Acetate assimilation by Nitrobacter agilis in relation to its "obligate autotrophy"

Acetate (1 to 10 mm) had no effect on the rate of nitrite oxidation or exponential growth by Nitrobacter agilis. However, acetate-1-(14)C and -2-(14)C were both assimilated by growing cultures, and acetate carbon contributed 33 to 39% of newly synthesized cell carbon. Carbon from acetate was incorporated into all of the major cell constituents, including most of the amino acids of cell protein and poly-beta-hydroxybutyrate (PHB). Cultures grown in the presence of acetate showed a significant increase in turbidity, attributable in part to protein synthesis and the accumulation of PHB in the "post-exponential phase," when the supply of nitrite was completely exhausted. Cell suspensons of N. agilis assimilated acetate in the absence of bicarbonate and even in the absence of nitrite. However, the addition of nitrite increased the rate of acetate assimilation by cell suspensions. The distribution of (14)C-acetate incorporated by cell suspensions was qualitatively similar to that found with growing cultures. Cell suspensions of N. agilis slowly oxidized acetate to CO(2). Addition of nitrite suppressed CO(2) production from acetate but increased the assimilation of acetate carbon into cell material. N. agilis contained all the enzymes of the tricarboxylic acid cycle. Growth of N. agilis in the presence of acetate did not significantly affect the levels of the enzymes of the tricarboxylic acid cycle, but did result in a 100-fold increase in the specific activity of isocitratase. In contrast, carboxydismutase was partially repressed. N. agilis was grown heterotrophically through seven transfers on a medium containing acetate and casein hydrolysate. The addition of nitrite increased the rate of heterotrophic growth. Heterotrophically grown organisms still retained their ability to grow autotrophically with nitrite. However, these organisms oxidized nitrite at a slower rate. Organisms from autotrophic and heterotrophic cultures were analyzed to determine the mean guanine plus cytosine content of their deoxyribonucleic acid; in both cases this mean was 61.2 +/- 1%. We concluded that N. agilis is not an obligate autotroph; it appears to be a facultative autotroph which resembles the novel facultative autotroph, Thiobacillus intermedius, very closely.     

Effects of Pesticides on Nitrite Oxidation by Nitrobacter agilis

The influence of pesticides on the growth of Nitrobacter agilis in aerated cultures and on the respiration of N. agilis cell suspensions and cell-free extracts was studied. Two pesticides, aldrin and simazine, were not inhibitory to growth of Nitrobacter, but five compounds [isopropyl N-(3-chlorophenyl) carbamate (CIPC), chlordane, 1,1-dichloro-2,2-bis (p-chlorophenyl) ethane (DDD), heptachlor, and lindane] prevented growth when added to the medium at a concentration of 10 mug/ml. Whereas CIPC and eptam prevented nitrite oxidation by cell suspensions, the addition of DDD and lindane resulted in only partial inhibition of the oxidation. Heptachlor and chlordane also caused only partial inhibition of oxidation, but were more toxic with cell-free extract nitrite oxidase. None of the pesticides inhibited the nitrate reductase activity of cell-free extracts, but most caused some repression of cytochrome c oxidase activity. Heptachlor was the most deleterious compound.     

Permeability of Nitrobacter agilis to Organic Compounds.

Ida, S. (Cornell University, Ithaca, N.Y.), and M. Alexander. Permeability of Nitrobacter agilis to organic compounds. J. Bacteriol. 90:151-156. 1965.-None of a variety of inorganic ions or organic compounds served as a sole energy source for the growth of Nitrobacter agilis, and the test substrates were not oxidized by either intact cells or extracts of the obligate chemoautotroph. The organic substances did not serve as sole carbon sources for the bacterium in a synthetic medium, and they failed to enhance the rate of nitrite oxidation. The organism was permeable to acetate and a number of other simple carbon compounds, however, and exogenously supplied acetate was converted to a number of products. On the basis of these findings, possible reasons are examined for the inability of the chemoautotroph to use exogenous organic compounds as energy or carbon sources.     

Growth of obligate autotrophic bacteria on glucose in a continuous flow-through apparatus

Nitrosomonas europaea, Nitrobacter agilis, Thiobacillus denitrificans, T. neapolitanus, and T. thioparus (all obligate autotrophic bacteria) have been grown in dialysis culture, on glucose salts media, in the absence of their specific inorganic energy source. Metabolic products for N. agilis grown on nitrite salts medium were identified as keto acids. Pyruvic acid inhibited this organism at 5 x 10(-5)m. Keto acids were not inhibitory for the thiobacilli grown on thiosulfate medium. However, when T. denitrificans was grown on glucose with dialysis, addition of 5 x 10(-4)m pyruvate inhibited growth. Thus, it appears pyruvate may be inhibitory for other autotrophs, as has been reported for T. thiooxidans.     

Effect of nitrite concentration and pH on most probable number enumerations of non-growing Nitrobacter spp.

Abstract Enumerations of nitrite-oxidizing bacteria in soil samples by a Most Probable Number technique, often showed relatively high cell numbers at a low nitrite concentration compared with the numbers of ammonium-oxidizing bacteria. It was hypothesized that the high numbers enumerated at low nitrite concentration would represent non-growing or organotrophically growing cells of nitrite-oxidizing species. In this paper, the sensitivity of non-growing Nitrobacter species to high nitrite concentrations as well as to low pH was examined. Different Nitrobacter species were pre-cultured at 0.5 mM nitrite. Non-growing cells differing in age were enumerated at different nitrite concentrations and pH values. The incubation period lasted for 5 months at 20°C. However, during the incubation periods of the older non-growing cells, it appeared that a period of 5 months might have been too short for reaching constant numbers. Early stationary cells of all species that were studied appeared not to be affected by high nitrite concentrations or low pH. Eight- and 18-month-old non-growing cells of Nitrobacter hamburgensis were also insensitive to 5 mM nitrite. The numbers of 8- and 18-month-old resting cells of N. vulgaris were only repressed by a combination of 5 mM nitrite and a low pH. Eight-month-old non-growing cells of N. winogradskyi were sensitive to 5 mM irrespective of pH, but 18-month-old cells only to 5 mM nitrate at low pH. The numbers of 8- and 18-month-old resting cells of N. winogradskyi serotype agilis were repressed by low pH rather than high nitrite concentration. Hence, it was concluded that the large differences in numbers of nitrite-oxidizing bacteria obtained with low and high nitrite concentrations in the incubation medium, was not likely to be due to the presence of non-growing Nitrobacter species in soil samples, but rather to the existence of organotrophically growing Nitrobacter cells.     

Microbiological Assay for Organic Compounds in Seawater

A method for the quantitative identification of organic compounds in seawater has been developed. When auxotrophic mutants of Serratia marinorubra were incubated at 21 to 24 C for 72 hr with constant agitation, standard bioassay reference curves were obtained. Sodium glycerophosphate (400 mg per liter), ammonium dibasic citrate (5 g per liter), and glycerol (25 ml per liter) supplied the needed nutrients for maximal growth with a limited concentration of the required metabolite. Data are presented for the microbiological assay for biotin in waters of the Gulf of Mexico and adjacent bays. The range of sensitivity for the biotin mutant A101V is 5 to 12 mmug per liter in seawater, with a growth response from 2 to 16 mmug per liter of seawater. The possible ecological and chemical significance of biotin occurrence in spring-summer off-shore water is discussed.     

Ultrastructure of Nitrobacter agilis Grown Under Autotrophic and Heterotrophic Conditions

Nitrobacter agilis, grown through seven transfers heterotrophically in the absence of nitrite, was examined in the electron microscope. The ultrastructure of such cells closely resembled that of autotrophically grown N. agilis. It was thus futher established that the organisms growing heterotrophically were indeed N. agilis and, therefore, that N. agilis is a facultative autotroph. Acetate incorporation into poly-beta-hydroxybutyrate was confirmed cytologically.     

Icosahedral inclusions (carboxysomes) of Nitrobacter agilis.

The icosahedral bodies of Nitrobacter agilis are about 120 nm in diameter and, as viewed by electron microscopy, consist of an outer shell enclosing 10-nm particles. The inner 10-nm particle is the enzyme D-ribulose 1,5-bisphosphate carboxylase. The bodies isolated from cells incubated 1 month without nitrite had a specific activity for the enzyme of 0.54 mu mol of CO2 fixed per min per mg of protein.     

Growth of Nitrobacter in the presence of organic matter

1. Culture filtrates of heterotrophic bacteria were tested for their stimulatory effect on nitrification of three strains of Nitrobacter.
2. Yeast extract-peptone solution, in which Pseudomonas fluorescens had grown, after removal of the cells was added to autotrophically growing cultures of Nitrobacter agilis; it caused a stimulated nitrite oxidation and growth of Nitrobacter agilis.
3. The degree of stimulation depended on: a) the proportion of the culture filtrate to the autotrophic medium; b) the composition of the complex medium in which Pseudomonas fluorescens had been grown; c) the time the heterotrophic bacterium had been grown in the complex medium.
4. The stimulatory effect was highest with Nitrobacter agilis, less with Nitrobacter winogradskyi and negligible with Nitrobacter K ₄.
5. It was possible to adapt nitrifying cells of Nitrobacter agilis to higher concentrations of yeast extract and peptone. After the nitrite had been completely oxidized the cell-N still increased up to 30% before growth stopped.

     

Immunofluorescence studies of Nitrobacter populations in soils.

Certain steps of a protocol to enumerate a bacterium directly in soil by immunofluorescence were studied with respect to the enumeration of Nitrobacter in soils of diverse properties. Maximal counts of Nitrobacter were obtained by varying factors involved in the release of bacteria from the soil. Differences with respect to these factors were related to soil-colloidal properties. Enumeration protocols modified with regard to soil properties were used with strain-specific fluorescent antibodies (FA) to enumerate Nitrobacter populations (a) in soil during storage, (b) in comparison with most probable number (MPN) enumeration, and (c) occurring in a spectrum of soil samples. FA counting was rapid and precise and gave counts generally 10- to 100-fold higher than obtained by MPN. Nitrobacter cells of the two serotypes studied, designated as agilis and Winogradsky, occurred in each soil at levels of 10(4)-10(5) per gram.     

Growth ofCandida albicans in a minimal synthetic medium without biotin

Summary Growth ofCandida albicans strain B 311-10 was observed in a minimal synthetic biotin-free medium, using different glucose concentrations, during the first 30 hours of its development at 28 °C. The yeast's growth was observed spectrophotometrically at 675 nm reading its optical density every hour. The minimal medium of Shepherdet al. [12], with glucose (15 g/L) and biotin was modified: this vitamin was eliminated and the concentration of glucose was gradually lowered to 0.5 g/L. At 5 g/L of glucose and without biotin very good growth was obtained. Based on our results during the first 30 hours of growth, biotin has no influence on the yeast's growth. This medium would be useful for the study of the physiology ofC. albicans during the first period of its development.     

VITAMIN B12, THIAMINE,AND BIOTIN CONTENTS OF MARINE PHYTOPLANKTON1

An extraction procedure was developed for determining vitamin B₁₂, thiamine, and biotin contents of marine phytoplankton. Phytoplankters were collected either by centrifugation or by retention on a glass fiber filter, then heated at 100 C for I hr in 100 ml of vitamin-free seawater acidified to pH 3.5 with HCl. The extract, after debris removal, was filter-sterilized and analyzed, for vitamin B₁₂, thiamine, and biotin with standard vitamin assay procedures. The vitamin contents of haeodactylum tricornutum, Skeletonema costatum, Stephanopyxis turris, and occolithus liuxleyi were determined during growth in batch cultures. P. tricornutum (non-vitamin requirer) growing in aerated cultures contained 0.29–0.96 ng B₁₂, 5–15 ng thiamine, and 0.45–1.70 ng biotin/mg C. Under similar conditions S. costatum (B₁₂-requirer) contained about 0.06 ng B₁₂, 5–36 ng thiamine, and 0.16–2.10 ng biotin/mg C. The concentrations of vitamin were generally similar during some portion of the growth curve, eg, logarithmic growth. The vitamin B₁₂, content of S. costatum growing under nonaerated conditions decreased when medium B₁₂, was reduced. The biotin content did not change when medium B₁₂ was decreased. The thiamine content per unit weight of C. huxleyi (thiamine-requirer) growing with either 10 or 120 ng/liter thiamine decreased under both medium concentrations, indicating no net synthesis of the vitamin.     

Catalysis of intermolecular oxygen atom transfer by nitrite dehydrogenase of Nitrobacter agilis

Nitrobacter agilis, which contains a very active nitrite dehydrogenase, was studied in vivo under anaerobic conditions by the 15N NMR technique. When incubated with equimolar 15NO3- and unlabeled nitrite (or 15NO2- and unlabeled nitrate) the bacterium catalyzed an isotope exchange reaction at rates about 10% those observed in the nitrite oxidase assay. When incubated with 18O-labeled 15NO2- and 18O-labeled 15NO3-, the 18O was observed to exchange at similar rates from both species into water. Finally, when incubated with equimolar [18O]nitrate and 15NO2-, intermolecular 18O transfer was observed to result in formation of double labeled nitrate and nitrite at similar rates. 18O was transferred from nitrate to a 15N species or to water at approximately equal rates under the conditions of the experiments. It is argued that the enzyme responsible for these exchange reactions is nitrite dehydrogenase and not nitrate reductase. This work and the related experiments of DiSpirito and Hooper (DiSpirito, A.A., and Hooper, A.B. (1986) J. Biol. Chem. 261, 10534-10537) represent the first demonstrations of intermolecular oxygen atom transfer among oxotransferases. Mechanistic implications are discussed.     

Stoichiometric and kinetic characterisation of Nitrobacter in mixed culture by decoupling the growth and energy generation processes

The growth, maintenance and lysis processes of Nitrobacter were characterised. A Nitrobacter culture was enriched in a sequencing batch reactor (SBR). Fluorescent in situ hybridisation showed that Nitrobacter constituted 73% of the bacterial population. Batch tests were carried out to measure the oxygen uptake rate and/or nitrite consumption rate when both nitrite and CO2 were in excess, and in the absence of either of these two substrates. The results obtained, along with the SBR performance data, allowed the determination of the maintenance coefficient and in situ cell lysis rate of Nitrobacter. Nitrobacter spends a significant amount of energy for maintenance, which varies considerably with the specific growth rate. At maximum growth, Nitrobacter consume nitrite at a rate of 0.042 mgN/mgCOD(biomass) . h for maintenance purposes, which increases more than threefold to 0.143 mgN/mgCOD(biomass) . h in the absence of growth. In the SBR, where Nitrobacter grew at 40% of its maximum growth rate, a maintenance coefficient of 0.113 mgN/mgCOD . h was found, resulting in 42% of the total amount of nitrite being consumed for maintenance. The above three maintenance coefficient values obtained at different growth rates appear to support the maintenance model proposed in Pirt (1982). The in situ lysis rate of Nitrobacter was determined to be 0.07/day under aerobic conditions at 22 degrees C and pH 7.3. Further, the maximum specific growth rate of Nitrobacter was estimated to be 0.02/h (0.48/day). The affinity constant of Nitrobacter with respect to nitrite was determined to be 1.50 mgNO2(-)-N/L, independent of the presence or absence of CO2.     

Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter

The alphaproteobacterium Nitrobacter hamburgensis X14 is a gram-negative facultative chemolithoautotroph that conserves energy from the oxidation of nitrite to nitrate. Sequencing and analysis of the Nitrobacter hamburgensis X14 genome revealed four replicons comprised of one chromosome (4.4 Mbp) and three plasmids (294, 188, and 121 kbp). Over 20% of the genome is composed of pseudogenes and paralogs. Whole-genome comparisons were conducted between N. hamburgensis and the finished and draft genome sequences of Nitrobacter winogradskyi and Nitrobacter sp. strain Nb-311A, respectively. Most of the plasmid-borne genes were unique to N. hamburgensis and encode a variety of functions (central metabolism, energy conservation, conjugation, and heavy metal resistance), yet approximately 21 kb of a approximately 28-kb "autotrophic" island on the largest plasmid was conserved in the chromosomes of Nitrobacter winogradskyi Nb-255 and Nitrobacter sp. strain Nb-311A. The N. hamburgensis chromosome also harbors many unique genes, including those for heme-copper oxidases, cytochrome b(561), and putative pathways for the catabolism of aromatic, organic, and one-carbon compounds, which help verify and extend its mixotrophic potential. A Nitrobacter "subcore" genome was also constructed by removing homologs found in strains of the closest evolutionary relatives, Bradyrhizobium japonicum and Rhodopseudomonas palustris. Among the Nitrobacter subcore inventory (116 genes), copies of genes or gene clusters for nitrite oxidoreductase (NXR), cytochromes associated with a dissimilatory nitrite reductase (NirK), PII-like regulators, and polysaccharide formation were identified. Many of the subcore genes have diverged significantly from, or have origins outside, the alphaproteobacterial lineage and may indicate some of the unique genetic requirements for nitrite oxidation in Nitrobacter.     

Nitrification on a coral reef.

We report that the algal pavement just behind the reef crest at Enewetak Atoll produces nitrate at measurable rates. In situ and in vitro incubations with N-Serve indicate that the autotrophic pathway involving two separate organisms is effective in this oxidation of ammonia to nitrate. Significant nitrification is indicated throughout the reef environment; Nitrobacter agilis has specifically been identified as at least one of the organisms responsible for the terminal oxidation of nitrite to nitrate.     

The Nutrition of the Freshwater Dinoflagellate Ceratium hirundinella*

A defined medium was devised for a freshwater isolate of the dinoflagellate Ceratium hirundinella. Highest cell yields were produced at 7,700–10,000 lux. The optimum pH range was between 7.0 and 7.5: the optimum temperature 21°C. Ceralium hirundinella tolerated a wide range (per liter) of Ca (0.1–100 mg) and Mg (0.1–50 mg) ion concentrations. The optimum range for growth was 20–30 rns Ca and 10–30 mg Mg. Cells cultured in media lacking Ca often became teratological yet motilp and viable. Variations in the Ca:Mg ratio had little effect on cell yield if the sum of the concentrations of the 2 ions remained the same. Organic as well as inorganic sources of N and P were utilized. NH₄ sources became toxic at elevated levels (7 mg N liter^-1). Methionine was not used as N source. Cells could not be completely depleted of P, but concentrations ≤ 0.01 mg P liter^-1 resulted in poor growth. Vitamin B₁₂, but not thiamine or biotin, was required. Highest cell yields were at a PII-metals concentration of 30 ml liter^-1; a t 100-ml liter^-1 cell yield was very low. Additions (per liter) of Fe (0.5 mg) and Mo (0.1 mg) to the basal medium produced higher cell yields, but Cu (0.1 mg) and V (0.1 mg) inhibited growth.     

Regulation of Biotin Transport in Saccharomyces cerevisiae

The metabolic control of biotin transport in Saccharomyces cerevisiae was investigated. Nonproliferating cells harvested from cultures grown in excess biotin (25 ng/ml) took up small amounts of biotin, whereas cells grown in biotin-sufficient medium (0.25 ng/ml) accumulated large amounts of the vitamin. Transport was inhibited maximally in cells grown in medium containing 9 ng (or more) of biotin per ml. When avidin was added to biotin-excess cultures, the cells developed the ability to take up large amounts of biotin. Boiled avidin was without effect, as was treatment of cells with avidin in buffer. Avidin did not relieve transport inhibition when added to biotin-excess cultures treated with cycloheximide, suggesting that protein synthesis was required for cells to develop the capacity to take up biotin after removal of extracellular vitamin by avidin. Cycloheximide did not inhibit the activity of the preformed transport system in biotin-sufficient cells. The presence of high intracellular free biotin pools did not inhibit the activity of the transport system. The characteristics of transport in biotin-excess cells (absence of temperature or pH dependence, no stimulation by glucose, absence of iodoacetate inhibition, independence of uptake on cell concentration, and nonsaturation kinetics) indicated that biotin entered these cells by diffusion. The results suggest that the synthesis of the biotin transport system in S. cerevisiae may be repressed during growth in medium containing high concentrations of biotin.     

Adaptation of the acetogen Clostridium thermoautotrophicum to minimal medium.

Clostridium thermoautotrophicum was adapted to minimal medium and cultivated at the expense of glucose, methanol, or H2-CO2. No supplemental amino acids were required for growth of the adapted strain, and nicotinic acid was the sole essential vitamin. Neither N2 nor nitrate could replace ammonium as the nitrogen source, and biotin was preferentially stimulatory for glucose cell lines. Growth in minimal medium yielded substantially higher acetate concentrations per unit of biomass formed than did growth in undefined medium.     

Isoniazid Uptake in Relation to Growth Inhibition of Mycobacterium tuberculosis

(14)C-isoniazid (INH) was used to study the relationship between drug uptake or binding by Mycobacterium tuberculosis and growth inhibition of the organism, which is dependent upon the concentration of drug and the duration of exposure. When strain H37R(a), grown in modified Sauton's liquid medium, was treated with 0.1 mug of INH per ml for 2 to 6 hr, followed by 10 mug of nicotinic hydrazide (NH) per ml to block further INH uptake, growth was retarded but not completely inhibited upon continued incubation. NH itself did not retard growth. However, cells treated in a similar manner with INH alone grew normally when diluted 1:100 in fresh, drug-free media. Uptake data showed that bacilli exposed to 0.1 mug of INH per ml accumulated 5.5, 9.7, and 12 mmug/mg of dry cells at 2, 4, and 6 hr, respectively. Other experiments suggested that once isoniazid is bound, it is not rapidly lost when NH is added or when the cells are diluted in fresh media. In the presence of 1.0 mug of INH per ml, tubercle bacilli took up 10 to 37 mmug/mg of dry cells in 20 to 90 min. These cells were not markedly inhibited when diluted 1:40 in fresh NH-containing media and incubated for 6 days. Growth inhibition of tubercle bacilli by INH depends on the uptake of sufficient drug, but the evidence obtained in this study suggests that the absolute concentration of bound INH is not as important in the action of the drug as is the maintenance of a critical cellular concentration for a requisite period of time.