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Author(s): Martina Preiner, William F. Martin Author Affiliations: Life in a carbon dioxide world Few chemicals have hit the headlines so widely that everyone knows their formula, but carbon dioxide [...], Microorganisms living in hydrothermal vents that emit carbon dioxide gas provide a striking example of metabolic finesse. This pathway sheds light on microbial ecology in extreme environments and offers clues to early life on Earth. Mechanism used by microbes to reverse the tricarboxylic acid cycle found.

The growth of a bacterial culture is one of the most familiar examples of exponential growth, with important consequences in biology and medicine. Bacterial growth involves more than just a rate constant. To sustain exponential growth, the cell must carefully coordinate the accumulation of mass, constant replication of the chromosome, and physical division. Hence, the growth rate is centrally important in any physical and chemical description of a bacterial cell. These aspects of bacterial growth can be described by empirical laws that suggest simple and intuitive models. Therefore, a quantitative discussion of bacterial growth could be a part of any undergraduate biophysics course. We present a general overview of some classic experimental studies and mathematical models of bacterial growth from a mostly physical perspective. [c] 2010 American Association of Physics Teachers. [DOI: 10.1119/1.3483278]

At present, Salmonella is considered to express two peroxiredoxin-type peroxidases, TsaA and AhpC. Here we describe an additional peroxiredoxin, Tpx, in Salmonella enterica and show that a single tpx mutant is susceptible to exogenous hydrogen peroxide ([H.sub.2][O.sub.2]), that it has a reduced capacity to degrade [H.sub.2][O.sub.2] compared to the ahpCF and tsaA mutants, and that its growth is affected in activated macrophages. These results suggest that Tpx contributes significantly to the sophisticated defense system that the pathogen has evolved to survive oxidative stress. doi: 10.1128/JB.01652-09

As one of the final steps in the bacterial growth cycle, daughter cells must be released from one another by cutting the shared peptidoglycan wall that separates them. In Escherichia coli, this delicate operation is performed by several peptidoglycan hydrolases, consisting of multiple amidases, lytic transglycosylases, and endopeptidases. The interactions among these enzymes and the molecular mechanics of how separation occurs without lysis are unknown. We show here that deleting the endopeptidase PBP 4 from strains lacking AmiC produces long chains of unseparated cells, indicating that PBP 4 collaborates with the major peptidoglycan amidases during cell separation. Another endopeptidase, PBP 7, fulfills a secondary role. These functions may be responsible for the contributions of PBPs 4 and 7 to the generation of regular cell shape and the production of normal biofilms. In addition, we find that the E. coli peptidoglycan amidases may have different substrate preferences. When the DD-carboxypeptidase PBP 5 was deleted, thereby producing cells with higher levels of pentapeptides, mutants carrying only AmiC produced a higher percentage of cells in chains, while mutants with active AmiA or AmiB were unaffected. The results suggest that AmiC prefers to remove tetrapeptides from peptidoglycan and that AmiA and AmiB either have no preference or prefer pentapeptides. Muropeptide compositions of the mutants corroborated this latter conclusion. Unexpectedly, amidase mutants lacking PBP 5 grew in long twisted chains instead of straight filaments, indicating that overall septal morphology was also defective in these strains.

Research points out that the polymerase chain reaction-denaturing gradient gel electrophoresis method is a non-culture-based technique that is applicable for studying vaginal microbiota. The microbiota of 19 premenopausal women is altered after the instillation of lactobacilli.

Research demonstrates that methanogenic bioreactor communities composed of different populations of bacteria exhibit functional stability based on their substrate processing type. Parallel substrate processing leads to more stability than serial substrate processing.

Research has been conducted on the cell organization and cell-cell interaction during colony development. The scanning electron micrographs of Saccharomyces cerevisiae colonies have been examined.

Research has been conducted on the Bradyrhizobium japonicum strain. The effect of carbon monoxide on the chemolithoautotrophic growth of this strain has been investigated.

Research has been conducted on the growth phase-dependent change in ribosome surcose density gradient centrifugation patterns. The analysis of this change for Escherichia coli strains is presented.

Research has been conducted on the catabolite repression control (Crc) in Pseudomonas putida. The investigation of the growth effect in 2xYT medium on Crc is discussed.

Results show that there is no change in the bacterial population dynamics in mesocosm diatom bloom and any observed changes are systemic in nature and are only responses to the changes in the environmental conditions.

Research was conducted to examine the effect of low temperature treatment on the survival of the lactococcus bacterial species after freezing (cryoprotection). Results show that cells shocked to 10 degrees C for 4 h exhibit 7 kD cold-induced proteins which confer a 100-fold cryoprotection.

The growth of Lactococcus lactis and bacteriocin production in salt-enriched defined medium has been studied. The osmoprotective effect of glycine betaine (GB) on bacterial growth and on lacticin 481 production has also been examined. Lacticin 481 is a bacteriocin produced by L. lactis subsp. lactis ADRIA 85LO30 which inhibits food spoilage bacterium Clostridium tyrobutyricum. Results show GB improves the growth of L. lactis under hyperosmotic constraints but contributes to a reduction in bacteriocin production.

The capacity of growing bacteria populations to adapt from one carbon source for growth on alternative substrates has been investigated. The bacteria strains used in the study are two natural isolates of beta-proteobacteria that can degrade the herbicide, 2,4-dichlorophenoxyacetic acid (2,4-D). Twenty lineages of bacteria were allowed to evolve with succinate as the sole carbon source and 2,4-D as the limiting substrate during experimental evolution. Results reveal that only three derived lines had a clear drop in fitness on the alternate substrate after adaptation to their selective substrate. Five derived lines showed improved fitness on both substrates.

A study was conducted to analyze the ecophysiological and phylogentic attributes of the neuston bacterium Nevskia ramosa which forms a conspicuous rosette-like microcolonies at the air-water interface. Pure cultures of the bacteria were gathered from a bog lake and fresh water ditch. Results revealed that these bacteria were sensitive to ultra violet radiation and they form a hydrophobic surface films with a dull appearance.

Organic carbon regulates the growth of bacteria found in drinking water. In Finland, it has been found that phosphorus also contributes to growth of microbes in drinking water. Phosphorus is used to treat corrosion in water pipelines but compromises the quality of drinking water. New technologies should be developed not only to reduce the total organic carbon but also the amount of phosphates in drinking water.

The growth kinetics of Pseudomonas sp. B13 on 3-chlorobenzoate (3CB) and acetate was investigated under conditions of minimum substrate concentration (Smin) in a recycling fermentor. Smin was different for batch, chemostat and recycling-fermentor cultures. There was a wide variation in the kinetic parameters for the three experimental conditions. Maintenance energy requirements for cells grown in acetate, 3CB or a mixture of both substrates were dependent on the kinetics of substrate transformation.

A copper-resistant rod-shaped methanogen has been isolated from a copper-mining region in Michigan's upper peninsula. The bacterium is a Methanobacterium bryantii strain capable of growing on formate and has been labeled M. bryantii BKYH. It grows on formate or H2-CO2 but not on acetate or methanol. Cells of the isolate in standing cultures form mats in the presence of H2-CO2, and are filamentous and intertwined in the presence of cupric salts. The CuSO4 MIC for the isolate is almost two to 36 times more than that for other methanogenic bacteria.

The addition of phosphorus (P) to cultures of Synechococcus cells isolated from the Mediterranean Sea decreases the duration of the G1 phase of the cell cycle. This causes the cells to enter and leave the S and G2 phases earlier than normal. The addition of nitrogen fails to affect the cell cycle. A study indicates that the Synechococcus cells are P-limited rather than N-limited during summers. The concentration of P that affects 50% of the bacterial cells is low during June and increases by July.

The growth of the naphthalene-degrading bacterial strain HH4 depends on naphthalene diffusion through water, air or porous media. The growth is inversely related to the distance between the bacteria and the naphthalene substrate. Bacterial growth and final naphthalene degradation rate are higher if naphthalene diffuses through air or unsaturated porous media, as naphthalene diffuses through air faster than through water. A mathematical model combining Monod growth kinetics and substrate diffusion explains the bacterial growth.

Gorgonian secondary metabolites are unable to suppress bacterial growth, and so bacteria are probably unable to act as selective agents in the evolution of the gorgonian secondary chemistry. A study of 39 species of Caribbean gorgonians from 14 genera, indicates that these invertebrates rarely produce potent antibiotics that are active against marine pathogens. Antibiotic activity is seen in only 15% of the tests, with 23% exhibiting no activity and 33% suppressing only one bacterial strain.

Methanotrophs are a diverse group of gram-negative bacteria that obtain carbon and energy from methane metabolism. On the basis of utilization of formaldehyde, these bacteria are classified into three groups. The type 1 and type X methanotrophs use the ribulose monophosphate pathway to assimilate formaldehyde. The type II methanotrophs use the serine pathway. The type I methanotrophs grow best in conditions of low methane concentration while the type II grow best in the presence of high methane levels.

Bacterial strains isolated by growth on biphenyl have greater ability to degrade polychlorinated biphenyl (PCB) than strains isolated by growth on naphthalene. Probes made from bph, nah and tod genes that code the iron sulfur protein of the dioxygenase complex are used to hybridize the strains. Hybridization patterns show no correspondence with the substrate used for isolation indicating diversity in the genes in nature. Strains showing high degradation capacity hybridize to the bhp probe but some strains having high hybridization have low PCB-degrading ability.

The production of organic C, P and N compounds by viral lysis stimulates the growth of noninfected bacteria in marine environments suggesting that viral activity recycles nutrients in the microbial food web. The growth efficiency of noninfected bacteria decreases in the presence of viruses. The extracellular breakdown of polymeric organic nitrogen and phosphorous in cell lysates probably causes an increase in energy consumption and a decrease in growth ability. The addition of viruses to cultures with low P enhances the uptake of organic C and alkaline phosphatase activity.

A decreased capacity of multiple-peptidase mutants of Lactococcus lactis, to break down peptides to free amino acids, leads to a reduction in their ability to grow in milk. An increase in the number of peptidase gene mutants leads to a lesser growth rate in milk giving rise to smaller amounts of intracellular amino acids. Single deficiencies in the genes, however, PepX, PepO, PepC, and PepT, barring PepN produce little effect on the growth rates of the mutants in milk.

The intestines of deep-sea fish contain a large number of bacteria which are mainly barophilic. The size of the bacteria populational and number of culturable cells is more at in situ pressures than atmospheric pressure. The facultative and obligate barophilic bacteria play a major role in the intestinal microfloras while barotolerant bacteria have a minor role. The intestines of deep-sea fish probably supply sufficient nutrients to maintain significant bacterial growth in the deep sea.

The expression of htrA is completely dependent on the rpoE gene in vivo and is essential for bacterial growth at high temperature. This is so because the reconstituted RNA polymerase containing EsigmaE projects htrA in vitro. Construction of an rpoE-defective strain by gene disruption by using cloned rpoE gene is also reflected.

Analysis of the plasmid contents of various B. thurigiensis subsp. israelensis isolates, aggregation mutants, plasmid-cured derivatives, transconjugants and recured transconsjugants showed that the Agr+ phenotype and Agr- of B. thuringiensis subsp. israelensis are correlated with the presence of plasmid pXO16. The evidence of this fact is presented.

Sequencing of a region from the pgm locus of Yersinia pestis KIM6+ which transmits sensitivity to the bacteriocin pesticin to certain strains of Y. pestis and Escherichia coli showed that the Y. Pestis sequence is almostidentical to the pesticin receptor from Yersinia enterocolitica and is homologous to other outer membrane TonB-dependent proteins. The protein manufactured by the irp2 mutant suggests that HMWP2 may be indirectly involved for the maximal expression of the pesticin receptor.

Experimental studies on the energetics of bacterial growth reveal a close link between the anabolic steps of cellular biosynthesis and the free energy change associated with catabolic reactions, under restricted energy source conditions. Total energy flux is divided between maintenance and growth activities. Under nutrient restricted conditions ATP spill occurs in reactions that are related to maintenance. Futile ion cycles through the cell membrane are used by the bacteria for the hydrolysis of ATP. Fast restarting of growth or cell protection against toxic substances occurs through energy spilling.

Outer leaves of broad-leaved endive plants have higher fluorescent and pectolytic epiphytic bacterial population densities than inner leaves. The frequency distribution and variability of bacterial population size are influenced by the age of the leaves. Immigration of fluorescent bacteria on new leaves is inhibited by adjacent leaves. Leaves of younger plants have higher bacterial population sizes.

Results of a series of incubation experiments to ascertain the rate of release of dissolved organic carbon (DOC) by jellyfish Aurelia aurita revealed that this scyphozoan jellyfish is a major source of DOC. Since DOC quantities directly influence bacterial abundance, bacterial growth was ascertained to be simulated in the presence of A. aurita.

Experiments involving complementation of the Bacillus subtilis narA1 strain QB692 help isolate the Bacillus subtilis narA locus, which has narQ and narA genes. Experimental data reveal the similarity of the product of narQ with that of FdhD, which is essential for formate dehydrogenase activity in Escherichia coli. NarA exhibits homology to a protein MoaA, which is associated with the biosynthesis of the molybdenum cofactor for nitrate reductase and formate dehydrogenase. Characterization of mutants shows that both nitrate assimilation and respiration require narA rather than narQ.

Digital image analysis and continuous-flow slide culture help examine the influence of nutrient status on the morphology and surface colonization characteristics of an Acinetobacter sp. Experimental data indicate that high-nutrient medium induces biphasic transition from coccoid to bacillar morphology. Morphological changes accompany changes in the stability of cell attachment. Coccoid and bacillar Acinetobacter sp. morphotypes, and their behavior are physiological adaptations for colonization and attachment in low-nutrient system.

Mass spectrometric studies of the influence of isoprenoid supplementation on the mosquito pathogenic fungus Langenidium giganteum reveal that isoprenoid induces significant modifications in molecular species of glycerophosphocholine (GPC), glycerophosphoethanolamine (GPE) and glycerophosphoinositol (GPI). Ether linkages are present in majority of GPC and GPI isolated from mycelia and nuclei. Sterol auxotrophic nature of the fungus is suggested as the reason for the higher levels of ether lipids.

Amino acids that are essential for the growth of Clostridium difficile in chemically defined medium are leucine, tryptophan, valine, cysteine, isoleucine and proline. Growth is increased by threonine, histidine, glycine, methionine and arginine. Pyridoxine, biotin and pantothenate are the essential vitamins for the growth. Adenine is an efficient substitute for threonine and glycine, indicating that both amino acids are precursors of purine nucleotides.

Oxygen tension and growth phase control the enzymes catalase and superoxide dismutase in Xanthomonas species. Enzyme levels are optimum within 1h of growth, while the enzyme activities decrease as the growth continues. Enzyme activities are stimulated by high oxygen tension and major forms of the enzymes are an 80,000-Da monofunctional catalase and a manganese superoxide dismutase. Various Xanthomonas strains exhibit this unusual regulatory types and these patterns are vital during the initial stage of the interaction between plant and microorganisms.

Examination of the growth of Listeria monocytogenes reveals that the di- and tripeptide permeases transport the essential amino acids required for the growth. This proton motive force-dependent di- and tripeptide transport system facilitates growth of this pathogens in different foods where proteolytic activity of the microorganisms supplies these peptides. The correlation of this transport system with osmoregulation and virulence of L. monocytogenes is analyzed.

Analysis of purified NAD- and glutathione- dependent formaldehyde dehydrogenase (GD-FALDH) of Paracoccus denitrificans reveals the enzyme as a tetramer with a relative mass of 150 kDa. Genetic experiments helps isolate and sequence the gene encoding GD-FLADH. A mutant strain produced by the insertion of a kanamycin resistance gene fails to grow on choline, methanol or methylamine, while mutation exerts no influence on the heterotrophic growth. Oxidation of formaldehyde requires GD-FALDH of P. denitrificans during methylotrophic growth.

Examination of the growth of Azorhizobium caulinodans on N2 in supplemented-batch cultures, batch cultures and continuous culture as a function of different nicotinate levels reveals that nicotinate catabolism does not limit the growth in continuous cultures. In continuous cultures, the specific growth exhibits a linear relationship with the level of nicotinate present per unit of biomass, while in batch cultures anomalous growth curves are obtained. Nicotinate catabolism is dispensable for batch cultures and the experimental data suggest A. caulinodans as a tree diazotroph.

Analysis of wall teichoic acid (WTA) levels in Bacillus subtilis 168 during rod-sphere transition reveals 84% and 33% reduction in the WTA levels in the 113 tagF1 and 104 rodB1 strains during the rod-sphere transition. D-alanylation decreases during the transition while alpha-D-glucosylation and growth remain stable. A decrease of about 53 residues is seen in the chain length of WTA.

Growth rate of Helicobacter pylori in modified brucella broth medium attains the maximum value at a pH of 5.5 and is independent of the presence or absence of urea levels in the culture. The growth occurs at partial oxygen pressures, indicating the obligate microaerophilic and facultative acidophilic properties of the bacterium.

Restriction of inorganic nutrients such as P and N, directly and individually, induces the growth of phytoplanktons and bacterial organisms. Bacterial and phytoplankton growth are unrelated if N/P molar ratios of the two are less than 40. Increase of bacterial growth is correlated to phytoplanktons' acquiring different pi values.

Sunlight inactivation of fecal coliforms (FC) and enterococci (Ent) from sewage and meatworks effluents is measured by open-topped chambers containing 300-liter effluent-seawater mixtures. FC inactivation rate is more than that of Ent and varies for different experiments. The inactivation rates in long-pass optical filters occur in two specific regions only.