Bacteria isolated from a sugarcane agroecosystem: their potential production of polyhydroxyalcanoates and resistance to antibiotics

Polyhydroxyalkanoate recovery from newly screened Bacillus sp. LPPI-18 using various methods of extraction from Loktak Lake sediment sample

BACKGROUND

Nowadays, the conventional plastic wastes are very challenging to environments and its production cost also creates an economic crisis due to petrochemical-based plastic. In order to solve this problem, the current studies were aimed at screening and characterizing these polyhydroxyalkanoate (PHA)-producing isolates and evaluating the suitability of some carbon source for newly screened PHA-producing isolates.

MATERIAL AND METHODS

Some carbon sources such as D-fructose, glucose, molasses, D-ribose and sucrose were evaluated for PHA production. Data were analyzed using SPSS version 20. The 16SrRNA gene sequence of these isolates was performed. These newly isolated taxa were related to Bacillus species. It was designated as Bacillus sp. LPPI-18 and affiliated Bacillus cereus ATCC 14577^T (AE01687) (99.10%). Paenibacillus sp. 172 (AF273740.1) was used as an outgroup.

RESULTS

Bacillus sp. LPPI-18 is a gram-positive, rod-shaped, endospore former, and citrate test positive. This isolate showed positive for amylase, catalase, pectinase, and protease test. They produced intracellular PHA granules when this isolate was stained with Sudan Black B (SBB) and Nile blue A (NBA) preliminary and specific staining dyes, respectively. Both temperature and pH used to affect polyhydroxyalkanoates (PHA) productivity. Bacteria are able to reserve PHA in the form of granules during stress conditions. This isolate produces only when supplied with carbon sources. More PHA contents (PCs) were obtained from glucose, molasses, and D-fructose. In this regard, the maximum mean value of PC was obtained from glucose (40.55±0.7%) and the minimum was obtained from D-ribose (12.4±1.4%). Great variations (P≤0.05) of PCs were observed among glucose and sucrose, molasses and sucrose, and D-fructose and sucrose carbon sources for PHA productivity (PP) of cell dry weight (CDW) g/L. After extraction, PHA film was produced for this typical isolate using glucose as a sole carbon source. Fourier transform infrared spectrum was performed for this isolate and showed the feature of polyester at 1719.64 to 1721.16 wavelengths for these extracted samples. The peak of fingerprinting (band of carboxylic acid group) at this wavelength is a characteristic feature of polyhydroxybutyrate (PHB) and corresponds to the ester functional group (C=O).

CONCLUSION

In this study, newly identified Bacillus sp. LPPI-18 is found to be producing biodegradable polymers that are used to replace highly pollutant conventional plastic polymers. This isolate is also used to employ certain cost-effective carbon sources for the production of PHA polymers.

PHA Production from Cheese Whey and "Scotta": Comparison between a Consortium and a Pure Culture of Leuconostoc mesenteroides

It is urgent to expand the market of biodegradable alternatives to oil-derived plastics owing to (i) increasingly limited oil availability/accessibility, and (ii) the dramatic impact of traditional plastics on aquatic life, the food chain, all Earth ecosystems, and ultimately, human health. Polyhydroxyalkanoates (PHAs) are promising biodegradable polymers that can be obtained through microbial fermentation of agro-industrial byproducts, e.g., milk and cheese whey. Here, the PHA-accumulating efficiency of a mixed microbial culture (MMC, derived from activated sludges) grown on dairy byproducts (cheese and scotta whey) was measured. Bioreactor tests featuring temperature and pH control showed that both scotta and pre-treated Toma cheese whey could be used for PHA production by MMC, although scotta cheese whey supported higher PHA yield and productivity. The advantages of open MMCs include their plasticity and versatility to fast changing conditions; furthermore, no growth-medium sterilization is needed prior to fermentation. However, the use of pure cultures of efficient PHA producers may support better metabolic performances. Therefore, PHA-producing strains were isolated from a MMC, leading to the satisfactory identification of two bacterial strains, Citrobacter freundii and Leuconostoc spp., whose ability to accumulate PHAs in synthetic media was confirmed. A more detailed investigation by mass spectrometry revealed that the strain was L. mesenteroides. Although the validation of L. mesenteroides potential to produce PHA through fermentation of agro-industrial byproducts requires further investigations, this is the first study reporting PHA production with the Leuconostoc genus.

A laboratory case study of efficient polyhydoxyalkonates production by Bacillus cereus, a contaminant in Saccharophagus degradans ATCC 43961 in minimal sea salt media

A contaminating bacterium growing along with the stock culture of Saccharophagus degradans ATCC 43961 (Sde 2-40) on marine agar plate was isolated and investigated for its ability to produce polyhydoxyalkonates (PHA). Preliminary screening by Sudan black B and Nile blue A staining indicated positive characteristic of the isolate to produce PHA. The isolate was able to grow and produce PHA in minimal sea salt medium broth. PHA quantification studies with gas chromatographic analyses of the dry cells derived from culture broths revealed accumulation of PHA in bacterial cells. PHA production started after 20 h and increased with cell growth and attained maximum values of 61 % of dry cell weight at 70 h of cultivation. After 70 h, a slight decrease in the level of PHA content was observed. The nature/type of PHA was found to be poly(3-hydroxybutyraye) by Fourier transform-infrared spectroscopy. Microbiological and 16S rRNA gene sequencing analyses suggested that the PHA producing bacterial isolate belongs to Bacillus genera and shows 100 % nucleotide sequence similarity with Bacillus cereus species in GenBank. This study is a first report for ability of Bacillus species to grow in marine sea salt media and produce PHA. The media used for the polymer production was novel in the context of the genus Bacillus and the production of PHA was three-fold higher than Sde 2-40 using same growth medium. This study shows that the contaminant bacteria once properly investigated can be used for advantageous characteristic of metabolites production in place of original cultures.

Biotechnological Production of Polyhydroxyalkanoates: A Review on Trends and Latest Developments

Polyhydroxyalkanoates (PHA) producers have been reported to reside at various ecological niches which are naturally or accidently exposed to high organic matter or growth limited conditions such as dairy wastes, hydrocarbon contaminated sites, pulp and paper mill wastes, agricultural wastes, activated sludges of treatment plants, rhizosphere, and industrial effluents. Few among them also produce extracellular by-products like rhamnolipids, extracellular polymeric substances, and biohydrogen gas. These sorts of microbes are industrially important candidates for the reason that they can use waste materials of different origin as substrate with simultaneous production of valuable bioproducts including PHA. Implementation of integrated system to separate their by-products (intracellular and extracellular) can be economical in regard to production. In this review, we have discussed various microorganisms dwelling at different environmental conditions which stimulate them to accumulate carbon as polyhydroxyalkanoates granules and factors influencing its production and composition. A brief aspect on metabolites which are produced concomitantly with PHA has also been discussed. In conclusion, exploring of capabilities like of dual production by microbes and use of wastes as renewable substrate under optimized cultural conditions either in batch or continuous process can cause deduction in present cost of bioplastic production from stored PHA granules.

Isolation and characterisation of aerobic endospore forming Bacilli from sugarcane rhizosphere for the selection of strains with agriculture potentialities

Eighteen aerobic endospore forming strains were isolated from sugarcane rhizosphere in N-free medium. A phenotypic description and analysis of the 5' end hypervariable region sequences of 16S rRNA revealed a high diversity of Bacillus and related genera. Isolates were identified, and four genera were obtained: seven strains belonged to Bacillus (Bacillaceae family), four belonged to Paenibacillus, six belonged to Brevibacillus and one strain was identified as Cohnella (Paenibacillaceae family). Four Brevibacillus strains showed in vitro inhibitory activity against plant pathogens fungi Curvularia and Fusarium. Seventy-four percent of the isolated bacteria grew on pectin as the only carbon source, showing polygalacturonase activity. Pectate lyase activity was detected for the first time in a Brevibacillus genus strain. All isolates showed endoglucanase activity. Calcium phosphate solubilisation was positive in 83.3% of the isolates, with higher values than those reported for Bacillus inorganic phosphate solubilising strains. High ethylene plant hormone secretion in the culture medium was detected in 22% of the bacteria. This is the first report of ethylene secretion in Paenibacillaceae isolates. Indole-3-acetic acid production was found in a Brevibacillus genus isolate. It was reported for the first time the presence of Cohnella genus strain on sugarcane rhizosphere bearing plant growth promoting traits. The sugarcane isolate Brevibacillus B65 was identified as a plant growth inoculant because it showed wider spectra of plant stimulation capabilities, including an antifungal effect, extracellular hydrolases secretion, inorganic phosphate solubilisation and plant hormone liberation. In this work, sugarcane was shown to be a suitable niche for finding aerobic endospore forming 'Bacilli' with agriculture biotechnological purposes.

Surveillance of single-cell behavior in different subpopulations of Ralstonia pickettii AR1 during growth and polyhydroxybutyrate production phases by flow cytometry

Most bacterial strains accumulate intracellular polyhydroxybutyrate (PHB) granules as an energy reservoir, in response to fluctuations in their microenvironment. Flow cytometry was applied for the analysis of single cells of Ralstonia pickettii AR1 in response to changes in the culture conditions. Two parameters, the PHB production-related FL2 and side scatter (SSC) parameters, were used to monitor, distinguish and characterize different subpopulations in the growth and PHB production phases. A high SSC level was observed in the mid-log exponential growth phase. When the nitrogen source reached a limiting level, the SSC started to decrease, in contrast to the intracellular PHB granules-related FL2 parameter. The results show that ammonium limitation is a critical and important factor for the accumulation of reserve compounds. Four subpopulations were observed and distinguished upon entrance of the cells into the exponential growth phase. When the cells entered the late exponential growth or early stationary phase, two subpopulations had disappeared and only two, different subpopulations were dominant. One of the subpopulations with changed SSC and PHB production activity switched to another subpopulation that was only active in PHB production in the stationary phase. The whole cells of R. pickettii AR1 tended to form a homogeneous population at the end of the stationary phase. In fact, the changes in the subpopulations of a single strain are related to different physiological states of the cells. The observation of different subpopulations suggests that each subpopulation shows a specific response to changes in the surrounding microenvironment, nutrients and limiting factors.

Isolation, characterization, and effect of fluorescent pseudomonads on micropropagated sugarcane

In this study, we report on the isolation, identification, and characterization of seven fluorescent pseudomonads isolated from the roots, shoots, and rhizosphere soil of sugarcane and their impacts on the growth of sugarcane plantlets. 16S rRNA gene sequence of five isolates showed close homology with Pseudomonas putida, one with Pseudomonas graminis, and one with Pseudomonas fluorescens. Physiological and biochemical characterizations were determined using API50CH and QTS24 identification kits. The isolates were also subjected to tests for various known growth promoting properties including production of indole acetic acid, the ability to fix nitrogen via the presence of the nifH gene, and ability to solubilize phosphate. Biological control potential was determined from agar diffusion assays of HCN production and production of antifungal compounds against local isolates of Colletotrichum falcatum (that induces red-rot disease of sugarcane). Direct plant growth promoting effects were tested on sugarcane plantlets in tissue culture under gnotobiotic conditions. All seven isolates provided significant increases in fresh and dry masses but only five strains increased shoot height.

Tropicibacter naphthalenivorans gen. nov., sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from Semarang Port in Indonesia

An aerobic, Gram-negative, motile bacterium, strain C02(T), was isolated from seawater obtained from Semarang Port in Indonesia. Cells of strain C02(T) were peritrichously flagellated and rod-shaped. Strain C02(T) was able to degrade naphthalene, alkylnaphthalenes and phenanthrene. 16S rRNA gene sequence analysis revealed that this strain was affiliated with the family Rhodobacteraceae in the class Alphaproteobacteria and was related most closely to Marinovum algicola FF3(T) (95.7 % similarity) and Thalassobius aestuarii JC2049(T) (95.2 %). The DNA G+C content of strain C02(T) was 64.6 mol%. The major cellular fatty acids were C(18 : 1)omega7c (50.9 % of the total), C(16 : 0) (17.9 %), 11 methyl C(18 : 1)omega7c (14.7 %), C(18 : 1)omega9c (2.9 %) and C(19 : 0) cyclo omega8c (2.4 %), and the predominant respiratory lipoquinone was ubiquinone-10. Based on physiological, chemotaxonomic and phylogenetic data, strain C02(T) is suggested to represent a novel species of a new genus, for which the name Tropicibacter naphthalenivorans gen. nov., sp. nov. is proposed. The type strain of Tropicibacter naphthalenivorans is C02(T) (=JCM 14838(T)=DSM 19561(T)).

Tropicimonas isoalkanivorans gen. nov., sp. nov., a branched-alkane-degrading bacterium isolated from Semarang Port in Indonesia

An aerobic, Gram-negative, motile bacterium, strain B51(T), was isolated from seawater obtained from Semarang Port in Indonesia. Cells of strain B51(T) were peritrichously flagellated and rod-shaped. Strain B51(T) was able to degrade alkanes, branched alkanes and alkylnaphthalenes. 16S rRNA gene sequence analysis revealed that strain B51(T) was affiliated with the family Rhodobacteraceae, and was related most closely to Thioclava pacifica TL 2(T) (94.6 % similarity). The DNA G+C content of strain B51(T) was 66.5 mol%. The major cellular fatty acids were C(18 : 1)omega7c (84.9 %), C(18 : 1)omega9c (13.8 %), C(16 : 0) (8.7 %), C(18 : 0) (6.4 %) and anteiso-C(15 : 0) (5.8 %) and the major quinone was ubiquinone-10. Based on its phenotypic and phylogenetic characteristics, strain B51(T) is considered to represent a novel species of a new genus, for which the name Tropicimonas isoalcanivorans gen. nov., sp. nov. is proposed. The type strain of the type species is B51(T) (=JCM 14837(T)=DSM 19548(T)).

Tranquillimonas alkanivorans gen. nov., sp. nov., an alkane-degrading bacterium isolated from Semarang Port in Indonesia

Strain A34(T), an obligately halophilic, Gram-negative, non-motile, rod-shaped bacterium, was isolated from seawater obtained from Semarang Port in Indonesia. It possesses a pink pigment and degrades short-chain alkanes. It is positive for catalase and oxidase and reduces nitrate to nitrite. Analyses of 16S rRNA gene sequences revealed a clear affiliation of this strain with the family 'Rhodobacteraceae' in the class Alphaproteobacteria, with its closest relatives being Salipiger mucosus A3(T) (94.9% sequence similarity) and Palleronia marisminoris B33(T) (93.4%). The DNA G+C content was 69.1 mol%. The major cellular fatty acids of strain A34(T) were C(18:1)omega7c (56.2%), C(19:0) cyclo omega8c (26.0%) and C(16:0) (9.1%), while the predominant respiratory lipoquinone was ubiquinone-10. Based on the physiological and phylogenetic data, it is proposed that strain A34(T) should be classified in a new genus and species, for which the name Tranquillimonas alkanivorans gen. nov., sp. nov. is proposed. The type strain of Tranquillimonas alkanivorans is strain A34(T) (=JCM 14836(T) =DSM 19547(T)).

Screening and isolation of PHB-producing bacteria in a polluted marine microbial mat

The characteristics of microbial mats within the waste stream from a seafood cannery were compared to a microbial community at a pristine site near a sandy beach at Puerto San Carlos, Baja California Sur, Mexico. Isolation of poly-beta-hydroxybutyrate (PHB)-producing bacteria, recognition of brightly refractile cytoplasmatic inclusions, lipophilic stains with Sudan Black and Nile Red, and chemical extraction of PHB were used as a culture-dependent strategy for the detection of PHB-producing bacteria. The culture-independent approach included denaturing gradient gel electrophoresis of phylotypes of 16S rRNA of microbial communities from environmental samples. Significant differences in community structure were found among the polluted and pristine sites. These differences were correlated with the physicochemical characteristics of the seawater column. At the polluted site, the seawater was rich in nutrients (ammonia, phosphates, and organic matter), compared to the pristine location. Partial sequencing of 16S rDNA of cultures of bacteria producing PHB included Bacillus and Staphylococcus at both sites; Paracoccus and Micrococcus were found only at the polluted site and Rhodococcus and Methylobacterium were found only at the pristine site. Bands of the sequences of 16S rDNA from both field samples in the denaturing gradient gel electrophoresis (DGGE) analyses affiliated closely only with bacterial sequences of cultures of Bacillus and Staphylococcus. High concentrations of organic and inorganic nutrients at the polluted site had a clear effect on the composition and diversity of the microbial community compared to the unpolluted site.

Fourier transform infrared spectroscopy for rapid identification of nonfermenting gram-negative bacteria isolated from sputum samples from cystic fibrosis patients

The accurate and rapid identification of bacteria isolated from the respiratory tract of patients with cystic fibrosis (CF) is critical in epidemiological studies, during intrahospital outbreaks, for patient treatment, and for determination of therapeutic options. While the most common organisms isolated from sputum samples are Pseudomonas aeruginosa, Staphylococcus aureus, and Haemophilus influenzae, in recent decades an increasing fraction of CF patients has been colonized by other nonfermenting (NF) gram-negative rods, such as Burkholderia cepacia complex (BCC) bacteria, Stenotrophomonas maltophilia, Ralstonia pickettii, Acinetobacter spp., and Achromobacter spp. In the present study, we developed a novel strategy for the rapid identification of NF rods based on Fourier transform infrared spectroscopy (FTIR) in combination with artificial neural networks (ANNs). A total of 15 reference strains and 169 clinical isolates of NF gram-negative bacteria recovered from sputum samples from 150 CF patients were used in this study. The clinical isolates were identified according to the guidelines for clinical microbiology practices for respiratory tract specimens from CF patients; and particularly, BCC bacteria were further identified by recA-based PCR followed by restriction fragment length polymorphism analysis with HaeIII, and their identities were confirmed by recA species-specific PCR. In addition, some strains belonging to genera different from BCC were identified by 16S rRNA gene sequencing. A standardized experimental protocol was established, and an FTIR spectral database containing more than 2,000 infrared spectra was created. The ANN identification system consisted of two hierarchical levels. The top-level network allowed the identification of P. aeruginosa, S. maltophilia, Achromobacter xylosoxidans, Acinetobacter spp., R. pickettii, and BCC bacteria with an identification success rate of 98.1%. The second-level network was developed to differentiate the four most clinically relevant species of BCC, B. cepacia, B. multivorans, B. cenocepacia, and B. stabilis (genomovars I to IV, respectively), with a correct identification rate of 93.8%. Our results demonstrate the high degree of reliability and strong potential of ANN-based FTIR spectrum analysis for the rapid identification of NF rods suitable for use in routine clinical microbiology laboratories.

Relationship between pH and medium dissolved solids in terms of growth and metabolism of lactobacilli and Saccharomyces cerevisiae during ethanol production

The specific growth rates of four species of lactobacilli decreased linearly with increases in the concentration of dissolved solids (sugars) in liquid growth medium. This was most likely due to the osmotic stress exerted by the sugars on the bacteria. The reduction in growth rates corresponded to decreased lactic acid production. Medium pH was another factor studied. As the medium pH decreased from 5.5 to 4.0, there was a reduction in the specific growth rate of lactobacilli and a corresponding decrease in the lactic acid produced. In contrast, medium pH did not have any significant effect on the specific growth rate of yeast at any particular concentration of dissolved solids in the medium. However, medium pH had a significant (P < 0.001) effect on ethanol production. A medium pH of 5.5 resulted in maximal ethanol production in all media with different concentrations of dissolved solids. When the data were analyzed as a 4 (pH levels) by 4 (concentrations of dissolved solids) factorial experiment, there was no synergistic effect (P > 0.2923) observed between pH of the medium and concentration of dissolved solids of the medium in reducing bacterial growth and metabolism. The data suggest that reduction of initial medium pH to 4.0 for the control of lactobacilli during ethanol production is not a good practice as there is a reduction (P < 0.001) in the ethanol produced by the yeast at pH 4.0. Setting the mash (medium) with > or =30% (wt/vol) dissolved solids at a pH of 5.0 to 5.5 will minimize the effects of bacterial contamination and maximize ethanol production by yeast.