A predictive model for the growth rate of Bacillus cereus in broth by response surface methodology

A response surface methodology (RSM) was developed for predicting the growth rate of Bacillus cereus in a tryptic soy broth medium as a function of temperature (10 to 40°C), pH (5.5 to 8.5), and the NaCl concentration (0 to 8%). The primary model showed a good fit (r² = 0.920 to 0.999) to a Gompertz equation to obtain growth rates each condition. The quadratic polynomial model was found to be significant (p < 0.0001) and predicted values were found to be in good agreement with experimental values (R² value of 0.9486). The evaluation of RSM for describing the growth rate of B. cereus used the bias factor (B_f) and the accuracy factor (A_f). Both the B_f value (1.11) and the A_f value (1.50) were within acceptable ranges. This model was provided an efficient and accurate method for predicting the growth of B. cereus as a function of the controlling factors.     

The trade-off between growth rate and yield in microbial communities and the consequences for under-snow soil respiration in a high elevation coniferous forest

Soil microbial respiration is a critical component of the global carbon cycle, but it is uncertain how properties of microbes affect this process. Previous studies have noted a thermodynamic trade-off between the rate and efficiency of growth in heterotrophic organisms. Growth rate and yield determine the biomass-specific respiration rate of growing microbial populations, but these traits have not previously been used to scale from microbial communities to ecosystems. Here we report seasonal variation in microbial growth kinetics and temperature responses (Q₁₀) in a coniferous forest soil, relate these properties to cultured and uncultured soil microbes, and model the effects of shifting growth kinetics on soil heterotrophic respiration (R_h). Soil microbial communities from under-snow had higher growth rates and lower growth yields than the summer and fall communities from exposed soils, causing higher biomass-specific respiration rates. Growth rate and yield were strongly negatively correlated. Based on experiments using specific growth inhibitors, bacteria had higher growth rates and lower yields than fungi, overall, suggesting a more important role for bacteria in determining R_h. The dominant bacteria from laboratory-incubated soil differed seasonally: faster-growing, cold-adapted Janthinobacterium species dominated in winter and slower-growing, mesophilic Burkholderia and Variovorax species dominated in summer. Modeled R_h was sensitive to microbial kinetics and Q₁₀: a sixfold lower annual R_h resulted from using kinetic parameters from summer versus winter communities. Under the most realistic scenario using seasonally changing communities, the model estimated R_h at 22.67 mol m⁻² year⁻¹, or 47.0% of annual total ecosystem respiration (R_e) for this forest.     

Molecular and Structural Characterization of Barley Vernalization Genes

Vernalization, the requirement of a period of low temperature to induce transition from the vegetative to reproductive state, is an evolutionarily and economically important trait in the Triticeae. The genetic basis of vernalization in cultivated barley (Hordeum vulgare subsp. vulgare) can be defined using the two-locus VRN-H1/VRN-H2 model. We analyzed the allelic characteristics of HvBM5A, the candidate gene for VRN-H1, from ten cultivated barley accessions and one wild progenitor accession (subsp. spontaneum), representing the three barley growth habits – winter, facultative, and spring. We present multiple lines of evidence, including sequence, linkage map location, and expression, that support HvBM5A being VRN-H1. While the predicted polypeptides from different growth habits are identical, spring accessions contain a deletion in the first intron of HvBM5A that may be important for regulation. While spring HvBM5A alleles are typified by the intron-localized deletion, in some cases, the promoter may also determine the allele type. The presence/absence of the tightly linked ZCCT-H gene family members on chromosome 4H perfectly correlates with growth habit and we conclude that one of the three ZCCT-H genes is VRN-H2. The VRN-H2 locus is present in winter genotypes and deleted from the facultative and spring genotypes analyzed in this study, suggesting the facultative growth habit (cold tolerant, vernalization unresponsive) is a result of deletion of the VRN-H2 locus and presence of a winter HvBM5A allele. All reported barley vernalization QTLs can be explained by the two-locus VRN-H1/VRN-H2 model based on the presence/absence of VRN-H2 and a winter vs. spring HvBM5A allele. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users.     

Transient Accumulation of Metabolic Intermediates of p-Cresol in the Culture Medium by a Pseudomonas sp. Strain A Isolated from a Sewage Treatment Plant

Summary Activated sludge from a sewage treatment plant in Kanpur, India, was screened for bacterial strains metabolizing p-cresol exclusively under aerobic conditions. One such isolate was identified to be belonging to the genus Pseudomonas based on morphological and physiological criteria as well as 16S ribosomal RNA gene sequence analysis. Two intermediates were identified from the culture medium during the growth phase of Pseudomonas sp. strain A that indicated that the strain degraded p-cresol via the protocatechuate (PCA) pathway. p-Cresol was rapidly converted into p-hydroxybenzaldehyde (PHB) during early growth phase, which was later utilized after p-cresol depletion. p-Hydroxybenzoate (PHBA) accumulation was observed during the later stages of exponential growth phase. Kinetic constants for the degradation of p-cresol were determined using Haldane’s model. High μ_max and inhibitory constant (K_I) values along with the observed accumulation of significant amounts of PHB in culture filtrates seem to indicate that the isolated Pseudomonas sp. strain A may be of potential use in biotransformations.     

Kinetic studies on autohydrogenotrophic growth of <Emphasis Type="Italic">Ralstonia eutropha</Emphasis> with nitrate as terminal electron acceptor

Autohydrogenotrophic batch growth of Ralstonia eutropha H16 was studied in a stirred-tank reactor with nitrate and nitrite as terminal electron acceptors and the sole limiting substrates. Assuming product inhibition by nitrite, saturation kinetics with the two limiting substrates and a simple switching function, which allows growth on nitrite only at low nitrate concentrations, resulted in a kinetic growth model with nine model parameters. The data of two batch experiments were used to identify the kinetic model. The kinetic model was validated with two additional batch experiments. The model predictions are in very good agreement with the experimental data. The maximum nitrite concentration was estimated to be 30.7 mM (total inhibition of growth). After complete reduction of nitrate, the growth rate decreases almost to zero before it increases again because of the following nitrite respiration. The maximum autohydrogenotrophic growth rate of Ralstonia eutropha with nitrate as a final electron acceptor (0.509 d⁻¹) was found to be reduced by 90–95% compared to the so far reported autohydrogenotrophic growth rates with oxygen.     

Modeling of growth and sporulation of <Emphasis Type="Italic">Bacillus thuringiensis</Emphasis> in an intermittent fed batch culture with total cell retention

An extended dynamical model for growth and sporulation of Bacillus thuringiensis subsp. kurstaki in an intermittent fed-batch culture with total cell retention is proposed. This model differs from reported models, by including dynamics for natural death of cells and substrate consumption for cell maintenance. The proposed model uses sigmoid functions to describe these kinetic parameters. Equations for time evolution of substrate, vegetative, sporulated and total cell concentration were taken from previous works. Model parameters were determined from batch experimental data obtained in pilot plant. Parameter identification was developed in two stages: (1) coarse identification using a multivariable optimization with constraints algorithm, (2) fine identification by heuristic fit of model parameters looking for a minimal model error. The proposed model estimates adequate time evolution of the process variables with a mean error of 2.6% on substrate concentration and 6.7% on biomass concentration.     

Insight into the basis of root growth in Arabidopsis thaliana provided by a simple mathematical model

Plant organ growth changes under genetic and environmental influences can be observed as altered cell proliferation and volume growth. The two aspects are mutually dependent and intricately related. For comprehensive growth analysis, it is necessary to specify the relationship quantitatively. Here, we develop a simple mathematical model for this purpose. Our model assumes that the biological activity of a given organ is proportional to the cell number of the organ and is allocated into three aspects: cell proliferation, volume growth, and organ maintenance. We analyzed the growth of primary roots of Arabidopsis thaliana (L.) Heynh. in one tetraploid and four diploid strains using this model. The analysis determined various growth parameters, such as specific cost coefficients of cell proliferation and volume growth for each strain. The results provide insight into the basis of interstrain variations and ploidy effects in root growth.     

Validation of the <Emphasis Type="Italic">VRN-H2</Emphasis>/<Emphasis Type="Italic">VRN-H1</Emphasis> epistatic model in barley reveals that intron length variation in <Emphasis Type="Italic">VRN-H1</Emphasis> may account for a continuum of vernalization sensitivity

The epistatic interaction of alleles at the VRN-H1 and VRN-H2 loci determines vernalization sensitivity in barley. To validate the current molecular model for the two-locus epistasis, we crossed homozygous vernalization-insensitive plants harboring a predicted “winter type” allele at either VRN-H1 (Dicktoo) or VRN-H2 (Oregon Wolfe Barley Dominant), or at both VRN-H (Calicuchima-sib) loci and measured the flowering time of unvernalized F₂ progeny under long-day photoperiod. We assessed whether the spring growth habit of Calicuchima-sib is an exception to the two-locus epistatic model or contains novel “spring” alleles at VRN-H1 (HvBM5A) and/or VRN-H2 (ZCCT-H) by determining allele sequence variants at these loci and their effects relative to growth habit. We found that (a) progeny with predicted “winter type” alleles at both VRN-H1 and VRN-H2 alleles exhibited an extremely delayed flowering (i.e. vernalization-sensitive) phenotype in two out of the three F₂ populations, (b) sequence flanking the vernalization critical region of HvBM5A intron 1 likely influences degree of vernalization sensitivity, (c) a winter habit is retained when ZCCT-Ha has been deleted, and (d) the ZCCT-H genes have higher levels of allelic polymorphism than other winterhardiness regulatory genes. Our results validate the model explaining the epistatic interaction of VRN-H2 and VRN-H1 under long-day conditions, demonstrate recovery of vernalization-sensitive progeny from crosses of vernalization-insensitive genotypes, show that intron length variation in VRN-H1 may account for a continuum of vernalization sensitivity, and provide molecular markers that are accurate predictors of “winter vs spring type” alleles at the VRN-H loci.     

Effects of the loss of clonal integration on four sedges that differ in ramet aggregation

Although clonal growth is a dominant mode of plant growth in wetlands, the importance of clonal integration, resource sharing among ramets, to individual ramet generations (mother and daughter) and entire clones of coexisting species has not been well investigated. This study evaluated the significance of clonal integration in four sedge species of varying ramet aggregations, from clump-forming species (Clumpers –Carex sterilis, Eleocharis rostellata), with tightly aggregated ramets (rhizomes<1cm), to runner species (Runners –Schoenoplectus acutus, Cladium mariscoides), with loosely aggregated ramets. We manipulated clonal integration by either severing connections between target mother and daughter ramets or leaving connections intact, and then planted them in an intact neighborhood of a fen in Michigan, USA. We measured growth parameters of original and newly produced ramets over two growing seasons and conducted a final biomass harvest, to address four hypotheses. First, we expected integrated clones to accumulate more biomass than severed clones. However, final clone-level biomass and ramet production were the same for both treatments in all species although severing initially stimulated ramet production by Schoenoplectus and produced a more compact ramet aggregation in Cladium. Second, we hypothesized that mother ramets would experience a cost of integration, through reduced ramet or biomass production, while daughters would experience a benefit, through increased resource availability from mothers. Mother ramets of Cladium suffered a cost from integration, while Schoenoplectus mothers suffered a slight cost and Carex daughters saw a slight benefit. Finally, we hypothesized that integration would be more active in runner species than in clumper species. Indeed, we documented more active integration in runners than clumpers, but none of the study species were dependent upon integration for growth or survival once daughter ramets were established with their own roots and shoots. This study demonstrates that integration between established ramets may not be the most important advantage to clonal growth in this wetland field site. The loss of integration elicited varied responses among coexisting species in their natural habitat, somewhat but not completely related to their growth form, suggesting that a combination of plant life history traits contributes to the dependence upon clonal integration among established ramets of clonal species.     

CO2-induced growth enhancements of co-occurring tree species decline at different rates

To elucidate how enriched CO₂ atmospheres, soil fertility, and light availability interact to influence the long-term growth of tree seedlings, six co-occurring members of temperate forest communities including ash (Fraxinus americana L.), gray birch (Betula populifolia), red maple (Acer rubrum), yellow birch (Betula alleghaniensis), striped maple (Acer pensylvanicum), and red oak (Quercus rubra L.) were raised in a glasshouse for three years in a complete factorial design. After three years of growth, plants growing in elevated CO₂ atmospheres were generally larger than those in ambient CO₂ atmospheres, however, magnitudes of CO₂-induced growth enhancements were contingent on the availability of nitrogen and light, as well as species identity. For all species, magnitudes of CO₂-induced growth enhancements after one year of growth were greater than after three years of growth, though species' growth enhancements over the three years declined at different rates. These results suggest that CO₂-induced enhancements in forest productivity may not be sustained for long periods of time. Additionally, species' differential growth responses to elevated CO₂ may indirectly influence forest productivity via long-term species compositional changes in forests.     

An energetics model of an aquatic predator and its application to life-history optima

Summary A bioenergetics simulation model of the growth and life history of the aquatic predator Nephelopsis obscura Verrill was developed and validated using both experimentation and sensitivity analysis. Sensitivity analysis demonstrated that the model's internal feedbacks resulted in stability similar to homeostatic biological mechanisms. The experimental validation showed the model very accurately predicts growth at 10°C and 15°C but is slightly biased at 20°C. Simulation output was also consistent with the observed data on Nephelopsis from the site from which the simulation input data were obtained and indicated that Nephelopsis growth is more sensitive to prey variation among years than to temperature variation. Although built using data from a population at one extreme of the spectrum observed in life history and growth, the model was able to emulate the growth of Nephelopsis throughout its range. Thus, the variability in size and life history observed in the field can be explained as the result of a plastic phenotype responding to different habitat conditions.     

Growth responses of the mixotrophic dinoflagellates, Cryptoperidiniopsis sp. and Pfiesteria piscicida, to light under prey-saturated conditions

Recent research emphasis on the ecology of Pfiesteria spp. (Dinophyceae) has led to recognition of several morphologically similar heterotrophic dinoflagellates that often co-occur with Pfiesteria spp. in estuaries along the United States Atlantic coast. These include cryptoperidiniopsoid dinoflagellates, which resemble Pfiesteria spp. in having complex life cycles that include zoospores capable of kleptoplastidy. To examine and compare the role of kleptoplastidy in Cryptoperidiniopsis sp. and Pfiesteria piscicida, we tested the effects of irradiance on growth under prey-saturated (Storeatula major, Cryptophyceae) conditions. Growth of Cryptoperidiniopsis was strongly influenced by light intensity while no major effects were observed in P. piscicida. In Cryptoperidiniopsis, highest cell numbers and specific growth rates, but lowest specific cryptophyte consumption rates, were found at the highest light intensity tested (100 μmol photons m⁻² s⁻¹). A growth model was developed and used to estimate that the average half-life of chloroplasts ingested by Cryptoperidiniopsis decreased 3.4-fold from 12.6 h at high light to 3.7 h in the dark. These results show that light strongly enhances specific growth rate and growth efficiency of Cryptoperidiniopsis feeding on cryptophytes, and suggest that retained kleptochloroplasts may play a quantitatively significant role in carbon and energy metabolism of this organism. Differences in the effects of light between Cryptoperidiniopsis and P. piscicida may reflect different nutritional strategies, and allow these closely related dinoflagellates to occupy different niches and co-exist.     

Bioactivity of intra and extracellular substances from cyanobacteria and lactic acid bacteria on “wood blue stain” fungi

Cyanobacteria (photoautotrophic prokariota) have potential for the control of pathogenic bacteria and fungi. The effect of intra and extracellular products from cyanobacterial strains on the growth of fungi isolated from “wood blue stain,” was tested. Extracellular products were obtained by concentration and sterilization of the culture medium where cyanobacteria were grown. Cyanobacterial substances promoted or inhibited fungal growth according to the fungal and cyanobacterial strains tested. Extracellular products from Nostoc muscorum 79a and the methanolic extract from Microchaete tenera 84b biomass inhibited growth of Sphaeropsis sapinea 2157 (64.7 and 775.6%, respectively). Extracellular products of Nostoc piscinale 59 and biomass methanolic extract from N. muscorum 79a produced the highest growth promotion of Trichoderma boningii 452 (105.0%) and T. viride 993 (136.7%). Extracellular products of the heterotrophic lactic acid bacterium Streptococcus termophilus were also tested and strongly inhibited (64–92%) all the fungal strains. The tested fungi have different sensitivity to the bioactive substances present in the biomass and/or the culture medium of the studied cyanobacteria and lactic acid bacterium. N. muscorum 79a, M. tenera 84b, and S. termophilus have potential to control the wood blue stain fungi by a friendly environmental alternative.     

The relationship between kinetics of substrate-limited transitions and steady-state growth in continuous cultures ofAquaspirillum autotrophicum limited by pyruvate

Heterotrophic growth at steady state and during transient states caused by the sudden change of the concentration of the limiting factor in the feed medium was investigated experimentally for continuous cultures ofAquaspirillum autotrophicum limited by pyruvate. A model for describing the growth at steady state was selected from three unstructured models after statistical tests of the data. This model postulates that the growth yield increases linearly with the growth rate. Growth during transitions where the substrate remained limiting at all times was fitted with first-order kinetics. Theoretical predictions of these kinetics were derived from the unstructured models used to describe steady state. The predicted rate coefficients of the transients were compared to the experimental coefficients. It appeared that the model which best described steady-state growth also provided the best predictions for growth during the transient state. It is a widespread opinion that unstructured models are adequate to describe growth under steady-state conditions but not to predict transitions in continuous culture. However, for the particular case studied here, no higher degree of complexity was required to describe transitions, provided the growth of the culture was always limited by the substrate.     

The clam sipho as indicator for growth indices in the soft-shell clam <Emphasis Type="Italic">Mya arenaria</Emphasis>

Due to the species’ deep burrowing behaviour, growth parameters of the soft-shell clam Mya arenaria L. 1758 are difficult to estimate, especially in deeper habitats which are not directly accessible. In this study, we analysed 192 specimens of M. arenaria and found, contrary to results of most other studies that the sigmoid Gompertz growth model (GGM) is appropriate to describe the growth. Predictions from this model confirm the finding of a life span up to 8 years and as a consequence of this, a maximum shell-length of 60 mm. Individual growth rates calculated from the first deviation indicate a nearly exponential growth in young individuals. The relationship between the clam sipho-width and age, shell-length and biomass conform to the GGM. This is a new approach to assess growth of M. arenaria and to solve practical problems that arise in field studies.     

Comparison of carbonic anhydrase activity among various species of plantlets

During plant tissue culture, the culture container is small and sealed; the concentration of CO₂ in the microenvironment is relatively low. The plantlet growth is restrained for the shortage of CO₂ in the culture container. Carbonic anhydrase is a zinc-containing metalloenzyme that catalyzes the reversible conversion of bicarbonate to CO₂. The determination of carbonic anhydrase of leaves from Atractylodes lancea (thunb.) DC, Orychophragmus violaceus (L.) O.E. Schulz, Brassica juncea (L.) Czern.et Coss. cv. Luzhousileng, Brassica campestris L. cv. Chuanyou No.8, Brassica napus L cv. Oro, Brassica carinata Braun, Raphanus sativa L. var. raphanistroides Makino and their plantlets indicates that the carbonic anhydrase activity of leaves from both plantlets and fields varies from plant species to plant species, the carbonic anhydrase activity of leaves of Atractylodes lancea (thunb.) DC is the lowest among those plants, and the leaves of all plantlets are lower in carbonic anhydrase activity than the same species of plants from fields. The comparison of the growth rates of those plantlets shows that their relative growth rates are significantly different, plantlets of Atractylodes lancea have the slowest relative growth rate among those plants, and plantlets of Brassica juncea have the greatest relative growth rate. The relationship between RGR of plantlets and their CA activities is a significant linear function. It seems that there was certain correlation between carbonic anhydrase activities of plants and their growth rates. It suggests that in vitro, the greater the carbonic anhydrase activity of plantlet is, the higher its net photosynthetic rate, and the faster its growth rate. Those results offer a foundation to a rational medium choice in plant tissue culture.     

Psychrophilic <Emphasis Type="Italic">Pseudomonas syringae</Emphasis> requires <Emphasis Type="Italic">trans</Emphasis>-monounsaturated fatty acid for growth at higher temperature

A psychrophilic bacterium, Pseudomonas syringae (Lz4W) from Antarctica, was used as a model system to establish a correlation, if any, between thermal adaptation, trans-fatty acid content and membrane fluidity. In addition, attempts were made to clone and sequence the cti gene of P. syringae (Lz4W) so as to establish its characteristics with respect to the cti of other Pseudomonas spp. and also to in vitro mutagenize the cti gene so as to generate a cti null mutant. The bacterium showed increased proportion of saturated and trans-monounsaturated fatty acids when grown at 28°C compared to cells grown at 5°C, and the membrane fluidity decreased with growth temperature. In the mutant, the trans-fatty acid was not synthesized, and the membrane fluidity also decreased with growth temperature, but the decrease was not to the extent that was observed in the wild-type cells. Thus, it would appear that synthesis of trans-fatty acid and modulation of membrane fluidity to levels comparable to the wild-type cells is essential for growth at higher temperatures since the mutant exhibits growth arrest at 28°C. In fact, the cti null mutant-complemented strain of P. syringae (Lz4W-C30b) that was capable of synthesizing the trans-fatty acid was indeed capable of growth at 28°C, thus confirming the above contention. The cti gene of P. syringae (Lz4W) that was cloned and sequenced exhibited high sequence identity with the cti of other Pseudomonas spp. and exhibited all the conserved features.     

Differential sensitivity of green algae to allelopathic substances from Chara

Three short-term laboratory experiments were conducted to investigate allelopathic effects of a mixture of Chara globularis var. globularis Thuillier and Chara contraria var. contraria A. Braun ex Kützing on three different green algae. Single phytoplankton species were exposed to filtered water originating from charophyte cultures. Phytoplankton growth was monitored by determination of chlorophyll concentrations in batch cultures. The change in chlorophyll concentration during the experiments was analysed with a logistic growth model, resulting in an estimate of the exponential growth rate and the duration of the lag phase of the single green algae. The results indicate allelopathic effects of Chara on the growth of the green algae Selenastrum capricornutum Printz and Chlorella minutissima Fott et Nováková, whereas Scenedesmus obliquus (Turpin) Kützing did not seem to be affected. The exponential growth rate of S. capricornutum decreased 7% in the presence of water from a charophyte culture, while the growth rate of C. minutissima decreased with 3%. The allelopathic effect of Chara did not increase when the green alga C. minutissima was P-limited. The effect of Chara was different when young sprouts were used. With young sprouts the duration of the lag phase of C. minutissima was extended (25%), whilst for old plants the growth rate of this green alga decreased. Although the inhibiting effect of charophytes on specific phytoplankton species is rather small, the differential sensitivity of the species to Chara might influence the composition and biomass of phytoplankton communities in the field.     

Modification of an algal culture medium for sustained growth of a saxitoxin-producing isolate of Alexandrium minutum

In order to study saxitoxin (STX) production bymicro-algae in the laboratory, a defined algal culture medium which supports optimum growth over a longtime-period is a requirement. In the development of such a medium, a number of modifications were made to a standard algal culture medium (GP) and growth of a STX-producing isolate of Alexandrium minutum in the different formulations was assessed by measuring maximum cell densities and mean generation times (MGT). All experiments were carried out under controlled conditions in an aerobic atmosphere with increased CO₂. Whilst maximum cell densities in the different modifications were similar, the MGT was significantly shortened by the addition of Tris buffer and the trace metals strontium, selenium and molybdenum. Replacement of natural with artificial seawater and removal of soil extract did not adversely affect algal growth. Five of the six media formulations supported the growth of A. minutumover a 9-month period. This revised version was published online in August 2006 with corrections to the Cover Date.     

Host plant growth response to inoculation withFrankia

Optimum growth conditions and inoculation regimes were determined for severalFrankia strains isolated from both Alnus and Casuarina host plants. Growth conditions were estabilished that allowed a reduction in generation time to less than 15 hours for certain Alnus derivedFrankia. Differences in plant growth response were observed with differing inoculum levels and soil mixtures. Elite strains of Alnus derivedFrankia were isolated that elicited similar growth reponses in allAlnus species tested; however, differences were observed betweenFrankia strains and plant growth response of variousCasuarina species tested.