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NADPH oxidase, Nramp1 and nitric oxide synthase 2 in the host antimicrobial response.

Using highly conserved, complex enzyme systems, leukocytes utilize the toxic nature of free radical intermediates, derived from oxygen and nitrogen, to control microbial pathogens as part of the innate immune response. Upon activation, NADPH oxidase generates superoxide anion radicals, which in turn give rise to further reactive oxygen intermediates. Similarly, activated nitric oxide synthase 2 catalyses the production of nitric oxide radicals, which leads to the formation of reactive nitrogen intermediates. Nitrogen- and oxygen-centered reactive intermediates can interact to form further reactive species. In addition, presence of the cationic transporter, Nrampl, may exacerbate the effects of these toxic compounds on invading microbes. While each of these antimicrobial systems can operate independently, the combination of their activities is synergistic in the successful containment of almost all invading pathogens. These systems are activated and modulated by microbial products and a series of temporally expressed cytokines. They also feed directly into the initiation of the adaptive immune response, which culminates in lasting specific immunity. The effector molecules, generated in the early innate immune response, are not specific to the invading pathogen and may also cause damage to the host. It is the critical balance of these processes in the initial stages of infection that determines the outcome of infectious disease.

Animals↗

Microbial Biomass and Community Structure in a Sequence of Soils with Increasing Fertility and Changing Land Use.

The microbial biomass and community structure of eight Chinese red soils with different fertility and land use history was investigated. Two community based microbiological measurements, namely, community level physiological profiling (CLPP) using Biolog sole C source utilization tests and phospholipid fatty acid (PLFA) profiles, were used to investigate the microbial ecology of these soils and to determine how land use alters microbial community structure. Microbial biomass-C and total PLFAs were closely correlated to organic carbon and total nitrogen, indicating that these soil microbial measures are potentially good indices of soil fertility in these highly weathered soils. Metabolic quotients and C source utilization were not correlated with organic carbon or microbial biomass. Multivariate analysis of sole carbon source utilization patterns and PLFAs demonstrated that land use history and plant cover type had a significant impact on microbial community structure. PLFAs showed these differences more than CLPP methods. Consequently, PLFA analysis was a better method for assessing broad-spectrum community differences and at the same time attempting to correlate changes with soil fertility. Soils from tea orchards were particularly distinctive in their CLPP. A modified CLPP method, using absorbance readings at 405 nm and different culture media at pH values of 4.7 and 7.0, showed that the discrimination obtained can be influenced by the culture conditions. This method was used to show that the distinctive microbial community structure in tea orchard soils was not, however, due to differences in pH alone.

Journal Article↗

Polyacrylamide added as a nitrogen source stimulates methanogenesis in consortia from various wastewaters.

Polyacrylamides are widely used as flocculants to enhance clarification of drinking waters and domestic wastewaters, for stabilization of agricultural soils, and to aid in managing mine tailings. The flocs produced with polyacrylamide may be deposited into retention areas that become anaerobic. Although it is unlikely that the carbon backbone of these polymers would be cleaved by microbial activity, the amide group could serve as a nitrogen source for microorganisms. Previous studies have shown that aerobic bacteria utilize the nitrogen from polyacrylamide. This study assessed whether methanogenesis was stimulated when an anionic polyacrylamide (Magnafloc LT27AG) was the sole fixed nitrogen source in serum-bottle microcosms. Microorganisms from two oil sands tailings sources, and a domestic anaerobic sewage sludge were used, with benzoate or acetate provided as carbon and energy sources. In each inoculum-substrate combination, the presence of polyacrylamide-enhanced methane production, indicating that polyacrylamide may stimulate microbial activities in anaerobic environments that are rich in fermentable carbon, but lack nitrogen sources.

Acetates↗

Aspects of urea metabolism in ruminants with reference to the goat.

In goats and other ruminants, urea functions as a source of nitrogen for protein biosynthesis in the digestive tract. Ammonia can be absorbed in the digestive system when formed in excessive quantitites and enhance formation of urea, or it can be derived from urea of blood plasma when its formation from feed sources is small. Entry rates of urea into plasma may vary from 4 to 80 mumol/min per kg.75 body weight depending on dietary conditions. Urea formation is related to nitrogen intake of which approximately 70% passes into the urea pool of plasma. Irreversible losses of urea of plasma into the digestive tract vary between 10 and 90% depending on the protein to energy ratios of the diet. Entry of urea from plasma into the rumen appears to be a passive process which is sensitive to short-term changes of urea concentrations in plasma. Permeability of ruminal epithelium to urea may be altered by fermentation products of rumen (ammonia, carbon dioxide, volatile fatty acids). The influx of nitrogen into the rumen is related to needs for nitrogen of microbial populations and is associated with changes of renal excretion and tubular reabsorption of urea. Combined gastrointestinal and renal responses exert a synergistic effect on improved utilization of urea of plasma when uptake of dietary nitrogen is limited in goats and other ruminants.

Animals↗

Effect of barley and its amylopectin content on ruminal fermentation and nitrogen utilization in lactating dairy cows.

The effect of type of grain (corn vs. barley) and amylopectin content of barley grain (normal vs. waxy) on ruminal fermentation, digestibility, and utilization of ruminal ammonia nitrogen for milk protein synthesis was studied in a replicated 3 x 3 Latin square design trial with 6 lactating dairy cows. The experimental treatments were (proportion of dietary dry matter): CORN, 40% corn grain, NBAR, 30% normal Baronesse barley:10% corn grain, and WBAR, 30% high-amylopectin (waxy) Baronesse barley:10% corn grain. All grains were steam-rolled and fed as part of a total mixed ration. The NBAR and WBAR diets resulted in increased ruminal ammonia concentrations compared with CORN (8.2, 7.4, and 5.6 mM, respectively), but other ruminal fermentation parameters were not affected. Ruminal digestibility of dietary nutrients and microbial protein synthesis in the rumen were also not affected by diet. Corn grain had greater in situ effective ruminal dry matter degradability (62.8%) than the barley grains (58.2 and 50.7%, respectively), and degradability of the normal barley starch was greater than that of the waxy barley (69.3 and 58.9%, respectively). A greater percentage of relative starch crystallinity was observed for the waxy compared with the normal barley grain. Total tract apparent digestibility of dry matter and organic matter were decreased by WBAR compared with CORN and NBAR. Total tract starch digestibility was greater and milk urea nitrogen content was lower for CORN compared with the 2 barley diets. In this study, the extent of processing of the grain component of the diet was most likely the factor that determined the diet responses. Minimal processing of barley grain (processing indexes of 79.2 to 87.9%) reduced its total tract digestibility of starch compared with steam-rolled corn (processing index of 58.8%). As a result of the increased ammonia concentration and reduced degradability of barley dry matter in the rumen, the utilization of ruminal ammonia nitrogen for microbial protein synthesis was decreased with the barley diets compared with the corn-based diet. In this study, waxy Baronesse barley was less degradable in the rumen and the total digestive tract than its normal counterpart. The most likely reasons for these effects were the differences in starch characteristics and chemical composition, and perhaps the different response to processing between the 2 barleys.

Amylopectin↗

Using pyrosequencing to shed light on deep mine microbial ecology.

BACKGROUND: Contrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence data was a costly and time-consuming process in defining an environment. Here we have used pyrosequencing, a rapid and relatively inexpensive sequencing technology, to generate environmental genome sequences from two sites in the Soudan Mine, Minnesota, USA. These sites were adjacent to each other, but differed significantly in chemistry and hydrogeology. RESULTS: Comparisons of the microbes and the subsystems identified in the two samples highlighted important differences in metabolic potential in each environment. The microbes were performing distinct biochemistry on the available substrates, and subsystems such as carbon utilization, iron acquisition mechanisms, nitrogen assimilation, and respiratory pathways separated the two communities. Although the correlation between much of the microbial metabolism occurring and the geochemical conditions from which the samples were isolated could be explained, the reason for the presence of many pathways in these environments remains to be determined. Despite being physically close, these two communities were markedly different from each other. In addition, the communities were also completely different from other microbial communities sequenced to date. CONCLUSION: We anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages. Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.

Bacteria↗

Factors affecting the biodegradation of cyanide by Burkholderia cepacia strain C-3.

The utilization of cyanide as a nitrogen source for growth in a liquid minimal medium by Burkholderia cepacia strain C-3 isolated from soil was demonstrated. The effects of various parameters on the biodegradation of cyanide by the strain were investigated. Growth at the expense of cyanide occurred over a pH range from 8 to 10, and was optimal at pH 10. Growth and cyanide biodegradation were optimal at 30 degrees C. The presence of Cu2+ or Fe2+ in the liquid medium at a concentration of 1 mM inhibited both the growth of the bacterium and its cyanide degradation. The effects of Ni2+ and Co2+, and to a lesser extent Mn2+ and Mo2+, on cyanide degradation rate were concentration dependent. Addition of the cyanide-containing waste contaminants ethanol and methanol reduced the cyanide utilization of the isolate, but phenol was completely inhibitory. Microbial depletion of cyanide occurred even in the presence of other organic and inorganic nitrogen sources. Fructose, glucose, and mannose were the preferred carbon sources for cyanide biodegradation. The highest rate of cyanide degradation by B. cepacia C-3, 1.85 mg CN h(-1), was observed with 0.25% (w/v) fructose; the degradation rate decreased progressively thereafter with increasing fructose concentration.

Journal Article↗

Do mammals, birds, reptiles and fish have similar nitrogen conserving systems?

Comparative physiological studies are a powerful tool for revealing common animal adaptations. Amino acid catabolism produces ammonia which is detoxified through the synthesis of urea (mammals, some fish), uric acid (birds), or urea and uric acid (reptiles). In mammalian herbivores and omnivores, urea nitrogen is salvaged by a series of steps involving urea transfer into the intestine, microbial mediated urea hydrolysis with synthesis of amino acids utilizing the liberated ammonia and transfer of the amino acids back to the host. A similar series of steps occur in omnivorous/granivorous and herbivorous birds, although in this case urine, containing uric acid, is refluxed directly into the intestine where microbes degrade the uric acid and utilize the liberated ammonia for amino acid synthesis. These amino acids are transferred back to the host. In reptiles and ureotelic fish not all of these steps have been experimentally confirmed. Reptiles like birds, reflux urine into the intestine where it is exposed to the microflora. However, the capacity of these microbes to breakdown the uric acid and urea and utilize ammonia for amino acid synthesis has not been documented. Ureotelic fish transfer urea into the intestine where urease (presumably of bacterial origin) hydrolyzes the urea. However, the amino acid synthesizing capacity of the intestinal microflora has not been studied. The series of steps, as outlined, would define the prevailing nitrogen conservation system for herbivores and omnivores at least. However, it would appear that some animals, in particular the fruit-eating bat and perhaps the fruit-eating bird, may have evolved alternative, as yet uncharacterized, adaptations to a very limited nitrogen intake.

Ammonia↗

The nutritive value of rumen micro-organisms in ruminants. 4. The limiting amino acids of microbial protein in growing sheep determined by a new approach.

Four experiments were carried out to identify and quantify the limiting amino acids (AA) in rumen microbial protein (RMP). A method was developed which involved first, an assessment of the efficiency of utilization of absorbed AA-nitrogen (U) of RMP, defined as the retention of AA-N from RMP absorbed from the small intestine, and second, addition of a mixture of AA similar to the absorbed AA profile in a quantity defined by the U of RMP and equal to (1-U)/U. Third, it involved removal of each AA in turn and measurement of the resultant N retention. Using this approach it was possible to calculate both the order and extent of AA limitations in RMP. Apart from methionine which was found to be the most limiting AA, only lysine, arginine and histidine reduced N retention when omitted, and accordingly only these AA were limiting in RMP. The method is discussed in detail and the amount of supplementary AA required to utilize RMP fully is calculated.

Amino Acids↗

Chemical and biological interactions during nitrate and goethite reduction by Shewanella putrefaciens 200.

Although previous research has demonstrated that NO(3)(-) inhibits microbial Fe(III) reduction in laboratory cultures and natural sediments, the mechanisms of this inhibition have not been fully studied in an environmentally relevant medium that utilizes solid-phase, iron oxide minerals as a Fe(III) source. To study the dynamics of Fe and NO(3)(-) biogeochemistry when ferric (hydr)oxides are used as the Fe(III) source, Shewanella putrefaciens 200 was incubated under anoxic conditions in a low-ionic-strength, artificial groundwater medium with various amounts of NO(3)(-) and synthetic, high-surface-area goethite. Results showed that the presence of NO(3)(-) inhibited microbial goethite reduction more severely than it inhibited microbial reduction of the aqueous or microcrystalline sources of Fe(III) used in other studies. More interestingly, the presence of goethite also resulted in a twofold decrease in the rate of NO(3)(-) reduction, a 10-fold decrease in the rate of NO(2)(-) reduction, and a 20-fold increase in the amounts of N(2)O produced. Nitrogen stable isotope experiments that utilized delta(15)N values of N(2)O to distinguish between chemical and biological reduction of NO(2)(-) revealed that the N(2)O produced during NO(2)(-) or NO(3)(-) reduction in the presence of goethite was primarily of abiotic origin. These results indicate that concomitant microbial Fe(III) and NO(3)(-) reduction produces NO(2)(-) and Fe(II), which then abiotically react to reduce NO(2)(-) to N(2)O with the subsequent oxidation of Fe(II) to Fe(III).

Culture Media↗

Nitrogen metabolism by the microbial flora of the rabbit caecum.

The dense microbial flora of the rabbit caecum consisted chiefly of bacteria (10(11)/g) with small numbers of yeast cells (10(6)/g). Using strictly anaerobic technique, 23% of the direct microscopic cell count was cultivated and 55% of the cultivatable bacteria utilized ammonia as the sole source of nitrogen. Ureolytic bacteria were isolated from the caecal lumen and mucosa and were identified as Bacteroides vulgatus, Clostridium clostridiiforme, Bacillus spp. and Staphylococcus spp. Ammonia assimilation by the bacterial flora of the caecum was by incorporation into alpha-oxoglutarate catalysed by NADPH-linked glutamate dehydrogenase.

Ammonia↗

Microbial metabolism of amino alcohols. Biosynthetic utilization of ethanolamine for lipid synthesis by bacteria.

1. Ten bacteria utilizing [2-14C]ethanol-2-amine as the sole or major source of nitrogen for growth on glycerol + salts medium incorporated radioactivity into a variety of bacterial substances. A high proportion was commonly found in lipid fractions, particularly in the case of Erwinia carotovora. 2. Detailed studies of [14C]ethanolamine incorporation into lipids by five bacteria, including E. carotovora, showed that all detectable lipids were labelled. Even where phosphatidylethanolamine was the major lipid labelled, radioactivity was predominantly in the fatty acid rather than the base moiety. The labelled fatty acids were identified in each case. 3. The addition of acetate to growth media decreased the incorporation of radioactivity from ethanolamine into both fatty acid and phosphatidyl-base fragments of lipids from all the bacteria except Mycobacterium smegmatis. Experiments with [3H]ethanolamine and [14C]acetate confirmed that unlabelled acetate decreased the incorporation of both radioactive isotopes into lipids, except in the case of M. smegmatis. 4. Enzyme studies suggested one of two metabolic routes between ethanolamine and acetyl-CoA for each of four bacteria. A role for ethanolamine O-phosphate was not obligatory for the incorporation of [14C]ethanolamine into phospholipids, but correlated with CoA-independent aldehyde dehydrogenase activity.

Acetates↗

Microbial metabolism of aromatic nitriles. Enzymology of C-N cleavage by Nocardia sp. (Rhodochrous group) N.C.I.B. 11216.

1. An organism utilizing benzonitrile as sole carbon and nitrogen source was isolated by the enrichment-culture technique and identified as a Nocardia sp. of the rhodochrous group. 2. Respiration studies indicate that nitrile degradation proceeds through benzoic acid and catechol. 3. Cell-free extracts of benzonitrile-grown cells contain an enzyme that catalyses the conversion of benzonitrile directly into benzoic acid without intermediate formation of benzamide. 4. This nitrilase enzyme was purified by DEAE-cellulose chromatography and gel filtration on Sephadex G-100 in the presence and absence of substrate. The purity of the enzyme was confirmed by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis and isoelectric focusing on polyacrylamide gel. 5. The enzyme shows a time-dependent substrate-activation process in which the substrate catalyses the association of inactive subunits of mol.wt. 45000 to form the polymeric 12-unit active enzyme of mol.wt. 560000. The time required for complete association is highly dependent on the concentration of the enzyme, temperature and pH. 6. The associated enzyme has a pH optimum of 8.0 and K(m) with benzonitrile as substrate of 4mm. The activation energy of the reaction as deduced from the Arrhenius plot is 51.8kJ/mol. 7. Enzyme activity is inhibited by thiol-specific reagents and several metal ions. 8. Studies with different substrates indicate that the nitrilase is specific for nitrile groups directly attached to the benzene ring. Various substituents in the ring are compatible with activity, though ortho-substitution, except by fluorine, renders the nitrile invulnerable to attack. 9. The environmental implications of these findings and the possible significance of the enzyme in the regulation of metabolism are discussed.

Aminohydrolases↗

Microbial mineralization of ring-substituted anilines through an ortho-cleavage pathway.

Moraxella sp. strain G is able to utilize as sole source of carbon and nitrogen aniline, 4-fluoroaniline, 2-chloroaniline, 3-chloroaniline, 4-chloroaniline (PCA), and 4-bromoaniline but not 4-iodoaniline, 4-methylaniline, 4-methoxyaniline, or 3,4-dichloroaniline. The generation time on PCA was 6 h. The pathway for the degradation of PCA was investigated by analysis of catabolic intermediates and enzyme activities. Mutants of strain G were isolated to enhance the accumulation of specific pathway intermediates. PCA was converted by an aniline oxygenase to 4-chlorocatechol, which in turn was degraded via a modified ortho-cleavage pathway. Synthesis of the aniline oxygenase was inducible by various anilines. This enzyme exhibited a broad substrate specificity. Its specific activity towards substituted anilines seemed to be correlated more with the size than with the electron-withdrawing effect of the substituent and was very low towards anilines having substituents larger than iodine or a methyl group. The initial enzyme of the modified ortho-cleavage pathway, catechol 1,2-dioxygenase, had similar characteristics to those of corresponding enzymes of pathways for the degradation of chlorobenzoic acid and chlorophenol, that is, a broad substrate specificity and high activity towards chlorinated and methylated catechols.

Aniline Compounds↗

Microbial metabolism of quinoline and related compounds. XVII. Degradation of 3-methylquinoline by Comamonas testosteroni 63.

A bacterial strain which utilizes 3-methylquinoline as sole source of carbon, nitrogen and energy was isolated from activated sludge. On the basis of its morphological and physiological characteristics, this isolate was classified as Comamonas testosteroni. Four metabolites of 3-methylquinoline degradation were isolated from the culture supernatant and identified as 3-methyl-2-oxo-1,2-dihydroquinoline, 6-hydroxy-3-methyl-2-oxo-1,2-dihydroquinoline, 5,6-dihydroxy-3-methyl-2-oxo-1,2-dihydroquinoline and 2,5,6-trihydroxy-3-methylpyridine. Based on these results, a degradation pathway for 3-methylquinoline is proposed.

Culture Media↗

Isolation and preliminary characterization of mutants of the cyanobacterium Nostoc muscorum resistant to growth inhibition by methylamine.

The wild-type heterocystous and nitrogen-fixing (Het+Nif+) N. muscorum and its non-heterocystous non-nitrogen-fixing (Het-Nif-) mutant strain both fail to grow in different inorganic nitrogen media containing 1 mM methylamine hydrochloride (MA). Mutants of the Het+Nif+ and Het-Nif- parents resistant to growth inhibition by 5 mM MA and thus designated as MAR strains were isolated with a frequency of 2.5(+/- 2.4) x 10(6). A MAR strain of the Het+Nif+ and a MAR strain of the Het-Nif- parent were characterized for growth, heterocyst formation and acetylene reducing activity in the presence and absence of methylamine in N2 medium. The Het+Nif+ MAR strain grows better in MA containing than in MA-free N2 medium, and all cultures grown with MA are found to lack both acetylene reducing activity and heterocyst. The Het-Nif-MAR strain shows good growth in MA-containing N2 medium but no growth in MA-free N2 medium. Furthermore, both the Het+Nif+MAR and Het-Nif-MAR strains show better growth in the presence than in the absence of MA in NO3- and HN4+ media. These results appear to suggest that the MAR phenotype in N. muscorum is due to the metabolic utilization of the ammonium analog as a nitrogen source.

Cyanobacteria↗

Community structure of ammonia-oxidizing bacteria within anoxic marine sediments.

The potential for oxidation of ammonia in anoxic marine sediments exists through anaerobic oxidation by Nitrosomonas-like organisms, utilizing nitrogen dioxide, coupling of nitrification, manganese reduction, and anaerobic oxidation of ammonium by planctomycetes (the Anammox process). Here we describe the presence of microbial communities with the potential to carry out these processes in a natural marine sediment system (Loch Duich, Scotland). Natural microbial communities of Planctomycetales-Verrucomicrobia and beta- and gamma-proteobacterial ammonia-oxidizing bacteria were characterized by analysis of 16S rRNA genes amplified using group-specific primers by PCR- and reverse transcription-PCR amplification of 16S rDNA and RNA, respectively. Amplification products were analyzed by sequencing of clones and by denaturant gradient gel electrophoresis (DGGE). Amplification of primers specific for Planctomycetales-Verrucomicrobia and beta-proteobacterial ammonia-oxidizing bacteria generated products at all sampling sites and depths, but no product was generated using primers specific for gamma-proteobacterial ammonia-oxidizing bacteria. 16S rDNA DGGE banding patterns indicated complex communities of beta-proteobacterial ammonia-oxidizing bacteria in anoxic marine sediments. Phylogenetic analysis of sequences from clones and those excised from DGGE gels suggests dominance of Nitrosospira cluster 1-like organisms and of strains belonging to a novel cluster represented in dominant bands in 16S rRNA DGGE banding patterns. Their presence indicates a group of organisms closely related to recognized beta-proteobacterial ammonia-oxidizing bacteria that may be selected in anoxic environments and may be capable of anoxic ammonia oxidation. Sequence analysis of planctomycete clone libraries and sequences excised from DGGE gels also demonstrated a diverse microbial community and suggested the presence of new subdivisions, but no sequence related to recognized Anammox organisms was detected.

Ammonia↗

The impact of saponins or saponin-containing plant materials on ruminant production--a review.

Saponins are steroid or triterpene glycoside compounds found in a variety of plants. Some saponin-containing plants, mainly legumes, have been used as animal feed, but others are toxic. Several studies on the effect of saponins on ruminant production have also been reported. Some in vitro and in vivo experiments that demonstrate the beneficial effects of saponin such as defaunation of the rumen and manipulation of the end products of fermentation are described. Defaunation is the selective removal of protozoa from the rumen microbial ecosystem by a cell membrane cholesterol-saponin interaction, which causes cell rupture. Because protozoa in the rumen cause protein turnover by predating on bacteria, defaunation increases the nitrogen utilization of the ruminant and may lead to an increase in growth, milk, or wool production. The growth-promoting effect was evident in the high roughage diet suggesting that the application of saponins or saponin-containing plant materials may be beneficial for the subsistence farmers in developing countries. Saponins are deglycosylated by rumen microbes. Some sapogenins have been detected in the digestive tract of ruminants; however, the direct action of these compounds on the host animal is still unclear. No information on the effects of saponin on ruminant reproduction is available. There is an urgent need for a systematic evaluation of the most active structural components of the saponins, and their interaction with the microbial community, the host animal, and the diet. Along with these studies, the direct effects of saponins or their microbial degradation products on the host must be examined in order to get the full understanding of the metabolism and beneficial effects of saponins on animals.

Animals↗