Effect of oxygen and peroxide on Bacteroides fragilis cell and phage survival after treatment with DNA damaging agents

Abstract Bacteroides fragilis Bf-2 cells were more sensitive to far-UV radiation, N -methyl- N '-nitrosoguanidine, ethylmethane sulphonate, acriflavine and mitomycin C under aerobic conditions than under anaerobic conditions. The opposite effect was observed with H₂O₂-treated cells and exposure to O₂ enhanced the survival of H₂O₂-treated cells. Pretreatment of cells with sublethal concentrations of H₂O₂ also increased the survival of H₂O₂-treated cells. Reactivation of UV- and X-irradiated and methylmethane sulphonate and H₂O₂-treated phage b-1 was induced by O₂ and H₂O₂ in B. fragilis .     

A strict anaerobic extreme thermophilic hydrogen-producing culture enriched from digested household waste

Aims:  The aim of this study was to enrich, characterize and identify strict anaerobic extreme thermophilic hydrogen (H₂) producers from digested household solid wastes.
Methods and Results:  A strict anaerobic extreme thermophilic H₂ producing bacterial culture was enriched from a lab-scale digester treating household wastes at 70°C. The enriched mixed culture consisted of two rod-shaped bacterial members growing at an optimal temperature of 80°C and an optimal pH 8·1. The culture was able to utilize glucose, galactose, mannose, xylose, arabinose, maltose, sucrose, pyruvate and glycerol as carbon sources. Growth on glucose produced acetate, H₂ and carbon dioxide. Maximal H₂ production rate on glucose was 1·1 mmol l⁻¹ h⁻¹ with a maximum H₂ yield of 1·9 mole H₂ per mole glucose. 16S ribosomal DNA clone library analyses showed that the culture members were phylogenetically affiliated to the genera Bacillus and Clostridium. Relative abundance of the culture members, assessed by fluorescence in situ hybridization, were 87 ± 5% and 13 ± 5% for Bacillus and Clostridium , respectively.
Conclusions:  An extreme thermophilic, strict anaerobic, mixed microbial culture with H₂-producing potential was enriched from digested household wastes.
Significance and Impact of the Study:  This study provided a culture with a potential to be applied in reactor systems for extreme thermophilic H₂ production from complex organic wastes.     

Enterobacteriaceae facilitate the anaerobic degradation of glucose by a forest soil

Anoxic micro zones that occur in soil aggregates of oxic soils may be temporarily extended after rainfall and thus facilitate the anaerobic degradation of organic compounds in soils. The microbial degradation of glucose by anoxic slurries of a forest soil yielded acetate, CO₂, H₂, succinate, and ethanol, products indicative of mixed acid fermentation. Prokaryotes involved in this process were identified by time-resolved 16S rRNA gene-targeted stable isotope probing with [¹³C-U]-glucose. All labeled phylotypes from the ¹³C-enriched 16S rRNA gene were most closely related to Rahnella and Ewingella , enterobacterial genera known to catalyze mixed acid fermentation. These results indicate that facultative aerobes, in particular Enterobacteriaceae , (1) can outcompete obligate anaerobes when conditions become anoxic in forest soils and (2) may be involved in the initial decomposition of monosaccharides in anoxic micro zones of aerated forest soils.     

The application of compound bi-directional flow diffusion chemostats to the study of microbial interactions

Abstract A multi-stage bi-directional chemostat system has been developed in which solutes but not cells are allowed to diffuse between the individual growth chambers which are separated by 0.2 micron pore size polyvinyledene difluoride membranes. The experimental system enables the generation of physico-chemical gradients which, together with the spatial separation of the individual microbial processes, provides a useful laboratory model to study microbial interactions. This paper describes the construction of a multi-stage diffusion chemostat and its application in studying carbon flow in anaerobic estuarine sediments. Populations of Clostridium butyricum, Desulfovibrio desulfuricans and Chromatium vinosum were grown in the compound diffusion chemostat at a dilution rate of 0.03 h⁻¹ at 25°C, and the effects of inorganic nitrogen source and availability on carbon flow and individual cell populations were determined. C. butyricum and D. desulfuricans both used NO⁻₃ as an e⁻ acceptor with an increase in cell numbers. Under these growth conditions, free S²⁻ concentrations were lower, resulting in more stable cell populations than in comparable cultures grown on NH⁺₄ as nitrogen source.     

Peroxide inducible phage reactivation in Bacteroides fragilis

Abstract Reactivation of UV-irradiated phage b-1 was induced by H₂O₂ and UV in Bacteroides fragilis . The characteristics of H₂O₂ and UV induced phage reactivation differ from a previously reported oxygen induced reactivation system. The survival of B. fragilis cells after UV irradiation was also increased by pretreatment with H₂O₂. DNA synthesis was not inhibited in the host cells exposed to H₂O₂ concentrations which induced phage reactivation. The pattern of DNA degradation and synthesis after UV irradiation with and without H₂O₂ differed from the effect of O₂ on DNA synthesis in irradiated B. fragilis cells.     

Gas exchange in intact isolated chloroplasts from Chlamydomonas reinhardtii during starch degradation in the dark

During starch degradation in intact isolated chloroplasts from Chlamydomonas reinhardtii gas exchange was studied with a mass spectrometer. Oxygen uptake by intact chloroplasts in the dark never exceeded 1.5% of the starch degradation rate [maximum 15 nmol O₂ (mg Chl)⁻¹ h⁻¹ consumed. 1 000 nmol glucose (mg Chl)⁻¹h⁻¹ degraded]. Evolution of CO₂ under aerobic conditions [9.8–28 nmol (mg Chl)⁻¹ h⁻¹] was stimulated by addition of 0.1–0.5 m M oxaloacetate [393–425 nmol CO₂ (mg Chl)⁻¹ h⁻¹]. Pyridoxal phosphate (5 m M ) inhibited starch degradation by more than 80%, but had no effect on O₂ uptake. Starch degradation rates and CO₂ evolution did not differ under acrobic and anaerobic conditions. Increasing P_i in the reaction medium from 0.5 m M to 5.0 m M stimulated starch degradation by 230 and 260% under aerobic and anaerobic conditions, respectively. A rapid autooxidation of reduced ferredoxin was observed in a reconstituted system consisting of purified Chlamydomonas ferredoxin, purified Chlamydomonas NADP-ferredoxin oxidoreductase (EC 1.6.7.1) and NADPH. Addition of isolated thylakoids from C. reinhardtii did not affect the rate of O₂ uptake. Our results clearly indicate the absence of any oxygen requirement during starch degradation in isolated chloroplasts.     

End products of metabolism in the anaerobic ciliate Trimyema compressum

Abstract The products of anaerobic and micro-aerobic (0.8% O₂) metabolism of the sapropelic ciliate Trimyema compressum strain N were studied. Under anaerobic conditions ethanol was formed in large amounts representing 44% of the total carbon excreted. Acetate, lactate, formate, CO₂ and H₂ were minor products, while succinate was formed in hardly detectable amounts. Under micro-aerobic conditions O₂ was consumed, CO₂ and formate were produced as major end products and no H₂, ethanol and succinate were formed.     

Associative cellulolysis and N2 fixation by co-cultures of Trichoderma harzianum and Clostridium butyricum: the effects of ammonium-N on these processes

Mixed cultures of the cellulolytic fungus Trichoderma harzianum with the anaerobic diazotroph Clostridium butyricum were shown to co-operatively degrade cellulose and utilize the degradation products for N₂ fixation. Cellulose degradation and N₂ fixation were stimulated by small (0.1 mg/ml) additions of (NH₄)₂SO₄. The (NH₄₂SO₄ stimulates cellulolysis thereby increasing the supply of cellulose degradation products to the diazotroph. In aerobic environments the anaerobe depends on the respiration of the aerobe to create anaerobic microsites. The N source increased O₂ uptake by the fungus increasing the number of sites suitable for the development of the anaerobe. Stimulation in the growth of T. harzianum by (NH₄₂SO₄ resulted in increased growth and N₂ fixation by Cl. butyricum.     

Induction of proteins during phage reactivation induced by UV irradiation, oxygen and peroxide in Bacteroides fragilis

Abstract Phage reactivation systems in Bacteroides fragilis were induced by far-UV irradiation, O₂ and H₂O₂. These three treatments also induced the synthesis of 3, 6, and 4 protein bands, respectively, which were easily detectable by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Two proteins with apparent M _r s of approx. 90 000 and 70 000 were induced by all three treatments. Caffeine completely inhibited UV- and O₂-induced phage reactivation and prevented the synthesis of the M _r 90 000 and M _r 70 000 proteins. The results suggest that these two proteins may be involved in phage reactivation processes induced by UV, O₂ and H₂O₂ in B. fragilis .     

Hydrogen-dependent control of the continuous thermophilic anaerobic digestion process using membrane inlet mass spectrometry

The control of a thermophilic continuous anaerobic digestion system when subjected to potential inhibitory shock loadings was achieved through the regulation of dissolved H₂, monitored using membrane inlet mass spectrometry, by the controlled addition of carbon source. At a feed pump switching threshold equivalent to 1 μmol/1 H₂ a steady state rate of methanogenesis of approximately 40 μmol/1/min was obtained. Higher H₂ thresholds resulted in an inhibition of methanogenesis, but precise control of H₂ concentration was demonstrated with an oscillatory response of period 2·5–5·0 min.     

In vivo phosphorylation of proteins in Clostridium sphenoides

Abstract Cell contents of Clostridium sphenoides , labeled with [³²P]orthophosphate under strict anaerobic conditions, were analyzed by two-dimensional gel electrophoresis. Autoradiography of these gels demonstrated the presence of at least 15 ³²P-labeled protein species, of which M _r and iso-electric point were determined. Treatment of the radioactively labeled cell contents with alkaline phosphatase and acid phosphatase showed that all these proteins were modified by phosphorylation. These findings demonstrate for the first time the presence of phosphorproteins in a strictly anaerobic bacterium.     

Oxygen control prevents denitrifiers and barley plant roots from directly competing for nitrate

Abstract Two denitrifying bacteria ( Pseudomonas chlororaphis and P. aureofaciens ) and a plant (barley, Hordeum vulgare ) were used to study the effect of O₂ concentration on denitrification and NO₃⁻ uptake by roots under well-defined aeration conditions. Bacterial cells in the early stationary phase were kept in a chemostat vessel with vigorous stirring and thus a uniform O₂ concentration in the solution. Both Pseudomonads lacked N₂O reductase and so total denitrification could be directly measured as N₂O production.
Denitrification decreased to 6–13% of the anaerobic rate at 0.01% O₂ saturation (0.14 μM O₂) and was totally inhibited at 0.04% O₂ saturation (0.56 μM O₂). In this well-mixed system denitrification was 10-times more oxygen sensitive than stated in earlier reports. Uptake of nitrate by plants was measured in the same system under light. The NO₃⁻ uptake rate decreased gradually from a maximum in 21% O₂-saturated medium (air saturated) to zero at 1.6% O₂ saturation (22.4 μM O₂). Owing to the very different non-overlapping oxygen requirements of the two processes, direct competition for nitrate between plant roots and denitrifying bacteria cannot occur.     

Convenient anaerobic techniques, science from the supermarket shelf

We describe the application and evaluation of a widely available commercial jar as an anaerobic container suitable for the growth of a wide variety of anaerobes. A system for generating stable anaerobiosis was developed by combining standard anaerobic environment generators with Click-Clack jars produced by Click-Clack Ltd. This system was simple, reliable, and reduced capital outlay on anaerobic jars by at least an order of magnitude.     

An Egg-yolk Agar Diffusion Assay for Monitoring Phospholipase C in Cultures of Clostridium welchii

An egg-yolk agar diffusion assay of phospholipase C has been developed and investigated. The results demonstrate the necessity for strict control of the pH and volume of the egg-yolk agar and of the temperature and duration of incubation of the assay plates. The method has been used to monitor phospholipase C production in cultures of Clostridium welchii sparged continuously with CO₂ in N₂ and shows that maximal concentration occurs after ca. 6-8 h incubation at 37°C. The concentration falls slowly during subsequent anaerobic incubation supporting the opinion that Cl. welchii may elaborate a proteinase which destroys phospholipase C.     

Temperature profile of oxygen activation and defense against oxygen toxicity in a psychrophilic member of the Bacteroidaceae

Abstract The temperature profiles have been determined for O₂ reduction by activating substrates for whole cells and cell extracts of the psychrophilic, obligately anaerobic bacterium, strain B6, belonging to the Bacteroidaceae. The profiles were similar whether the cells were grown at 15 or 1°C, and also for cells harvested in the exponential or stationary phase. The H₂O producing pyruvate oxidase displayed in cell-free extracts a considerably higher activity than the H₂O₂ producing NADH and NADPH oxidases at all temperatures in the range 30–1°C, and characteristically makes up a larger proportion of the total O₂ reduction capacity the lower the temperature. It thus seems that the O₂ scavenging property of the pyruvate oxidase, postulated to be utilized in a defense mechanism against the detrimental effects of the H₂O₂ producing pyridine nucleotide oxidases, is particularly well adapted to function at the low temperatures of the Barents Sea, from which this obligately anaerobic organism originates.     

Behavioural and physiological adaptations to a burrowing lifestyle in the snake blenny, Lumpenus lampretaeformis, and the red band-fish, Cepola rubescens

Observations have been made on the mode of burrow construction in the snake blenny, Lumpenus lampretaeformis , under laboratory conditions. It appears that head probing and lateral oscillations of the body are principally responsible for the excavation of the burrow which is completed within 24 h. The burrow structure has been analysed in detail, showing a mean depth of 7.2 cm with a maximum observed length of 73 cm, with most systems between 20 and 35 cm in length. Initially linear burrows with two openings are usually provided with a small side tunnel, giving the system a characteristic Y-shape.
Burrow irrigation was investigated for the first time in L. lampretaeformis. The mean duration of burrow irrigation, by flexions of the tail of the fish, was 21 s with over 13 min h⁻¹ spent in irrigating the burrow. The mean water displacement per irrigation period was 3.1 ml. The PO ₂ and PCO ₂ were measured in both surface water and within the burrow system of L. lampretaeformis. Surface water values for PO ₂ were high (> 150 Torr) and PCO ₂ low (<0.4 Torr). Hypoxic and hypercapnic conditions were measured in the burrow system itself, with PO ₂ values ranging between 57 and 129 Torr and PCO ₂ rising to > 1.3 Torr in some burrows.
A comparative study of Cepola rubescens burrows indicated similar surface water PO ₂ and PCO ₂ values as in L. lampretaeformis. Burrow water PO ₂ values ranged between 60 and 94 Torr, with PCO ₂ values as high as 1.5 Torr being recorded. These results are discussed in relation to the adaptation of both species to a burrowing lifestyle.     

Vertical distribution of methane metabolism in microbial mats of the Great Sippewissett Salt Marsh

Methane metabolism was investigated with respect to depth in intertidal microbial mats of the Great Sippewissett Salt Marsh, Massachusetts. Although sulfate-reducing organisms dominate anaerobic carbon consumption in marine microbial mats, methanogens persist and their activity varies vertically and temporally in the mat system. In the Sippewissett mats, potential methane production for all mat layers was higher in the spring (17.2 ± 4.5 nmol CH₄ cm⁻² day⁻¹) than in the fall (3.0 ± 1.1 nmol CH₄ cm⁻² day⁻¹) and maximal rates were consistently observed in proximity to the chemocline (5–10 mm depth). The methane flux from the mat surface did not vary appreciably over time due to the ability of methanotrophic activity to limit net methane production. Evidence indicates that both aerobic and anaerobic oxidation of methane occurs in this system. The importance of H₂ as a substrate for methanogenesis appeared to be the greatest at the mat surface (0–10 mm), and the proportion of methylotrophic methanogens generally increased with depth. These results suggest that both non-equilibrium H₂ dynamics and the use of non-competitive substrates permit coexistence of methanogens and sulfate-reducing organisms in the mat system.     

The use of PCR to monitor the population abundance of six human intestinal bacterial species in an in vitro semicontinuous culture system

Abstract Six PCR primer sets complementary to the 16S rDNAs (rRNA genes) were developed and shown to be specific for the following anaerobic bacteria: Clostridium clostridiiforme, C. perfringens, C. leptum, Bacteroides vulgatus, B. distasonis , and B. thetaiotaomicron , respectively. These primers were used for PCR to detect and monitor the bacteria in a semicontinuous culture system designed to mimic intestinal microflora in the human gastrointestinal tract. Except for C. perfringens , the five species of Bacteroides and Clostridia present in the in vitro culture system were detected by the PCR, and the titers varied from 10⁻² to 10⁻⁶ dilutions. The role of azo dye reduction by these bacterial species in the system was examined and discussed.     

Sporulation of Clostridium putrefaciens and the Resistance of the Spores to Heat, γ-Radiation and Curing Salts

Clostridium putrefaciens grew well in most media used routinely for culturing anaerobes, but produced spores only on lactose-egg yolk agar. The D_80° was 8–14 min, z value was 4°–6° and D _γ, 0.16 Mrad. The inhibitory interactions of pH, NaCl, NaNO₂ and incubation temperature are described.     

Post-exercise metabolic rate in Atlantic cod and its dependence upon the method of exhaustion

This study tests whether or not post-exercise oxygen consumption rates ( M o₂) in fish are dependent upon how exhaustion is induced. A group of eight Atlantic cod ( Gadus morhua ) were each exercised using (1) a critical swimming speed ( U _crit) protocol, (2) an exercise protocol designed to measure anaerobic capacity of fish ( U _burst), and (3) a protocol in which the fish were chased to exhaustion manually. M o₂ was measured for a 2-h period following exhaustion induced by all three exercise regimes ( U _crit, U _burst and chase). Post-exercise M o₂ following exhaustion from the U _burst and chase protocols were significantly higher than post-exercise M o₂ following the U _crit protocol. Each fish during the U _crit protocol exhibited maximal M o₂ during exercise rather than during recovery, yet 75% of the fish during U _brust recovery and 100% during chase recovery exhibited M o₂ higher than that measured during U _crit exercise. These results, as well as the large interindividual variations in M o₂ among the eight fish, show that post-exhaustion M o₂ is specific to the exercise regime employed, thus, investigators must exercise caution when combining results from different exercise protocols and/or individuals.