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DOI 10.1007/s00449-016-1628-3
ORIGINAL PAPER
Received: 30 March 2016 / Accepted: 16 May 2016 / Published online: 9 June 2016
Ó Springer-Verlag Berlin Heidelberg 2016
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1528 Bioprocess Biosyst Eng (2016) 39:1527–1537
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compounds aliquots (20 lL) were injected and analyzed Searches against protein data bases with the priority order
using an Agilent 1260 HPLC with a 5C18-250A column of non-redundant protein sequences in NCBI(NR) were
(Agilent, 4.6 mm id 9 250 mm, 5 lm) thermostated at carried out by Kyoto Encyclopedia of Genes and Genomes
35 °C. The mobile phase consists of water: acetonitrile (70: database (KEGG, Ver. 1.67x, http://www.genome.jp/kegg/
30 [v/v]) at a flow rate of 0.8 mL/min. Analytes were ) [21]. Furthermore, searches for Clusters of Orthologous
detected at 361 nm. Groups (COG, http://clovr.org/docs/clusters-of-ortholo
VB12 was qualitative by HPLC connected to an elec- gous-groups-cogs/) [22] were conducted with acritical
trospray mass spectrometer (Micromass Esquire 3000 plus; E value B1e-3. Based on the results of the protein database
Bruker Daltonics, Germany) [15]. The electron spray ion- annotation, Blast2GO (https://www.blast2go.com/) [23]
ization–mass spectrum (ESI–MS) was performed in posi- was applied to obtain the functional classification of the
tive mode using 0.01 % (v/v) formic acid in 15 % (v/v) genomic sequences based on gene ontology (GO) terms.
acetonitrile as mobile phase. Separation was performed at The Nr database was used to perform the GO functional
room temperature at 1 mL/min and the injection volume classification for all genomic sequences.
was 50 lL. Nitrogen was used as both desolvation gas at a
flow rate of 350 L/h and cone gas at 50 L/h. The desol- Optimization of fermentation temperature
vation temperature was set at 350 °C. The ionization
source was working at 105 °C. Capillary and cone voltages The optimal fermentation temperature of strain S. meliloti 320
were 4000 and 180 V, respectively [15, 16]. was tested using the following medium: Sucrose, 60 g L-1;
CSL, 20 g L-1; (NH4)2SO4, 2g L-1; CoCl2, 0.006 g L-1;
Identification of the isolates by 16S rDNA KH2PO4, 2.6 g L-1; betaine, 6 g L-1; DMBI, 1 g L-1. Fer-
sequencing mentation was carried out in 250 mL-Erlenmeyer flasks
containing 30 mL of medium at an agitation rate of 200 rpm
Genomic DNA was isolated from the bacterial isolate and for 7 days. After 7 days fermentation at 25, 30, 35, 40 and
was used as template for polymerase chain reaction (PCR). 45 °C, respectively, fermentation broth was used to assay the
Primers used for the amplification of part of 16S rDNA concentration of VB12.
were 16SF (50 -AGAGTTTGATCCTGGCTCAG-30 ) and
16SR (50 -TACGG TTACCTTGTTACGACTT-30 ). PCR Selection of the optimal carbon source and nitrogen
was carried out in a 50 lL reaction volume containing source
50 ng of genomic DNA, 20 pmol of each primer, 1.25 units
of Q5 High-Fidelity DNA polymerase (New England Applied media for the determination of the optimal carbon
Biolabs, USA), 200 lM of each dNTPs and 1X PCR buf- source contained CSL, 20 g L-1; (NH4)2SO4, 2 g L-1;
fer. PCR was carried out for 30 cycles in a MycyclerTM CoCl2, 0.006 g L-1; KH2PO4, 2.6 g L-1; betaine, 6 g L-1;
(Bio-Rad, USA) with the initial denaturation at 98 °C for DMBI 1 and 60 g L-1 of one of five carbon sources
5 min, cyclic denaturation at 98 °C for 30 s, annealing at (glucose, maltose, sucrose, fructose or starch). VB12-con-
55 °C for 30 s and extension at 72 °C for 1 min with a final centrations in 7 days fermentation broth were determined
extension of 10 min at 72 °C. The PCR product was by HPLC as described above.
checked by agarose gel electrophoresis and was further To determine the most suitable organic nitrogen source,
subjected to sequencing. The sequence data was checked the following medium was used: Sucrose, 60 g L-1;
by BLAST analysis [17]. The phylogenetic analysis of the (NH4)2SO4, 2 g L-1; CoCl2, 0.006 g L-1; KH2PO4,
16S rDNA sequence of the isolate obtained in this study 2.6 g L-1; betaine, 6 g L-1 and DMBI, 1 g L-1. Organic
was conducted with MEGA 5 using neighbor joining nitrogen sources and amounts tested were as following: (1)
method with 1000 bootstrap replicates [18]. 2 % yeast powder (YP), 1 % peptone; (2) 2 % yeast extract
(YE), 1 % peptone; (3) 2 % yeast extract powder (YEP),
Genome analysis of S. meliloti 320 strain 1 % peptone; (4) 2 % yeast extract concentrate (YEC), 1 %
peptone; (5) 2 % autolyzed yeast powder (AYP), 1 %
The genomic DNA of strain S. meliloti 320 was extracted peptone; (6) 2 % CSL; (7) 2 % CSL, 1 % peptone.
from purified bacterial isolates using OMEGA Bacterial Experiments were conducted in 250 mL-Erlenmeyer-flasks
DNA kits (Omega bio-tek, Feyou Biotechnology, China). containing 30 mL of each medium at 30 °C at an agitation
Sinorhizobium meliloti 320 was completely sequenced rate of 200 rpm in rotary shakers for 7 days.
using the sequencing platform on NGS-QC-Toolkit, Response surface methodology (RSM)-central compos-
deleting overlapping sequences. The cut-off-level (cut off ite design (CCD) was employed to find out the optimum
Qual Score) was set to 30 [19]. The resulting genomic concentrations of the optimal carbon source and nitrogen
sequences were determined by BLASTX(V2.2.17) [20]. source and to study their interactions [24]. Experimental
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Fig. 2 a The microscope image of S. meliloti 320 dyed by 1 % base Strain selection and identification of VB12
fuchsin; b 6 d fermentation broth of S. meliloti 320 and negative
control
50 bacterial strains were isolated from soil samples and
design, model calculation, graph drawing and other data cultivated in minimum media. Among these strains, only
analysis were all performed on Design Expert software the color of S. meliloti 320 fermentation broth was red
(Version 8.0.6, Stat-Ease Inc., Minneapolis, USA). Each (Fig. 2b) and the microscope image of S. meliloti 320
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Bioprocess Biosyst Eng (2016) 39:1527–1537 1531
Table 1 General information this product, HPLC–ESI–MS/MS was used to analyze the
Features Value
about sequenced S. meliloti 320 fermentation broth.
genome Genome size (bp) 7256751 Electrospray ionization of the cobalamines in a mass
GC-content 63.2 % spectrometer ion source leads to the formation of not only
Plasmid 0 of some molecular adducts, but also a pattern of frag-
Replicons 1 mentation ions (due to a low chemical stability of the
Total genes 6903 cobalamines). Proper selection of a sufficiently abundant
tRNA genes 3 fragment ion helps achieve the required quantification/de-
rRNA genes 5 tection limits. Results of the HPLC–ESI–MS/MS analysis
CDs 6895 from the cell cultures within the MS are shown in Fig. 3B.
Ionization of CN-Cbl using an ESI source leads to the
formation of the ions 678.3 [M?2H]2?, which was consist
with that reported by Szterk [25]. In this study, only CN-
shows it is a rod-shaped strain and the cell diameter is Cbl could be detected as different kinds of vitamin B12
about 1.0–1.2 lm (Fig. 2a). were all translated to CN-Cbl. Lou et al. [16] also reported
The 56 h fermentation broth was used to assay the the formation of multi-charged molecules during B12
amounts of VB12 by HPLC. In compliance with VB12 vitamin ionization. However, some of such adducts were
standards, mass spectroscopic measurements of corre- not found in this study. This is caused by the differences in
sponding HPLC retention peaks revealed spectra covering the electrospray source operation parameters and differ-
VB12-standard spectra (Fig. 3A). This shows that S. meli- ences in the chemical composition of the LC mobile phase.
loti 320 could produce VB12 when grown under aerobic The ionization process might be also affected by the
conditions. To further identification and characterization of composition of the analyzed matrix.
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Fig. 5 The network of porphyrin and chlorophyll metabolism has shown on KEGG which containing VB12 biosynthetic pathway. Enzyme
classes matching with KEGG analyses are highlighted
Phylogenetic classification of S. meliloti 320 variable regions. This gene is therefore suitable for phylo-
genetic and taxonomic classifications at various levels,
The 16s rDNA gene is a universal characteristic in including intrageneric differentiation [26]. A 1476 bp target
prokaryotes and has both conserved and sufficiently fragment was amplified by PCR using 16S rDNA primers.
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Bioprocess Biosyst Eng (2016) 39:1527–1537 1533
Fig. 6 a GO functional
classification of genes; b COG
functional classification of
genes
We conducted sequence similarity analysis of 16S rDNA Genomic features of S. meliloti 320
genes, and compared them with those of reference organ-
isms obtained from GenBank data libraries. The phyloge- Sinorhizobium meliloti 320 hosts one circular chromosome
netic analysis by MEGA5 [27] revealed that the isolated S. of 7,256,751 bp with an average GC-content of 63.2 %,
meliloti 320 belongs to the species of genus Sinorhizobium/ although no further plasmid was present. The genome
Ensifer (Fig. 4). Sinorhizobium sp. ZJB1101 and Ensifer comprises 6903 genes and 6895 putative genomic coding
adhaerens M14 represent the most related organisms with sequences (CDs). The genome includes 3 tRNA genes and
16S rDNA-sequence similarities of 99 %. 5 rRNA genes in total (Table 1).
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the highest concentration of VB12, 100 ± 2 mg L-1, was increase VB12 production. The experimental data in
obtained at 30 °C. This temperature was then used in Table 2 were correlated as a second-order polynomial
subsequent experiments. model by nonlinear regression. The empirical relationship
between variables and responses was expressed by the
Selection of carbon source and nitrogen source following second-order polynomial equation:
Y ¼ 126:46 þ 9:58A þ 18:08Bþ8:25AB 11:19A2
To select the optimum carbon source, five different carbon
9:94B2
sources were investigated initially, at pH 7.0, 30 °C and
200 rpm. When using sucrose, 98 ± 2.8 mg L-1 VB12 was where Y is the predicted response of VB12 production (mg
produced, which is the highest one (Fig. 7b). However, L-1), and A and B are the coded values of sucrose and
when employing starch as carbon source, VB12 concen- CSL, respectively.
tration is only 30 mg L-1. Thus, sucrose was then used in The sufficiency of the second-order model was checked
subsequent experiments. by the analysis of variance (ANOVA) presented in Table 3.
Replacing YP, YE, YEP, YEC or AYP in fermentation The F value of 5.37 implies that the model is significant, as
medium with 20.0 g L-1 CSL resulted in VB12 concen- there is only a 3.21 % probability that a large F value could
tration increased from 10 ± 0.8 to 130 ± 3.2 mg L-1 occur due to noise. The model presents a relatively high
(Fig. 7c). CSL is a cheap organic nitrogen source and is determination coefficient (R2 = 0.8172), explaining
available in large scale fermentation. Thus, in subsequent 81.7 % of the variability in the response. The P values
experiments CSL was chosen as suitable nitrogen source were used to identify the effects of each factor on VB12
and its concentration was further to be optimized. production. A P value below 0.05 indicates that the model
terms are significant. In this case, A2 (sucrose 9 sucrose),
Optimization of the concentration of sucrose B (CSL) and B2 (CSL 9 CSL) are significant (Table 4).
and CSL using RSM The interaction between these two factors is not significant.
The location of the optimum was determined to be
The concentrations of sucrose and CSL were optimized to A = -0.901, and B = 1.283, obtained by the differentia-
find the best combination of them for maximum VB12 tion of the quadratic model given by equation above. The
production. 1 % peptone was added to each experiment to corresponding uncoded values were: 69.0 g L-1 sucrose
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Table 4 Regression coefficients and significances obtained by RSM 4. Xia W, Chen W, Peng WF, Li KT (2015) Industrial vitamin B
production by Pseudomonas denitrificans using maltose syrup
Factor Coefficient estimate F value P value and corn steep liquor as the cost-effective fermentation sub-
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AB 8.25 0.82 0.3998
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Acknowledgments We are grateful for the support from State Key
analysis of vitamin B12 in food products and in multivitamins-
Development Program for Basic Research of China (973 Program,
multimineral tablets. Anal Chim Acta 562(2):185–189
2013CB733600), National Nature Science Foundation of China
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