Chelatococcus thermostellatus sp. nov., a new thermophile for bioplastic synthesis: comparative phylogenetic and physiological study
Received: 9 February 2016
Accepted: 19 May 2016
Published: 9 June 2016
Abstract
The poly(3-hydroxybutyrate), PHB, accumulating thermophilic strain MW9T, isolated from an aerobic organic waste treatment plant, was characterized by detailed physiological and phylogenetic studies. The strain is a Gram-stain-negative, rod shaped, non-spore forming member of Alphaproteobacteria. It shows optimum growth at 50 °C. Based on 16S rRNA gene sequence similarity, the strain together with five very similar isolates, was affiliated to the genus Chelatococcus (Ibrahim et al. in J Appl Microbiol 109:1579–1590, 2010). Rep-PCR genomic fingerprints and partial dnaK gene sequence also revealed that these isolates are very similar, but differ from other Chelatococcus type strains. The major fatty acids were similar to those of other strains of the genus Chelatococcus. DNA–DNA hybridization of strain MW9T with Chelatococcus species type strains revealed 11.0–47.7 % relatedness. G+C content of DNA was 67.1 mol%, which is comparable with the other strains of Chelatococcus species. The physiological and phenotypic characteristics of the new strain MW9T are sufficient to differentiate it from previously described species in the genus Chelatococcus. Strain MW9T is considered to represent a novel species of the genus Chelatococcus, for which the name Chelatococcus thermostellatus is proposed. The type strain is MW9T (=LMG 27009T = DSM 28244T). Compared to known Chelatococcus strains, strain MW9T could be a potent candidate for bioplastic production at elevated temperature.
Keywords
Introduction
Increased global demands for alternative energy and biodegradable materials have stimulated many studies for the utilization of renewable resources via microbial fermentation (Chiellini and Corti 2012). Microbially synthesized biodegradable plastics, polyhydroxyalkanoates (PHAs), have been revealed to possess similar properties as conventional oil-based plastics, however industrial production costs of PHAs are relatively high (Chen 2010). Alternatively, biofunctionalized PHAs nanobeads can be used in numerous precious biotechnological applications (Dinjaski and Auxiliadora Prieto 2015). Moreover, its monomers are of great interest for biomedical applications, and could also be converted to alternative fuel (Chen 2010). Recently, fermentative production of PHA using thermophiles has gained more interest because of the possibility to reduce costs of sterilization and cooling during high-cell density cultivation at industrial scale (Ibrahim and Steinbüchel 2010).
Composting is a self-heating aerobic solid phase process for partial biodegradation and conversion of organic waste materials. A large variety of mesophilic, thermotolerant and thermophilic aerobic microorganisms have been reported to be predominant in composting at temperatures between 20 and 60 °C (De Bertoldi et al. 1983). Temperature is revealed to be a major factor determining the type of microorganism, species diversity, and the rate of metabolic activities during composting. It has been reported that at temperature of 50–60 °C, thermophilic bacteria are very active composting organisms (Beffa et al. 1995).
In a previous study of thermophilic bacteria, which are able to produce poly(3-hydroxybutyrate), PHB, the aerobic organic waste composting process in Münster (Germany) was used as a source to screen for new thermophiles. From different samples collected at various positions inside the compost heap, six thermophilic PHB-accumulating isolates, MW9T, MW10, MW11, MW12, MW13 and MW14 were purified and characterized (Ibrahim et al. 2010). Despite sharing over 99 % sequence similarity with each other in 16S rRNA genes (Ibrahim et al. 2010), these isolates showed some differences in aggregates formation, colony morphology, color, and size. It also showed some other biochemical and physiological characteristics differences such as carbon substrate preference. The 16S rRNA gene sequences of these isolates showed high similarities to those of C. daeguensis K106T (98.96 %), C. sambhunathii HT4T (98.84 %), and C. asaccharovorans TE2 (95.84 %) (Ibrahim et al. 2010).
The new isolates, except MW10, form star-shaped cell aggregates (SSC aggregates) during normal growth in mineral salts medium (MSM). They all grow optimally at 50 °C. These isolates show fast growth and shorter cell length without aggregation when grown in rich media; nutrient broth and standard I nutrient broth (Merck KGaA) (Ibrahim et al. 2010). Furthermore, in all these new Chelatococcus isolates, a growth-associated accumulation of intracellular PHB granules was observed when growing in medium with excess carbon source (Ibrahim et al. 2010).
In the present study, detailed physiological and molecular investigations were done for a precise differentiation of the new isolates from other Chelatococcus type strains. PHB accumulation and SSC aggregates formation by the new strain MW9T and other strains of the genus Chelatococcus were also investigated.
Materials and methods
Isolation and cultivation of strains
Isolates MW9T, MW10, MW11, MW12, MW13 and MW14, were isolated from an aerobic compost of an organic waste treatment plant in Münster (Germany) (Ibrahim et al. 2010). Strains used for comparative study were C. asaccharovorans LMG 25503T, C. daeguensis LMG 25471T, C. sambhunathii LMG 26063T (Table 3). The 16S rRNA gene sequences for isolates MW9T, MW10, MW11, MW12, MW13 and MW14 were deposited in the NCBI database under the accession numbers: GQ871852, GQ871853, GQ871854, GQ871855, GQ871856 and GQ871857, respectively.
Cultivations were done in three media: (i) Luria–Bertani broth (LB broth) (AppliChem GmbH, 64291 Darmstadt, Germany), (ii) standard-1-nutrient broth containing (g/L): peptone 15.0; yeast extract 3.0; sodium chloride 6.0; D(+)glucose 1.0 (Merck KGaA, 64271 Darmstadt, Germany); (iii) mineral salt medium (MSM, Schlegel et al. 1961) containing (g/L): Na2HPO4·12H2O, 9.0; KH2PO4, 1.5; MgSO4·7H2O, 0.2; NH4Cl, 1.0; CaCl2·2H2O, 0.02; Fe(III)NH4-citrate, 0.0012. The MSM also included 1 mL of trace element solution containing the following compounds (g/L): EDTA, 50.0; FeCl3, 8.3; ZnCl2, 0.84; CuCl2·2H2O, 0.13; CoCl2·6H2O, 0.1; MnCl2·6H2O, 0.016; H3BO3, 0.1. Glucose (20 g/L) was added separately as sole carbon source. The pH of the medium was adjusted to 7.3 before sterilization. Agar (16 g/L) and/or Nile-red (final concentration 0.5 µg/mL), was added for solid media preparation.
Cultures for PHA accumulation
Erlenmeyer flasks (250 mL) containing 50 mL MSM with glucose (20 g/L) were inoculated with 3.5 mL of a 24-h grown pre-culture (7 % inoculum size). The pre-culture was inoculated with a full-loop of well-grown culture on MSM. Unless stated otherwise, flasks were incubated at 50 °C and 200 rpm for 72 h. Cells were harvested by centrifugation for 20 min at 3072×g and 4 °C, washed with distilled water, frozen and lyophilized.
Gas chromatography analysis of PHA content
PHA content in whole cell dry matter was determined by gas chromatography analysis after methanolysis and 3-hydroxybutyric acid methyl ester formation (Ibrahim et al. 2010).
Scanning electron microscopy (SEM)
Samples were fixed in 0.15 M cacodylate buffer (2.5 % glutaraldehyde) overnight. The samples were attached to poly-l-lysine prepared cover slips, alcohol dehydrated and critical point dried. Then they were mounted on aluminum and sputter coated with gold/palladium.
Transmission electron microscopy (TEM)
The cells were fixed in 0.1 M sodium cacodylate buffer (3 % glutaraldehyde) overnight, postfixed in 1 % osmium tetroxide for 1 h and dehydrated in ethanol. They were embedded in Epon (Taab), 50 nm thick sections were cut off with a diamond knife and stained with 2 % uranyl acetate and lead citrate, according to Reynolds (1963), and examined in a JEOL JEM 1230 transmission electron microscope.
Rep-PCR analysis
For rep-PCR, DNA preparations were made starting from one or two colonies of each isolate/strain and using the alkaline lysis protocol of Baele et al. (2003). Rep-PCR was performed as described by Gevers et al. (2001) using the (GTG)5 primer (5′-GTG GTG GTG GTG GTG-3′), and the resulting genomic fingerprints were processed using BioNumerics v. 5.1 software (Applied Maths).
Sequence analysis of dnaK
The same DNA preparations as used for rep-PCR were also used to amplify dnaK genes using the primers and protocol described previously (Stępkowski et al. 2003; Martens et al. 2007). Sequence analysis was performed using MEGA version 5 (Tamura et al. 2011). Using Muscle in MEGA, dnaK gene sequences of the new isolates were aligned with those of the related strains. A neighbor-joining tree was calculated and a bootstrap analysis using 1000 replications was performed.
Fatty acid analysis
Whole-cell fatty acid composition was analyzed for strain MW9T, as well as for the type strains of the three other Chelatococcus species. All strains were grown for 48 h on TSA (LMG medium 185) at 37 °C. Harvesting of cells, extraction and analysis were performed according to the recommendations of the manufacturer of the MIDI identification system (Microbial Identification System). The fatty acid methyl esters mixtures were separated using MIDI SHERLOCK Microbial Identification System (Microbial ID, Newark, DE, 19711, USA.) and an Agilent model 6890 series gas chromatograph fitted with a 7683 automatic sample injector. Peaks were assigned using the Sherlock MIS software and the TSBA50 peak naming method.
DNA–DNA hybridization
High-quality DNA for DNA–DNA hybridization was prepared by the method of Wilson (1987), with minor modifications (Cleenwerck et al. 2002). DNA–DNA hybridization was performed using the microplate method (Ezaki et al. 1989) with some modifications as described by Cleenwerck et al. (2002). The hybridization temperature was 45 ± 1 °C. Reciprocal reactions were performed for every hybridization pair and variation was within the limits of this method (Goris et al. 1998). The values presented are based on a minimum of four replicates (Table 3).
G+C content
The G+C content of DNA was determined by HPLC according to the method of Mesbah et al. (1989) using a Waters Breeze HPLC system and XBridge Shield RP18 column thermostabilised at 37 °C. The solvent was 0.02 M NH4H2PO4 (pH 4.0) with 1.5 % (v/v) acetonitrile. Non-methylated lambda phage (Sigma) and E. coli DNA were used as calibration reference and control, respectively.
Results
Morphological and physiological characterization
Differential characteristics between strains MW9T and the type strains of recognized Chelatococcus species
C. thermostellatus MW9T DSM 28244T(a) | C. asaccharovorans DSM 6462T (a) | C. daeguensis K106T CCUG 54519T (a) | C. sambhunathii HT4T DSM 18167T (a) | |
|---|---|---|---|---|
Isolation source | Organic waste compost (Ibrahim et al. 2010) | Wastewater, soil (Auling et al. 1993) | Textile waste matter (Yoon et al. 2008) | Hot spring (Panday and Das 2010) |
Cell morphology | Rods | Coccoid rods | Rods(b) | Short rods(b) |
Motility | + | − | +(b) | + |
Mucoid colony on MSM with glucose | − | ND | +(b) | −(b) |
Hydrolysis of gelatin | + | + | − | + |
Use of NTA as sole carbon and nitrogen source | − | + | − | + |
Utilisation of | ||||
Mannose, gluconate | + | + | + | − |
Xylose | − | + | + | − |
Mannose | + | + | + | − |
Glycerol | w | − | − | − |
Sucrose | w | − | − | − |
Growth temp. | ||||
Range | 37–55 °C | 4–41 °C | 20–51 °C | 20–50 °C |
Optimum | 50 °C(b) | 35–37 °C | 30–37 °C(b) | 37–42 °C(b) |
Growth pH | ||||
Range | 6.0–8.5 | 5.5–9.5 | 5.5–10.0 | 6.0–8.5 |
Optimum | 7.0–7.5 | 7.0–8.0 | 7.0–7.5 | 7.5–8.0 |
Star-shaped aggregates | +(b) | − | +(b) | +(b) |
PHB granules | +(b) | + | +(b) | +(b) |
Scanning electron microscopy (SEM) show the star-shaped cell aggregates (SSCAs) formed by the strain MW9T
PHA accumulation
Transmission electron microscopy (TEM) for cells of strain MW9T. Intracellular granules of PHB are distinguished inside cells of MW9T
Rep-PCR genomic fingerprints analysis
Comparison of genomic fingerprints obtained by rep-PCR. Profiles were compared using Pearson product moment correlation coefficients and UPGMA clustering using BioNumerics
Partial dnaK gene sequences comparison
Phylogenetic tree based on neighbor-joining analysis of partial dnaK gene sequences showing the relatedness of Chelatococcus isolates and closest neighbors. Partial dnaK gene sequence of strain MW9T was identical to MW10, MW11, MW12, MW13 and MW14 gene sequences. Bootstrap values expressed as percentages of 1000 replicates are shown at the branch nodes. Scale bar, five estimated base differences per sequence
Phylogenetic trees, updated from our 2010 study (Ibrahim et al. 2010), are available as supplementary figures (S1, 16S rRNA gene sequences Maximum Likelihood tree; S2, 16S rRNA gene sequences Neighbor Joining tree; S3, 16S rRNA gene sequences Maximum Parsimony tree; S4, partial dnaK gene sequences Maximum Likelihood tree). Because of the identity between the new isolates, only the isolate MW9T was selected as type strain and as a representative for further molecular characterization.
Utilization of nitrilotriacetic acid (NTA)
Isolate MW9T was investigated for NTA utilization as previously reported for the type strain C. asaccharovorans. Cells were cultivated in MSM (1 g/L NH4Cl) supplemented with glucose (20 g/L) at the standard conditions in comparison with growth in the same medium with NTA, but without both nitrogen and carbon sources. Isolate MW9T could not grow in the NTA-containing medium even after 4 days of incubation.
Fatty acid analysis
The new strain MW9T did not grow at the standard temperature of 28 °C. Its growth temperature range was previously determined to be 37–55 °C with an optimum of 50 °C, however, at this temperature the Chelatococcus reference strains failed to grow. The reference strains did grow at 37 °C, and therefore this temperature was used for all strains to allow comparison.
Fatty acid composition of strain MW9T and the type strains of Chelatococcus species, grown for 48 h on TSA (LMG medium 185) at 37 °C
Fatty acid | C. thermostellatus | C. asaccharovorans | C. daeguensis | C. sambhunathii |
|---|---|---|---|---|
MW9T | LMG 25503T | LMG 25471T | LMG 26063T | |
11 Methyl 18:1 ω7c | – | 0.2 | – | – |
14:00 | – | 0.3 | – | – |
15:0 3OH | 0.4 | 0.1 | – | – |
16:00 | 2 | 10.9 | 4.5 | 4.6 |
16:0 3OH | – | 0.8 | – | – |
17:00 | 0.9 | 0.8 | 3.6 | 4.4 |
17:0 Cyclo | 0.2 | 1.7 | – | – |
18:00 | 4.1 | 3.1 | 4.4 | 3.2 |
18:0 3OH | 5.2 | 2.8 | 4.8 | 2.2 |
18:1 2OH | 8.3 | – | 3.4 | 6.8 |
18:1 ω7c | 38.8 | 18.4 | 40 | 35.3 |
19:0 Cyclo ω8c | 27.8 | 48.7 | 31.4 | 25.4 |
19:0 10 Methyl | 0.3 | – | – | – |
20:1 ω7c | 1 | 1.4 | – | – |
20:2 ω6,9c | – | 0.1 | – | – |
Summed feature 1 | 0.5 | – | – | 1.5 |
Summed feature 2 | 10.1 | 10.1 | 7.2 | 16.5 |
Summed feature 3 | 0.2 | – | – | – |
Unknown ECL 14.502 | – | 0.2 | – | – |
Unknown ECL 14.959 | 0.4 | – | 0.7 | – |
G+C content and DNA–DNA homology study
DNA G+C content and DNA–DNA relatedness between strain MW9T and Chelatococcus species
Strain | DNA G+C content (mol%) | DNA–DNA relatedness (%) | ||
|---|---|---|---|---|
MW9T LMG 27009T | LMG 25503T | LMG 25471T | ||
C. thermostellatus MW9T LMG 27009T | 67.1 | |||
C. asaccharovorans LMG 25503T | 67.7 | 11.0 ± 2.8 | ||
C. daeguensis LMG 25471T | 64.0 | 47.7 ± 5.8 | 12.1 ± 1.8 | |
C. sambhunathii LMG 26063T | 67.8 | 42.5 ± 4.2 | 4.9 ± 0.6 | 22.1 ± 1.7 |
Low level of DNA–DNA hybridization was detected between strain MW9T and C. asaccharovorans LMG 25503T (11.0 %), C. daeguensis LMG 25471T (47.7 %), and C. sambhunathii LMG 26063T (42.5 %).
Discussion
The genus Chelatococcus was first described by Auling et al. (1993) and later by Egli and Auling (2005) as consisting of gram negative bacteria with the distinctive characteristics of utilizing the metal-chelating aminopolycarboxylic acid nitrilotriacetic acid (NTA). Following the first description of species C. asaccharovorans (Auling et al. 1993; Egli and Auling 2005), two distinct species were recently affiliated to the genus, C. daeguensis (Yoon et al. 2008) and C. sambhunathii (Panday and Das 2010). Ecologically, strains of the genus were isolated from different aquatic and waste treatment environments (Wilberg et al. 1993; Egli and Auling 2005; Ibrahim et al. 2010; Xu et al. 2014).
New physiological characteristics were reported for the new isolates, MW9T, MW10, MW11, MW12, MW13 and MW14, such as high optimum growth temperature, star-shaped cell aggregates, and PHA accumulation. The 16S rRNA gene sequences of these isolates are very similar and place them in the genus Chelatococcus (Ibrahim et al. 2010).
These new unusual characteristics made it important to conduct a more detailed study for a precise affiliation of these isolates within the genus Chelatococcus, possibly as a new species. Moreover, a clear differentiation between the new isolates is needed.
SSC aggregates have previously been found in several taxa within the Alphaproteobacteria (Biebl et al. 2007). However, this aggregation was not previously reported for any of the Chelatococcus species, possibly because growth was usually studied in nutrient-rich media. In the present study and during cultivation in mineral salts medium, the type strains C. daeguensis LMG 25471T and C. sambhunathii LMG 26063T showed SSC aggregation during growth.
Little information about PHA accumulation was reported for strains belonging to related Chelatococcus species: PHB granules were observed in the type strain of C. asaccharovorans (Egli and Auling 2005) (Table 1) and very recently, a new thermophilic denitrifying bacterial strain of C. daeguensis, TAD1, was reported to accumulate poly(3-hydroxybutyrate) at 45 and 50 °C from glucose (Xu et al. 2014). PHA accumulation can be regarded as a characteristic attribute of the genus Chelatococcus, especially after the confirmation of high PHB content in cells of strains C. daeguensis LMG 25471T and C. sambhunathii LMG 26063T in the present study, and the high content reported for our new thermophilic isolates (Ibrahim et al. 2010).
The identity of rep-PCR profiles and partial dnaK gene sequences between the new isolates together with the high similarity of their 16S rRNA gene sequences would suggest that they may not be classified as separate organisms, but rather be different colonies with slightly differences in carbohydrates preference (Ibrahim et al. 2010). We therefore chose the glucose utilizing isolate MW9T as representative of the new thermophilic isolates and describe it as a new species given the differences in 16S rRNA, rep-PCR, and partial dnaK gene sequences with other Chelatococcus species. This isolate was used for further investigations.
The dnaK gene sequence of the type strain of the type species C. asaccharovorans showed less similarity to all new Chelatococcus strains (Fig. 4), even though it did belong to the Chelatococcus cluster in 16S rRNA gene phylogeny (Ibrahim et al. 2010), indicating its dnaK sequence may be affected by lateral gene transfer. Comparison of the complete dnaK gene might clarify this possibility.
Utilization of NTA as the sole carbon and nitrogen source was investigated for the new strain MW9T. However, this strain was not able to grow on NTA alone. Similar results were also reported for strain C. daeguensis (Yoon et al. 2008). The emended genus description by Yoon et al. (2008) also stated that this characteristic could be positive or negative variable within different species of Chelatococcus.
DNA G+C content, together with the physiological properties summarized in Table 1, are in accordance with the genus amendment of Chelatococcus reported by Yoon et al. (2008). Considering the 70.0 mol% DNA–DNA relatedness cut-off point recommended for bacterial species delineation (Wayne et al. 1987), strain MW9T should be regarded as representing a novel species of the genus Chelatococcus.
The phylogenetic distinctiveness and low DNA–DNA relatedness with other Chelatococcus type strains reported here as well as phenotypic differences (Table 1), justify the creation of a new Chelatococcus species for strain MW9T, for which the name Chelatococcus thermostellatus sp. nov. is proposed. The species was isolated from aerobic organic waste compost in Germany, and DNA sequence data indicate it may be present in other compost systems. Indeed, a FASTA search with the 16S rRNA gene sequence of MW9T in the EMBL database Environmental subsection revealed highly similar Chelatococcus sequences from asparagus straw compost from China (99.9 %, accession number JQ740271, clone ASC373), from a pilot scale municipal drum compost from Finland (99.8 %, FN667527, clone PS3657), from dairy manure and rice chaff composting samples in China [99.6 %, JQ337129, clone NT-3-59 (Tian et al. 2013)], and from fermented composting material in China [99.3 %, FJ930065, clone 6 (Wang et al. 2011)].
As a conclusion, the present study, while presenting a new species in the genus Chelatococcus, also confirmed PHA accumulation as a new genus-wide feature and showed that the formation of SSC aggregates can be used to describe many strains of Chelatococcus species. Strain MW9T is capable of growing and producing high content of PHB at higher temperature compared to other related strains. This makes this new Chelatococcus strain a potent candidate for bioplastic production at thermophilic condition, where production costs can be minimized. Further physiological and proteomic investigations should facilitate a precise differentiation between isolates, MW9T, MW10, MW11, MW12, MW13 and MW14.
Description of Chelatococcus thermostellatus sp. nov
Chelatococcus thermostellatus [ther.mo.ste’llatus. Gr. adj. thermos, hot; N.L. v. stellatus, to form star-shape cell aggregates; N.L. part. adj. thermostellatus, referring to the formation of star-shaped cell aggregates at high temperatures].
Cells are Gram-negative, oxidase positive motile rods (0.2–0.4 × 1.0–2.5 μm), aerobic, and non-spore forming. Good growth occurs on LB broth, nutrients broth, standard I nutrient broth, and MSM-gluconate/glucose/glycerol after 1–3 days at 50 °C. No growth was detected below 37 °C or above 55 °C. Optimum pH 7.0–7.5. NTA was not utilized as a sole source for carbon and nitrogen. During optimum growth on MSM, star-shaped cell aggregates, and PHB intracellular granules were observed as well. Colonies on MSM are circular with bright white to beige color and 0.5–1.0 mm in diameter. The major fatty acids comprises (>10 %) 18:1 ω7c, 19:0 cyclo ω8c and summed feature 2 (12:0 aldehyde, 16:1 iso I and/or 14:0 3OH). The DNA G+C content of the type strain is 67.1 mol%.
The type strain MW9T (=LMG 27009T = DSM 28244T) was isolated from aerobic organic waste compost in Münster, Germany.
Declarations
Acknowledgements
Authors thank professor Rajni Hatti-Kaul and Ms. Rita Wallen from Lund University, Sweden, for electron microscope examination facility. Grant for MHAI from the cultural affairs and missions sector, Ministry of Higher Education, Egypt, is gratefully acknowledged.
Competing interests
The authors declare that they have no competing interests.
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
Authors’ Affiliations
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