a heat- and protease-sensitive protein (lectin) adhesin or a saccharide receptor, as coaggregation was reversed by sugars.

Purification and characterization of the heat-labile alpha-amylase secreted by the psychrophilic bacterium TAC 240B

A total of 59 bacteria samples from Antarctic sea water were collected and screened for their ability to produce alpha-amylase. The highest activity was recorded from an isolate identified as an Alteromonas species. The purified alpha-amylase shows a molecular mass of about 50,000 Da and a pI of 5.2. The enzyme is stable from pH 7.5 to 9 and has a maximal activity at pH 7.5. Compared with other alpha-amylases from mesophiles and thermophiles, the "cold enzyme" displays a higher activity at low temperature and a lower stability at high temperature. The psychrophilic alpha-amylase requires both Cl- and Ca2+ for its amylolytic activity. Br- is also quite efficient as an allosteric effector. The comparison of the amino acid composition with those of other alpha-amylases from various organisms shows that the cold alpha-amylase has the lowest content in Arg and Pro residues. This could be involved in the principle used by the psychrophilic enzyme to adapt its molecular structure to the low temperature of the environment.

Optimization of simultaneous chemical and biological mineralization of perchloroethylene

Optimization of the simultaneous chemical and biological mineralization of perchloroethylene (PCE) by modified Fenton's reagent and Xanthobacter flavus was investigated by using a central composite rotatable experimental design. Concentrations of PCE, hydrogen peroxide, and ferrous iron and the microbial cell number were set as variables. Percent mineralization of PCE to CO2 was investigated as a response. A second-order, quadratic response surface model was generated and fit the data adequately, with a correlation coefficient of 0.72. Analysis of the results showed that the PCE concentration had no significant effect within the tested boundaries of the model, while the other variables, hydrogen peroxide and iron concentrations and cell number, were significant at alpha = 0.05 for the mineralization of PCE. The 14C radiotracer studies showed that the simultaneous chemical and biological reactions increased the extent of mineralization of PCE by more than 10% over stand-alone Fenton reactions.

A corrinoid-dependent catabolic pathway for growth of a Methylobacterium strain with chloromethane

Methylobacterium sp. strain CM4, an aerobic methylotrophic alpha-proteobacterium, is able to grow with chloromethane as a carbon and energy source. Mutants of this strain that still grew with methanol, methylamine, or formate, but were unable to grow with chloromethane, were previously obtained by miniTn5 mutagenesis. The transposon insertion sites in six of these mutants mapped to two distinct DNA fragments. The sequences of these fragments, which extended over more than 17 kb, were determined. Sequence analysis, mutant properties, and measurements of enzyme activity in cell-free extracts allowed the definition of a multistep pathway for the conversion of chloromethane to formate. The methyl group of chloromethane is first transferred by the protein CmuA (cmu: chloromethane utilization) to a corrinoid protein, from where it is transferred to H4folate by CmuB. Both CmuA and CmuB display sequence similarity to methyltransferases of methanogenic archaea. In its C-terminal part, CmuA is also very similar to corrinoid-binding proteins, indicating that it is a bifunctional protein consisting of two domains that are expressed as separate polypeptides in methyl transfer systems of methanogens. The methyl group derived from chloromethane is then processed by means of pterine-linked intermediates to formate by a pathway that appears to be distinct from those already described in Methylobacterium. Remarkable features of this pathway for the catabolism of chloromethane thus include the involvement of a corrinoid-dependent methyltransferase system for dehalogenation in an aerobe and a set of enzymes specifically involved in funneling the C1 moiety derived from chloromethane into central metabolism.

Production of poly(3-hydroxybutyric acid-co-4-hydroxybutyric acid) and poly(4-hydroxybutyric acid) without subsequent degradation by Hydrogenophaga pseudoflava

A Hydrogenophaga pseudoflava strain was able to synthesize poly(3-hydroxybutyric acid-co-4-hydroxybutyric acid) [P(3HB-co-4HB)] having a high level of 4-hydroxybutyric acid monomer unit (4HB) from gamma-butyrolactone. In a two-step process in which the first step involved production of cells containing a minimum amount of poly(3-hydroxybutyric acid) [P(3HB)] and the second step involved polyester accumulation from the lactone, approximately 5 to 10 mol% of the 3-hydroxybutyric acid (3HB) derived from the first-step culture was unavoidably reincorporated into the polymer in the second cultivation step. Reincorporation of the 3HB units produced from degradation of the first-step residual P(3HB) was confirmed by high-resolution 13C nuclear magnetic resonance spectroscopy. In order to synthesize 3HB-free poly(4-hydroxybutyric acid) [P(4HB)] homopolymer, a three-stage cultivation technique was developed by adding a nitrogen addition step, which completely removed the residual P(3HB). The resulting polymer was free of 3HB. However, when the strain was grown on gamma-butyrolactone as the sole carbon source in a synthesis medium, a copolyester of P(3HB-co-4HB) containing 45 mol% 3HB was produced. One-step cultivation on gamma-butyrolactone required a rather long induction time (3 to 4 days). On the basis of the results of an enzymatic study performed with crude extracts, we suggest that the inability of cells to produce 3HB in the multistep culture was due to a low level of 4-hydroxybutyric acid (4HBA) dehydrogenase activity, which resulted in a low level of acetyl coenzyme A. Thus, 3HB formation from gamma-butyrolactone is driven by a high level of 4HBA dehydrogenase activity induced by long exposure to gamma-butyrolactone, as is the case for a one-step culture. In addition, intracellular degradation kinetics studies showed that P(3HB) in cells was completely degraded within 30 h of cultivation after being transferred to a carbon-free mineral medium containing additional ammonium sulfate, while P(3HB-co-4HB) containing 5 mol% 3HB and 95 mol% 4HB was totally inert in interactions with the intracellular depolymerases. Intracellular inertness could be a useful factor for efficient synthesis of the P(4HB) homopolymer and of 4HB-rich P(3HB-co-4HB) by the strain used in this study.

Multiple genes involved in chitin degradation from the marine bacterium Pseudoalteromonas sp. strain S91

A cluster of three closely linked chitinase genes organized in the order chiA, chiB and chiC, with the same transcriptional direction, and two unlinked genes, chiP and chiQ, involved in chitin degradation in Pseudoalteromnas sp. strain S91 were cloned, sequenced and characterized. The deduced amino acid sequences revealed that ChiA, ChiB and ChiC exhibited similarities to chitinases belonging to family 18 of the glycosyl hydrolases while ChiP and ChiQ belonged to family 20. ChiP and ChiQ showed different enzymic activities against fluorescent chitin analogues, but neither was able to degrade colloidal chitin. ChiA possessed chitinase activity but did not bind chitin; ChiB bound chitin but had no chitinase activity; ChiC possessed strong chitinase activity and also bound chitin. Production of ChiC in S91 appeared to be controlled by chiA expression, since insertion of a transposon into the ORF of chiA resulted in the loss of chitinase activity as well as loss of ChiC proteins in a chitinase-negative mutant. In Escherichia coli, ChiC appeared to be expressed from its own promoter.

Membrane-bound electron transfer chain of the thermohalophilic bacterium Rhodothermus marinus: characterization of the iron-sulfur centers from the dehydrogenases and investigation of the high-potential iron-sulfur protein function by in vitro reconstitution of the respiratory chain

Rhodothermus marinus, a thermohalophilic bacterium, has a unique electron-transfer chain, containing, besides a cbb3 and a caa3 terminal oxidases, a novel cytochrome bc complex [Pereira, M. M., Carita, J. N., and Teixeira, M. (1999) Biochemistry 38, 1268-1275]. The membrane-bound iron-sulfur centers of this bacterium were studied by electron paramagnetic resonance (EPR) spectroscopy, leading to the identification of its main electron-transfer complexes. The resonances typical for the Rieske-type centers are not detected. Clusters S1 and S3 from succinate dehydrogenase were identified; interestingly, center S3 is shown to be present in two different conformations, with g values at 2.035, 2.009, and 2.001 and at 2.025, 2.002, and 2.000. Upon addition of NADH and dithionite, EPR signals assigned to resonances characteristic of binuclear and tetranuclear clusters develop and are attributed to the iron-sulfur centers of complexes I and II. A high-potential iron-sulfur protein- (HiPIP-) type center previously detected in the membranes of this bacterium [Pereira et al. (1994) FEBS Lett. 352, 327-330] is shown to belong indeed to a canonical HiPIP. This protein was purified and extensively characterized. It is a small water-soluble protein of approximately 10 kDa, containing a single [4Fe-4S]3+/2+ cluster. The reduction potential, determined by EPR redox titrations in intact and detergent-solubilized membranes as well as by cyclic voltammetry in solution, has a pH-independent value of 260 +/- 20 mV, in the range 6-9. In vitro reconstitution of the R. marinus electron-transfer chain shows that the HiPIP plays a fundamental role in the chain, as the electron shuttle between R. marinus cytochrome bc complex and the caa3 terminal oxidase, being thus simultaneously identified a HiPIP reductase and a HiPIP oxidase.

[Occurrence of gram-negative non-fermenting rods in hemocultures and their sensitivity to antimicrobial agents]

In the period from January 1993 to June 1996 were at the Department of Microbiology of the University Hospital in Olomouc 122 strains of Gram-negative nonfermentative rod-shaped bacteria isolated from haemocultures. The majority represented the group of 51 strains of the genus Acinetobacter (41.8%), complex A. calcoaceticus-baumannii (Acb complex). The second largest group were 21 strains (17.2%) of Pseudomonas aeruginosa. These were followed by 17 strains (13.9%) of Stenotrophomonas maltophilia, 8 strains (6.6%) of non-Acb complex acinetobacters, 6 strains (4.9%) of Pseudomonas putida and 5 strains (4.1%) of Alcaligenes xylosoxidans. The remaining species were represented only by 1-2 strains. In three isolations was the identification impossible. The majority of strains (24.6%) were from the Department of Haematology of the University Hospital in Olomouc. The most frequent diagnoses in patients with positive haemocultures were leukemias and lymphomas (24.6%). The most effective tested antimicrobial agents were ceftazidime (93.4% of sensitive strains) and ofloxacin (91.7%). From the total number of 80 strains detected using the equipment BacT/Alert 120, 22 (27.5%) were isolated repeatedly confirming their role in the etiology of bacteriemic or septic episodes. Because only one blood sample was obtained in 34 cases (58.6%) of the remaining 58 only once detected strains, it was impossible to confirm their etiologic role by repeated isolation. (Tab. 6, Ref. 22.)

Direct antimicrobial susceptibility testing of gram-negative bacilli in blood cultures by an electrochemical method

Nonfastidious aerobic gram-negative bacilli (GNB) are commonly isolated from blood cultures. The feasibility of using an electrochemical method for direct antimicrobial susceptibility testing of GNB in positive blood cultures was evaluated. An aliquot (10 microliter) of 1:10-diluted positive blood cultures containing GNB was inoculated into the Bactometer module well (bioMérieux Vitek, Hazelwood, Mo.) containing 1 ml of Mueller-Hinton broth supplemented with an antibiotic. Susceptibility tests were performed in a breakpoint broth dilution format, with the results being categorized as resistant, intermediate, or susceptible. Seven antibiotics (ampicillin, cephalothin, gentamicin, amikacin, cefamandole, cefotaxime, and ciprofloxacin) were used in this study, with each agent being tested at the two interpretive breakpoint concentrations. The inoculated modules were incubated at 35 degreesC, and the change in impedance in each well was continuously monitored for 24 h by the Bactometer. The MICs of the seven antibiotics for each blood isolate were also determined by the standardized broth microdilution method. Of 146 positive blood cultures (1,022 microorganism-antibiotic combinations) containing GNB tested by the direct method, the rates of very major, major, and minor errors were 0, 1.1, and 2.5%, respectively. The impedance method was simple; no centrifugation, preincubation, or standardization of the inocula was required, and the susceptibility results were normally available within 3 to 6 h after inoculation. The rapid method may allow proper antimicrobial treatment almost 30 to 40 h before the results of the standard methods are available.

Detection and partial characterization of bacteriocin in the methanotrophic bacterium Methylobacter bovis

The strain Methylobacter bovis 98 was selected among methanotrophic bacteria as one of the most active producers of secretory bacteriocin-like compounds. In the above strain this compound was shown to be a protein with a molecular weight of about 70 kD, relatively thermostable, having a bactericidal effect on closely related organisms. Its properties as a whole are consistent with the accepted definition of bacteriocins, which so far have not been found in this group of microorganisms. A methodical approach that combines electrophoretic separation of secretory proteins and testing their antibacterial activity directly in polyacrylamide gel allowed us for the first time to identify bacteriocin in methanotrophic bacterial culture.

Acquired thermotolerance and temperature-induced protein accumulation in the extremely thermophilic bacterium Rhodothermus obamensis

Temperature-induced changes in thermotolerance and protein composition were examined in heat-shocked cells and high-temperature-grown cells of the extremely thermophilic bacterium Rhodothermus obamensis. The survival at temperatures superoptimal for growth (90 and 95 degrees C) was enhanced in both heat-shocked cells and high-temperature-grown cells relative to that of cells grown at optimal temperatures. In a comparison of protein composition using two-dimensional gel electrophoresis, putative heat shock proteins (HSPs) and high-temperature growth-specific proteins (HGPs) were detected. N-terminal amino acid sequence analysis revealed that the putative HSPs were quite similar to the ATP-binding subunits of ABC transporters and the HGPs were proteins corresponding to domains II and III of elongation factor Tu. These results suggested that this extreme thermophile has developed temperature-induced responses that include increased survival under hyperthermal conditions, changes in protein composition, and also the production of novel HSPs.

Cloning, sequencing and overexpression of a Rhodothermus marinus gene encoding a thermostable cellulase of glycosyl hydrolase family 12

A gene library from the thermophilic eubacterium Rhodothermus marinus, strain ITI 378, was constructed in pUC18 and transformed into Escherichia coli. Of 5400 transformants, 3 were active on carboxymethylcellulose. Three plasmids conferring cellulase activity were purified and were all found to contain the same cellulase gene, celA. The open reading frame for the celA gene is 780 base pairs and encodes a protein of 260 amino acids with a calculated molecular mass of 28.8 kDa. The amino acid sequence shows homology with cellulases in glycosyl hydrolase family 12. The celA gene was overexpressed in E. coli when the pET23, T7 phage RNA polymerase system was used. The enzyme showed activity on carboxymethylcellulose and lichenan, but not on birch xylan or laminarin. The expressed enzyme had six terminal histidine residues and was purified by using a nickel nitrilotriacetate column. The enzyme had a pH optimum of 6-7 and its highest measured initial activity at 100 degrees C. The heat stability of the enzyme was increased by removal of the histidine residues. It then retained 75% of its activity after 8 h at 90 degrees C.

An automated system for biocide testing on biofilms

The paper presents and discusses a novel on-line real-time non-destructive continuous-flow system for biocide testing on industrial biofilms. This laboratory system is capable of monitoring changes in growth, accumulation and respiratory activity of biofilms in response to biocidal treatment. The system incorporates a fouling monitor for continuous measuring of the rate of biofilm accumulation (heat transfer resistance), a sensor for monitoring of microbial activity (oxygen meter for monitoring the rate of biofilm respiratory activity), and subsystems necessary for microbial life support and control of operation parameters. Examples of system operation and testing of oxidizing and non-oxidizing biocides are presented.

Assignment of biochemical functions to glycosyl transferase genes which are essential for biosynthesis of exopolysaccharides in Sphingomonas strain S88 and Rhizobium leguminosarum

Glycosyl transferases which recognize identical substrates (nucleotide-sugars and lipid-linked carbohydrates) can substitute for one another in bacterial polysaccharide biosynthesis, even if the enzymes originate in different genera of bacteria. This substitution can be used to identify the substrate specificities of uncharacterized transferase genes. The spsK gene of Sphingomonas strain S88 and the pssDE genes of Rhizobium leguminosarum were identified as encoding glucuronosyl-(B1-->4)-glucosyl transferases based on reciprocal genetic complementation of mutations in the spsK gene and the pssDE genes by segments of cloned DNA and by the SpsK-dependent incorporation of radioactive glucose (Glc) and glucuronic acid (GlcA) into lipid-linked disaccharides in EDTA-permeabilized cells. By contrast, glycosyl transferases which form alternative sugar linkages to the same substrate caused inhibition of polysaccharide synthesis or were deleterious or lethal in a foreign host. The negative effects also suggested specific substrate requirements: we propose that spsL codes for a glucosyl-(beta1-->4)-glucuronosyl transferase in Sphingomonas and that pssC codes for a glucuronosyl-(beta1-->4)-glucuronosyl transferase in R. leguminosarum. Finally, the complementation results indicate the order of attachment of sphingan main-chain sugars to the C55-isoprenylphosphate carrier as -Glc-GlcA-Glc-isoprenylpyrophosphate.

Impact of inoculation protocols, salinity, and pH on the degradation of polycyclic aromatic hydrocarbons (PAHs) and survival of PAH-degrading bacteria introduced into soil

Degradation of polycyclic aromatic hydrocarbons (PAHs) and survival of bacteria in soil was investigated by applying different inoculation protocols. The soil was inoculated with Sphingomonas paucimobilis BA 2 and strain BP 9, which are able to degrade anthracene and pyrene, respectively. CFU of soil bacteria and of the introduced bacteria were monitored in native and sterilized soil at different pHs. Introduction with mineral medium inhibited PAH degradation by the autochthonous microflora and by the strains tested. After introduction with water (without increase of the pore water salinity), no inhibition of the autochthonous microflora was observed and both strains exhibited PAH degradation.

Research note: in vitro inhibition of Listeria monocytogenes growth by veillonellae cultures grown on tartrate media

Veillonellae cultures were grown on agar media supplemented with tartrate and examined for inhibitory effects on the growth of Listeria monocytogenes. Veillonellae cultures grown on media supplemented with 0 or 50 mmol l-1 of tartrate did not inhibit the growth of L. monocytogenes; however, veillonellae grown on media supplemented with 100, 150 or 200 mmol l-1 of tartrate did inhibit the growth of L. monocytogenes. The inhibition of the growth of L. monocytogenes by the veillonellae was correlated with the increased production of acetate and propionate from tartrate by veillonellae and with the reduction of the pH of the media by L. monocytogenes.

Enzymology of the degradation of (di)chlorobenzenes by Xanthobacter flavus 14p1

Xanthobacter flavus 14p1 used 1,4-dichlorobenzene as the sole source of carbon and energy but did not grow on other (chloro)aromatic compounds. 1,4-Dichlorobenzene was attacked by a chlorobenzene dioxygenase, and the intermediate chlorocatechol was metabolized by the modified ortho pathway. All enzymes necessary to convert 1, 4-dichlorobenzene to 3-oxoadipate showed a low substrate specificity and also accepted the respective intermediates of chlorobenzene or 1, 3-dichlorobenzene degradation. Of the three compounds chlorobenzene, 1,4-dichlorobenzene, and 1,3-dichlorobenzene, the latter was the most toxic for X. flavus 14p1. Furthermore, 1,3-dichlorobenzene did not induce chlorocatechol 1,2-dioxygenase activity of the organism. Chlorobenzene, however, induced chlorocatechol 1,2-dioxygenase, dienelactone hydrolase, and maleylacetate reductase activities. As demonstrated by chloride release, also chlorobenzene dioxygenase, chlorobenzene cis-dihydrodiol dehydrogenase, and chloromuconate cycloisomerase activities were present in chlorobenzene-induced cells, but chlorobenzene failed to support growth. Presumably a toxic compound was formed from one of the intermediates.

Structure of the capsular polysaccharide from Alteromonas nigrifaciens IAM 13010T containing 2-acetamido-2,6-dideoxy-L-talose and 3-deoxy-D-manno-octulosonic acid

A capsular polysaccharide was obtained from Alteromonas nigrifaciens IAM 13010T by saline extraction. On the basis of 1H and 13C NMR spectroscopy, including one-dimensional (1D) NOE spectroscopy, 2D rotating-frame NOE spectroscopy (ROESY), and 1H-detected heteronuclear 1H,13C multiple-quantum coherence (HMQC), it was concluded that the polysaccharide contained inter alia an acidic sugar, 3-deoxy-D-manno-octulosonic acid (Kdo), and a rare amino sugar, 2-acetamido-2,6-dideoxy-L-talose (L-6dTalNAc, N-acetylpneumosamine), and has a pentasaccharide repeating unit of the following structure: [equation: see text]

A fatty acid alpha-ketol, a product of the plant lipoxygenase pathway, is oxidized to 3(Z)-dodecendioic acid by a bacterial monooxygenase

The fatty acid alpha-ketol 13-hydroxy-12-oxo-9(Z)-octadecenoic acid (methyl ester) was incubated with a bacterial culture isolated from soil. The bacteria (tentatively identified as Ralstonia sp.) exhibited strong monooxygenase activity growing on 2-tridecanone as sole source of carbon. They catalyzed a Baeyer-Villiger type of oxidation and converted the alpha-ketol to 3(Z)-dodecendioic acid. 3(Z)-Dodecendioic acid was isolated from the incubation mixture and identified by comparison with an authentic reference compound. These findings offer both a physiological role for alpha-ketol fatty acids in plant lipid hydroperoxide metabolism and new insights into an alternative biosynthetic pathway leading to traumatic acid (2(E)-dodecendioic acid).

Osmoprotectants in Halomonas elongata: high-affinity betaine transport system and choline-betaine pathway

The osmoregulatory pathways of the moderately halophilic bacterium Halomonas elongata DSM 3043 have been investigated. This strain grew optimally at 1.5 to 2 M NaCl in M63 glucose-defined medium. It required at least 0.5 M NaCl for growth, which is a higher concentration than that exhibited by the H. elongata type strain ATCC 33173. Externally provided betaine, choline, or choline-O-sulfate (but not proline, ectoine, or proline betaine) enhanced the growth of H. elongata on 3 M NaCl-glucose-M63 plates, demonstrating the utilization of these compounds as osmoprotectants. Moreover, betaine and choline stimulated the growth of H. elongata DSM 3043 over the entire range of salinity, although betaine was more effective than choline at salinities below and above the optimum. We found that H. elongata DSM 3043 has at least one high-affinity transport system for betaine (K(m) = 3.06 microM and Vmax = 9.96 nmol of betaine min(-1) mg of protein(-1)). Competition assays demonstrated that proline betaine and ectoine, but not proline, choline, or choline-O-sulfate, are also transported by the betaine permease. Finally, thin-layer chromatography and 13C-nuclear magnetic resonance analysis showed that exogenous choline was taken up and transformed to betaine by H. elongata, demonstrating the existence of a choline-glycine betaine pathway in this moderately halophilic bacterium.

Improved large scale culture of Methylophilus methylotrophus for 13C/15N labeling and random fractional deuteration of ribonucleotides

Isotopic labeling of RNA with 13C and 15N has become a routine procedure in structural studies by NMR spectroscopy. The methodology in this paper describes the random fractional deuteration of RNA using the obligate methylotropic bacterium, Methylophilus methylotrophus. This bacterium was grown using a non-deuterated carbon source in 52:48 D20/H20 and we have shown that all protons in the ribonucleotides except for the ribose H1 become 52% randomly fractionally deuterated. Improved growth conditions for this organism are also described that yield higher cell densities in liquid culture, which is applicable for all labeling procedures.

Isolation and characterization of isopimaric acid-degrading bacteria from a sequencing batch reactor

We isolated two aerobic, gram-negative bacteria which grew on the diterpene resin acid isopimaric acid (IpA) as the sole carbon source and electron donor. The source of the isolates was a sequencing batch reactor treating a high-strength process stream from a paper mill. The isolates, IpA-1 and IpA-2, also grew on pimaric and dehydroabietic acids, and IpA-1 grew on abietic acid. Both strains used fatty acids, but neither strain used camphor, sitosterol, or betulin. Strain IpA-1 grew anaerobically with nitrate as an electron acceptor. Strains IpA-1 and IpA-2 had growth yields of 0.19 and 0.23 g of protein per g of IpA, respectively. During growth, both strains transformed IpA carbon to approximately equal amounts of biomass, carbon dioxide, and dissolved organic carbon. In both strains, growth on IpA induced an enzymatic system which caused cell suspensions to transform all four of the above resin acids. Cell suspensions of IpA-1 and IpA-2 removed IpA at rates of 0.56 and 0.13 mumol mg of protein-1 h-1, respectively. Cultures and cell suspensions of both strains failed to completely consume pimaric acid and yielded small amounts of an apparent metabolite from this acid. Cultures and cell suspensions of both strains yielded large amounts of three apparent metabolites from dehydroabietic acid. Analysis of 16S rDNA sequences indicated that the isolates are distinct members of the genus Pseudomonas sensu stricto.