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Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota.

Stieglmeier M, Klingl A, Alves RJ, Rittmann SK, Melcher M, Leisch N, Schleper C - Int. J. Syst. Evol. Microbiol. (2014)

Bottom Line: The organism gained energy by oxidizing ammonia to nitrite aerobically, thereby fixing CO2, but growth depended on the addition of small amounts of organic acids.The optimal growth temperature was 42 °C and the optimal pH was 7.5, with ammonium and pyruvate concentrations of 2.6 and 1 mM, respectively.Additionally, we propose the family Nitrososphaeraceae fam. nov., the order Nitrososphaerales ord. nov. and the class Nitrososphaeria classis nov.

View Article: PubMed Central - PubMed

Affiliation: University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstr. 14, 1090 Vienna, Austria.

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(a) Growth curve of a culture of strain EN76T grown at 42 °C with 2 mM NH4Cl and 1 mM pyruvate. Cell counts, ammonium consumption and nitrite production were used to follow growth. Data represent mean values of triplicate cultures with standard deviations plotted (sometimes smaller than symbols). (b) Acceleration of growth of strain EN76T since purification of the strain in 2010 (Tourna et al., 2011). The cultivation conditions were as follows: July 2010 and November 2010, 37 °C, 1 mM NH4Cl, 1 mM pyruvate; March 2013, 37 °C, 1 mM NH4Cl, 0.1 mM pyruvate; July 2013, 42 °C, 1 mM NH4Cl, 0.8 mM pyruvate; November 2013, 42 °C, 2 mM NH4Cl, 1 mM pyruvate. Nitrite production was used to follow growth. Data represent mean values of replicated cultures (three to five replicates) with standard deviations plotted (sometimes smaller than symbols). Data points previously published in Fig. 3(b) of Tourna et al. (2011) (i.e. July 2010) were included in the figure.
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f1: (a) Growth curve of a culture of strain EN76T grown at 42 °C with 2 mM NH4Cl and 1 mM pyruvate. Cell counts, ammonium consumption and nitrite production were used to follow growth. Data represent mean values of triplicate cultures with standard deviations plotted (sometimes smaller than symbols). (b) Acceleration of growth of strain EN76T since purification of the strain in 2010 (Tourna et al., 2011). The cultivation conditions were as follows: July 2010 and November 2010, 37 °C, 1 mM NH4Cl, 1 mM pyruvate; March 2013, 37 °C, 1 mM NH4Cl, 0.1 mM pyruvate; July 2013, 42 °C, 1 mM NH4Cl, 0.8 mM pyruvate; November 2013, 42 °C, 2 mM NH4Cl, 1 mM pyruvate. Nitrite production was used to follow growth. Data represent mean values of replicated cultures (three to five replicates) with standard deviations plotted (sometimes smaller than symbols). Data points previously published in Fig. 3(b) of Tourna et al. (2011) (i.e. July 2010) were included in the figure.

Mentions: In order to investigate optimal growth conditions for EN76T, a design of experiments (DoE) strategy was applied, using the factors temperature, pyruvate concentration and ammonium concentration. Based on our preliminary knowledge of the strain’s growth requirements (Tourna et al., 2011), the range for each factor (design space) was set as follows: 37–47 °C, 0.1–1.5 mM sodium pyruvate and 1–4 mM NH4Cl. As nitrite production was shown to follow biomass production (Tourna et al., 2011), it was used to calculate the growth rate (μ) and maximum growth rate (μmax), which were eventually used to develop the model (Design-Expert 8 software; Stat-Ease Inc.). Experiments were conducted in triplicate, except for the centre points of the initial two-level factorial screening design, which were set up in fivefold replicates. The two-level factorial design was applied in order to screen the design space rapidly. Due to a low model significance of data obtained from the initial two-level factorial screening design space, an augmented matrix was used in order to account for putative interactions of individual factors. Thus, the two-level factorial design space was extended by using a face-centred augmented matrix. Eventually, data points of all experiments (n = 51) were used to establish a response surface model (RSM). Data were analysed with the software Design-Expert 8. ANOVA, based on a stepwise regression elimination procedure, was used to develop the model. The desirability approach, as described elsewhere (Derringer & Suich, 1980), was used to maximize μ or μmax (variable) based on variation of quantitative factors, here c(ammonium), c(pyruvate) and temperature (within the design space). A score is given to each quantitative factor setting that can be used to maximize the variable. In this approach, desirability between 0 and 1 (corresponding to 0–100 %) can be assigned to a variable for optimization; factors identified as being outside a certain desirability function will not be considered for model generation. To verify the calculated optimal growth conditions identified by the established RSM model design space, one additional growth experiment (fivefold-replicated closed-batch cultures) was performed (Fig. 1a).


Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota.

Stieglmeier M, Klingl A, Alves RJ, Rittmann SK, Melcher M, Leisch N, Schleper C - Int. J. Syst. Evol. Microbiol. (2014)

(a) Growth curve of a culture of strain EN76T grown at 42 °C with 2 mM NH4Cl and 1 mM pyruvate. Cell counts, ammonium consumption and nitrite production were used to follow growth. Data represent mean values of triplicate cultures with standard deviations plotted (sometimes smaller than symbols). (b) Acceleration of growth of strain EN76T since purification of the strain in 2010 (Tourna et al., 2011). The cultivation conditions were as follows: July 2010 and November 2010, 37 °C, 1 mM NH4Cl, 1 mM pyruvate; March 2013, 37 °C, 1 mM NH4Cl, 0.1 mM pyruvate; July 2013, 42 °C, 1 mM NH4Cl, 0.8 mM pyruvate; November 2013, 42 °C, 2 mM NH4Cl, 1 mM pyruvate. Nitrite production was used to follow growth. Data represent mean values of replicated cultures (three to five replicates) with standard deviations plotted (sometimes smaller than symbols). Data points previously published in Fig. 3(b) of Tourna et al. (2011) (i.e. July 2010) were included in the figure.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4129164&req=5

f1: (a) Growth curve of a culture of strain EN76T grown at 42 °C with 2 mM NH4Cl and 1 mM pyruvate. Cell counts, ammonium consumption and nitrite production were used to follow growth. Data represent mean values of triplicate cultures with standard deviations plotted (sometimes smaller than symbols). (b) Acceleration of growth of strain EN76T since purification of the strain in 2010 (Tourna et al., 2011). The cultivation conditions were as follows: July 2010 and November 2010, 37 °C, 1 mM NH4Cl, 1 mM pyruvate; March 2013, 37 °C, 1 mM NH4Cl, 0.1 mM pyruvate; July 2013, 42 °C, 1 mM NH4Cl, 0.8 mM pyruvate; November 2013, 42 °C, 2 mM NH4Cl, 1 mM pyruvate. Nitrite production was used to follow growth. Data represent mean values of replicated cultures (three to five replicates) with standard deviations plotted (sometimes smaller than symbols). Data points previously published in Fig. 3(b) of Tourna et al. (2011) (i.e. July 2010) were included in the figure.
Mentions: In order to investigate optimal growth conditions for EN76T, a design of experiments (DoE) strategy was applied, using the factors temperature, pyruvate concentration and ammonium concentration. Based on our preliminary knowledge of the strain’s growth requirements (Tourna et al., 2011), the range for each factor (design space) was set as follows: 37–47 °C, 0.1–1.5 mM sodium pyruvate and 1–4 mM NH4Cl. As nitrite production was shown to follow biomass production (Tourna et al., 2011), it was used to calculate the growth rate (μ) and maximum growth rate (μmax), which were eventually used to develop the model (Design-Expert 8 software; Stat-Ease Inc.). Experiments were conducted in triplicate, except for the centre points of the initial two-level factorial screening design, which were set up in fivefold replicates. The two-level factorial design was applied in order to screen the design space rapidly. Due to a low model significance of data obtained from the initial two-level factorial screening design space, an augmented matrix was used in order to account for putative interactions of individual factors. Thus, the two-level factorial design space was extended by using a face-centred augmented matrix. Eventually, data points of all experiments (n = 51) were used to establish a response surface model (RSM). Data were analysed with the software Design-Expert 8. ANOVA, based on a stepwise regression elimination procedure, was used to develop the model. The desirability approach, as described elsewhere (Derringer & Suich, 1980), was used to maximize μ or μmax (variable) based on variation of quantitative factors, here c(ammonium), c(pyruvate) and temperature (within the design space). A score is given to each quantitative factor setting that can be used to maximize the variable. In this approach, desirability between 0 and 1 (corresponding to 0–100 %) can be assigned to a variable for optimization; factors identified as being outside a certain desirability function will not be considered for model generation. To verify the calculated optimal growth conditions identified by the established RSM model design space, one additional growth experiment (fivefold-replicated closed-batch cultures) was performed (Fig. 1a).

Bottom Line: The organism gained energy by oxidizing ammonia to nitrite aerobically, thereby fixing CO2, but growth depended on the addition of small amounts of organic acids.The optimal growth temperature was 42 °C and the optimal pH was 7.5, with ammonium and pyruvate concentrations of 2.6 and 1 mM, respectively.Additionally, we propose the family Nitrososphaeraceae fam. nov., the order Nitrososphaerales ord. nov. and the class Nitrososphaeria classis nov.

View Article: PubMed Central - PubMed

Affiliation: University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstr. 14, 1090 Vienna, Austria.

Show MeSH
Related in: MedlinePlus