Ammonium assimilation in Proteus vulgaris, Bacillus pasteurii, and Sporosarcina ureae

Microbially Induced Calcium Carbonate Precipitation by Sporosarcina pasteurii: a Case Study in Optimizing Biological CaCO3 Precipitation

Current production of traditional concrete requires enormous energy investment that accounts for approximately 5 to 8% of the world's annual CO2 production. Biocement is a building material that is already in industrial use and has the potential to rival traditional concrete as a more convenient and more environmentally friendly alternative. Biocement relies on biological structures (enzymes, cells, and/or cellular superstructures) to mineralize and bind particles in aggregate materials (e.g., sand and soil particles). Sporosarcina pasteurii is a workhorse organism for biocementation, but most research to date has focused on S. pasteurii as a building material rather than a biological system. In this review, we synthesize available materials science, microbiology, biochemistry, and cell biology evidence regarding biological CaCO3 precipitation and the role of microbes in microbially induced calcium carbonate precipitation (MICP) with a focus on S. pasteurii. Based on the available information, we provide a model that describes the molecular and cellular processes involved in converting feedstock material (urea and Ca2+) into cement. The model provides a foundational framework that we use to highlight particular targets for researchers as they proceed into optimizing the biology of MICP for biocement production.

A Study on Bio-Stabilisation of Sub-Standard Soil by Indigenous Soil Urease-Producing Bacteria

Sub-standard soils are of great concern worldwide due to diverse economic losses and the possibility of severe environmental hazards ranging from catastrophic landslides, building collapse, and erosion to loss of lives and properties. This study explored the potential of urease-producing bacteria, <i>Bacillus cereus</i> and <i>Bacillus paramycoides</i>, to stabilise sub-standard soil bio-stabilisation. The maximum urease activity measured by <i>B. cereus</i> and <i>B. paramycoides</i> was 665 U/mL and 620 U/mL, respectively. <i>B. cereus</i> and <i>B. paramycoides</i> precipitated 943 ± 57 mg/L and 793 ± 51 mg/L of CaCO₃ at an optical density (425 nm) of 1.01 and 1.09 and pH 8.83 and 8.59, respectively, after 96 hours of incubation. SEM microstructural analysis of the precipitated CaCO₃ revealed crystals of various sizes (2.0–23.0 µm) with different morphologies. XRD analysis confirmed that the precipitated CaCO₃ comprised calcite and aragonite crystals. SEM analysis of the microstructure of organic and sandy clay soils treated with <i>B. cereus</i> and <i>B. paramycoides</i> showed the formation of bio-precipitated calcium carbonate deposits on the soil particles (biocementing soil grains), with <i>B. cereus</i> precipitating more CaCO₃ crystals with a better biocementing effect compared to <i>B. paramycoides</i>. Overall, the experimental results attributed CaCO₃ formation to bacterial-associated processes, suggesting that soil ureolytic bacteria are potentially useful to stabilise sub-standard soil.

Transcriptome analyses reveal the utilization of nitrogen sources and related metabolic mechanisms of Sporosarcina pasteurii

In recent years, Sporosarcina pasteurii (S. pasteurii) has become one of the most popular bacteria in microbially induced calcium carbonate precipitation (MICP). Various applications have been developed based on the efficient urease that can induce the precipitation of calcium carbonate. However, the metabolic mechanism related to biomineralization of S. pasteurii has not been clearly elucidated. The process of bacterial culture and biomineralization consumes a large amount of urea or ammonium salts, which are usually used as agricultural fertilizers, not to mention probable environmental pollutions caused by the excessive use of these raw materials. Therefore, it is urgent to reveal the mechanism of nitrogen utilization and metabolism of S. pasteurii. In this paper, we compared the growth and gene expression of S. pasteurii under three different culture conditions through transcriptome analyses. GO and KEGG analyses revealed that both ammonium and urea were direct nitrogen sources of S. pasteurii, and the bacteria could not grow normally in the absence of ammonium or urea. To the best of our knowledge, this paper is the first one to reveal the nitrogen utilization mechanism of S. pasteurii through transcriptome methods. Furthermore, the presence of ammonium might promote the synthesis of intracellular ATP and enhance the motility of the bacteria. There should be an ATP synthesis mechanism associated with urea hydrolysis catalyzed by urease in S. pasteurii.

Calcite seed-assisted microbial induced carbonate precipitation (MICP)

Microbial-induced calcium carbonate precipitation (MICP) is a biological process inducing biomineralization of CaCO3. This can be used to form a solid, concrete-like material. To be able to use MICP successfully to produce solid materials, it is important to understand the formation process of the material in detail. It is well known that crystallization surfaces can influence the precipitation process. Therefore, we present in this contribution a systematic study investigating the influence of calcite seeds on the MICP process. We focus on the changes in the pH and changes of the optical density (OD) signal measured with absorption spectroscopy to analyze the precipitation process. Furthermore, optical microscopy was used to visualize the precipitation processes in the sample and connect them to changes in the pH and OD. We show, that there is a significant difference in the pH evolution between samples with and without calcite seeds present and that the shape of the pH evolution and the changes in OD can give detailed information about the mineral precipitation and transformations. In the presented experiments we show, that amorphous calcium carbonate (ACC) can also precipitate in the presence of initial calcite seeds and this can have implications for consolidated MICP materials.

Revealing nutritional requirements of MICP-relevant Sporosarcina pasteurii DSM33 for growth improvement in chemically defined and complex media

Microbial induced calcite precipitation (MICP) based on ureolysis has a high potential for many applications, e.g. restoration of construction materials. The gram-positive bacterium Sporosarcina pasteurii is the most commonly used microorganism for MICP due to its high ureolytic activity. However, Sporosarcina pasteurii is so far cultivated almost exclusively in complex media, which only results in moderate biomass concentrations at the best. Cultivation of Sporosarcina pasteurii must be strongly improved in order to make technological application of MICP economically feasible. The growth of Sporosarcina pasteurii DSM 33 was boosted by detecting auxotrophic deficiencies (L-methionine, L-cysteine, thiamine, nicotinic acid), nutritional requirements (phosphate, trace elements) and useful carbon sources (glucose, maltose, lactose, fructose, sucrose, acetate, L-proline, L-alanine). These were determined by microplate cultivations with online monitoring of biomass in a chemically defined medium and systematically omitting or substituting medium components. Persisting growth limitations were also detected, allowing further improvement of the chemically defined medium by the addition of glutamate group amino acids. Common complex media based on peptone and yeast extract were supplemented based on these findings. Optical density at the end of each cultivation of the improved peptone and yeast extract media roughly increased fivefold respectively. A maximum OD600 of 26.6 ± 0.7 (CDW: 17.1 ± 0.5 g/L) was reached with the improved yeast extract medium. Finally, culture performance and media improvement was analysed by measuring the oxygen transfer rate as well as the backscatter during shake flask cultivation.

Non-sterile corn steep liquor a novel, cost effective and powerful culture media for Sporosarcina pasteurii cultivation for sand improvement

AIMS

Microbial induced calcium carbonate precipitation (MICP) is one of the bio-cementation methods for improving granular soils. This study evaluate the feasibility of obtaining a bacterial solution with high optical density and urease activity by an inexpensive corn steep liquor (CSL) medium in non-sterile conditions in order to achieve sand improvement.

METHODS AND RESULTS

Corn steep liquor media with different concentrations (different dilution rates) were prepared and, without any autoclaving (non-sterile conditions), different percentage of the inoculum solutions were added to them and incubated. Effect of inoculum solution percentage and CSL dilution rates on specifications of bacterial solution was evaluated. Urease activity and scanning electron microscope (SEM) and X-Ray Diffraction (XRD) were used to efficiency of CLS media in sand improvement. The considerable urease activity was measured as 5·7 mS cm^-1  min^-1 using nonsterile CLS. By using CYNU (CSL-Yeast extract-NH4Cl-Urea) bacterial solution, the urease activity of 5·5 mS cm^-1  min^-1 for the OD₆₀₀ (optical density at 600 nm) of 1·88 and, consequently, specific urease activity of 2·93 mS cm^-1  min^-1  OD₆₀₀ ^-1 was obtained. The highest unconfined compressive strength (811 kPa) was obtained for the CYNU. XRD revealed new calcite peaks next to the quartz peaks.

CONCLUSIONS

Production of inexpensive bacterial solution using diluted CSL as the inexpensive, effective and powerful culture media for Sporosarcina pasteurii cultivation in nonsterile conditions, allows geotechnical and biotechnological engineers to use MICP technology more widely in land improvement and field-scale bio-cementation and bioremediation projects.

SIGNIFICANCE AND IMPACT OF THE STUDY

Obtaining high urease activity of inexpensive microbial solution using diluted CSL as the culture medium in nonsterile conditions, as the unique results of this study, can be significant in the field of bioremediation studies using MICP.

Diversity of Sporosarcina-like Bacterial Strains Obtained from Meter-Scale Augmented and Stimulated Biocementation Experiments

Microbially Induced Calcite Precipitation (MICP) is a biomediated soil cementation process that offers an environmentally conscious alternative to conventional geotechnical soil improvement technologies. This study provides the first comparison of ureolytic bacteria isolated from sand cemented in parallel, meter-scale, MICP experiments using either biostimulation or bioaugmentation approaches, wherein colonies resembling the augmented strain ( Sporosarcina pasteurii ATCC 11859) were interrogated. Over the 13 day experiment, 47 of the 57 isolates collected were strains of Sporosarcina and the diversity of these strains was high, with 20 distinct strains belonging to 5 species identified. Although the S. pasteurii inoculant used for augmentation was recovered immediately after introduction in the augmented specimen, the strain was not recovered after 8 days in either augmented or stimulated soils, suggesting that it competes poorly with indigenous bacteria. Past studies on the physiological properties of S. pasteurii ATCC 11859 suggest that close relatives may have selective advantages under the biogeochemical conditions employed during MICP; however, the extent to which these properties apply to isolates of the current study is unknown. Whole cell urease kinetic properties were investigated for representative isolates and suggest up to 100-fold higher rates of carbonate production when compared to other biomediated processes proposed for MICP.

Nitrogen assimilation in denitrifier Bacillus azotoformans LMG 9581T

Until recently, it has not been generally known that some bacteria can contain the gene inventory for both denitrification and dissimilatory nitrate (NO₃^-)/nitrite (NO₂^-) reduction to ammonium (NH₄⁺) (DNRA). Detailed studies of these microorganisms could shed light on the differentiating environmental drivers of both processes without interference of organism-specific variation. Genome analysis of Bacillus azotoformans LMG 9581^T shows a remarkable redundancy of dissimilatory nitrogen reduction, with multiple copies of each denitrification gene as well as DNRA genes nrfAH, but a reduced capacity for nitrogen assimilation, with no nas operon nor amtB gene. Here, we explored nitrogen assimilation in detail using growth experiments in media with different organic and inorganic nitrogen sources at different concentrations. Monitoring of growth, NO₃^- NO₂^-, NH₄⁺ concentration and N₂O production revealed that B. azotoformans LMG 9581^T could not grow with NH₄⁺ as sole nitrogen source and confirmed the hypothesis of reduced nitrogen assimilation pathways. However, NH₄⁺ could be assimilated and contributed up to 50% of biomass if yeast extract was also provided. NH₄⁺ also had a significant but concentration-dependent influence on growth rate. The mechanisms behind these observations remain to be resolved but hypotheses for this deficiency in nitrogen assimilation are discussed. In addition, in all growth conditions tested a denitrification phenotype was observed, with all supplied NO₃^- converted to nitrous oxide (N₂O).

Selective enrichment and production of highly urease active bacteria by non-sterile (open) chemostat culture

In general, bioprocesses can be subdivided into naturally occurring processes, not requiring sterility (e.g., beer brewing, wine making, lactic acid fermentation, or biogas digestion) and other processes (e.g., the production of enzymes and antibiotics) that typically require a high level of sterility to avoid contaminant microbes overgrowing the production strain. The current paper describes the sustainable, non-sterile production of an industrial enzyme using activated sludge as inoculum. By using selective conditions (high pH, high ammonia concentration, and presence of urea) for the target bacterium, highly active ureolytic bacteria, physiologically resembling Sporosarcina pasteurii were reproducibly enriched and then continuously produced via chemostat operation of the bioreactor. When using a pH of 10 and about 0.2 M urea in a yeast extract-based medium, ureolytic bacteria developed under aerobic chemostat operation at hydraulic retention times of about 10 h with urease levels of about 60 μmol min−1 ml−1 culture. For cost minimization at an industrial scale the costly protein-rich yeast extract medium could be replaced by commercial milk powder or by lysed activated sludge. Glutamate, molasses, or glucose-based media did not result in the enrichment of ureolytic bacteria by the chemostat. The concentration of intracellular urease was sufficiently high such that the produced raw effluent from the reactor could be used directly for biocementation in the field.

In Vitro and In Vivo Assessment of Intraintestinal Bacteriotherapy in Chronic Kidney Disease

Chronic kidney disease may progress to end-stage renal disease, which requires dialysis or kidney transplantation. No generally applicable therapies to slow progression of renal disease are available. Bacteriotherapy affords a promising approach to mitigate uremic intoxication by ingestion of live microbes able to catabolize uremic solutes in the gut. The present study evaluates the nonpathogenic soil-borne alkalophilic urease-positive bacterium Sporosarcina pasteurii (Sp) as a potential urea-targeted component for such "enteric dialysis" formulation. Data presented herein suggest that Sp survives through exposure to gastric juice retaining the ability to hydrolyze urea. In vitro, 10 cfu (colony forming units) of Sp removed from 21 +/- 4.7 mg to 228 +/- 6.7 mg urea per hour, depending on pH, urea concentration, and nutrient availability. Beneficial effects of Sp on fermentation parameters in the intestine were demonstrated in vitro in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) inoculated with fecal microbiota. Enumeration of marker organisms suggested that presence of Sp does not disturb microbial community of the SHIME. Additionally, a pilot study in 5/6th nephrectomized rats fed 10 cfu of live Sp daily throughout the study demonstrated that the tested regimen reduced blood urea-nitrogen levels and significantly prolonged the lifespan of uremic animals.

Isolation of a novel, phosphate-activated glutaminase from Bacillus pasteurii

In Bacillus pasteurii glutamine is being taken up efficiently by a sodium-dependent uptake system and subsequently hydrolysed to ammonium and glutamate. Concerning the latter process, a catabolic L-glutamine amidohydrolase (glutaminase) was isolated from the cytoplasm of this alkaliphilic bacterium and purified to homogeneity using liquid chromatography. Biochemical and physical parameters of the pure enzyme were examined in detail. Interestingly, analysis of the glutaminase revealed a marked increase in catalytic activity in the presence of phosphate, a property yet restricted to animal glutaminases. This is the first report on the presence of a phosphate-activated glutaminase in bacteria.

Properties of NAD-dependent glutamate dehydrogenase from the tylosin producer Streptomyces fradiae

Glutamate dehydrogenase is an enzyme responsible for ammonium assimilation and glutamate catabolism in organisms. The tylosin producer Streptomyces fradiae possesses both NADP- and NAD-dependent glutamate dehydrogenases. The latter enzyme was purified 498-fold with a 7.5% recovery by a six-step protocol. The enzyme is composed of two subunits, each of Mr 47 000, and could form active aggregates of four or eight subunits. Its activity was inactivated by alkaline pH or temperatures of −20 °C or above 40 °C. Activities assayed in the direction of oxidative deamination and reductive amination were optimal at pH 9.2 and 8.8, respectively, and at temperatures of 30–35 °C. No activity was found when NAD(H) was replaced with NADP(H). The Km values were 32.2 mM for L-glutamate, 0.3 mM for NAD+, 3.4 mM for 2-ketoglutarate, 14.2 mM for NH4+, and 0.05 mM for NADH. Deamination activity was partially inhibited by adenyl nucleotides and several divalent cations; amination activity was not affected by the nucleotides but significantly inhibited by Cu2+ or Ni2+.Key words: Streptomyces fradiae, NAD-dependent glutamate dehydrogenase, purification, properties.

Ammonium/urea-dependent generation of a proton electrochemical potential and synthesis of ATP in Bacillus pasteurii

The influence of ammonium and urea on the components of the proton electrochemical potential (delta p) and de novo synthesis of ATP was studied with Bacillus pasteurii ATCC 11859. In washed cells grown at high urea concentrations, a delta p of -56 +/- 29 mV, consisting of a membrane potential (delta psi) of -228 +/- 19 mV and of a transmembrane pH gradient (delta pH) equivalent to 172 +/- 38 mV, was measured. These cells contained only low amounts of potassium, and the addition of ammonium caused an immediate net decrease of both delta psi and delta pH, resulting in a net increase of delta p of about 49 mV and de novo synthesis of ATP. Addition of urea and its subsequent hydrolysis to ammonium by the cytosolic urease also caused an increase of delta p and ATP synthesis; a net initial increase of delta psi, accompanied by a slower decrease of delta pH in this case, was observed. Cells grown at low concentrations of urea contained high amounts of potassium and maintained a delta p of -113 +/- 26 mV, with a delta psi of -228 +/- 22 mV and a delta pH equivalent to 115 +/- 20 mV. Addition of ammonium to such cells resulted in the net decrease of delta psi and delta pH without a net increase in delta p or synthesis of ATP, whereas urea caused an increase of delta p and de novo synthesis of ATP, mainly because of a net increase of delta psi. The data reported in this work suggest that the ATP-generating system is coupled to urea hydrolysis via both an alkalinization of the cytoplasm by the ammonium generated in the urease reaction and a net increase of delta psi that is probably due to an efflux of ammonium ions. Furthermore, the findings of this study show that potassium ions are involved in the regulation of the intracellular pH and that ammonium ions may functionally replace potassium to a certain extent in reducing the membrane potential and alkalinizing the cytoplasm.

Molecular biology of microbial ureases

Urease (urea amidohydrolase; EC 3.5.1.5) catalyzes the hydrolysis of urea to yield ammonia and carbamate. The latter compound spontaneously decomposes to yield another molecule of ammonia and carbonic acid. The urease phenotype is widely distributed across the bacterial kingdom, and the gene clusters encoding this enzyme have been cloned from numerous bacterial species. The complete nucleotide sequence, ranging from 5.15 to 6.45 kb, has been determined for five species including Bacillus sp. strain TB-90, Klebsiella aerogenes, Proteus mirabilis, Helicobacter pylori, and Yersinia enterocolitica. Sequences for selected genes have been determined for at least 10 other bacterial species and the jack bean enzyme. Urease synthesis can be nitrogen regulated, urea inducible, or constitutive. The crystal structure of the K. aerogenes enzyme has been determined. When combined with chemical modification studies, biophysical and spectroscopic analyses, site-directed mutagenesis results, and kinetic inhibition experiments, the structure provides important insight into the mechanism of catalysis. Synthesis of active enzyme requires incorporation of both carbon dioxide and nickel ions into the protein. Accessory genes have been shown to be required for activation of urease apoprotein, and roles for the accessory proteins in metallocenter assembly have been proposed. Urease is central to the virulence of P. mirabilis and H. pylori. Urea hydrolysis by P. mirabilis in the urinary tract leads directly to urolithiasis (stone formation) and contributes to the development of acute pyelonephritis. The urease of H. pylori is necessary for colonization of the gastric mucosa in experimental animal models of gastritis and serves as the major antigen and diagnostic marker for gastritis and peptic ulcer disease in humans. In addition, the urease of Y. enterocolitica has been implicated as an arthritogenic factor in the development of infection-induced reactive arthritis. The significant progress in our understanding of the molecular biology of microbial ureases is reviewed.

Cloning, heterologous expression, and sequencing of the Proteus vulgaris glnAntrBC operon and implications of nitrogen control on heterologous urease expression

The glnAntrBC operon of Proteus vulgaris was cloned and heterologously expressed in Escherichia coli. The nucleotide sequence was determined. An open reading frame of 1407 bp was identified as the glnA gene and the deduced amino acid sequence showed 82% identity with the E. coli glutamine synthetase protein. Heterologous expression of the glnA gene in E. coli restored glutamine synthetase (GS) activity in a GS-negative mutant and a 52 kDa protein was detected and addressed as the GS subunit of P. vulgaris. Adjacent to the glnA gene the regulatory genes ntrB and ntrC were identified. Their coding regions comprised 1053 and 1452 bp, respectively, and the deduced gene products NRII (NtrB) and NRI (NtrC) shared 72% identity with the corresponding E. coli proteins. Heterologous expression in E. coli revealed only a 54 kDa protein which was shown to be NRI. NRII was not detectable using the methods employed.

Nickel availability and urease expression in Proteus mirabilis

Cells of Proteus mirabilis, previously grown in nutrient broth (NB), exhibited an increase in urease activity during subsequent incubation in mineral medium even when protein biosynthesis was inhibited. During growth in NB, degradation of amino acids obviously led to the formation of nickel-complexing metabolites, and nickel ions were therefore unavailable for maximal expression of enzymatically active urease; this inhibition of urease biosynthesis was overcome by the addition of nickel to the growth medium, and also by added glucose. Experiments concerning the incorporation of radioactive nickel into urease finally indicated that the observed increase in urease activity was caused by posttranslational insertion of nickel into performed apo-urease.