Serratia Plymuthica Strain Research Articles

Complete genome sequence of Serratia plymuthica SWSY-3.47.

Serratia plymuthica strain SWSY-3.47 is a Gram-negative, rod-shaped bacteria isolated for its high chitinolytic activity. Here, we report the complete genome of this strain comprised of a single circular chromosome of 5,636,345 bp with a G + C content of 56.0%.

Ni2+ and Cu2+ Biosorption by EPS-Producing Serratia plymuthica Strains and Potential Bio-Catalysis of the Organo–Metal Complexes

In this study, a biosorption system for nickel (Ni2+) and copper (Cu2+) removal by selected exopolymeric substance-producing bacterial strains was evaluated from the perspective of water remediation. A preliminary screening in a biofilm-based filtration system allowed the selection of two best-performing Serratia plymuthica strains for specific Ni2+ and Cu2+ removal from synthetic solutions, as well as the definition of the optimal growth conditions. Further tests were conducted in a planktonic cell system in order to evaluate: (i) the effect of contact time, (ii) the effect of initial metal concentration, and (iii) the effect of biomass dose. S. plymuthica strain SC3I(2) was able to remove 89.4% of Ni2+ from a 50 mg L−1 solution, and showed maximum biosorption capacity of 33.5 mg g−1, while S. plymuthica strain As3-5a(5) removed up to 91.5% of Cu2+ from a 200 mg L−1 solution, yielding maximum biosorption capacity of 80.5 mg g−1. Adsorption equilibria of both metals were reached within 30 min, most of the process occurring in the first 2–4 min. Only Ni2+ biosorption data were adequately described by Langmuir and Freundlich isothermal models, as Cu2+ was in part subjected to complexation on the exopolymeric substances. The capability of the exopolymeric substances to stably coordinate a transition metal as Cu2+ offers the possibility of the eco-friendly re-use of these new hybrid systems as catalysts for application in addition reaction of B2(pin)2 on α,β-unsaturated chalcones with good results. The systems formed by biomass and Ni2+ were instead evaluated in transfer hydrogenation of imines. The biosorption performances of both strains indicate that they have the potential to be exploited in bioremediation technologies and the obtained organo–metal complexes might be valorized for biocatalytic purposes.

Complete Genome Sequences of Five Gram-Negative Bacterial Strains Comprising Synthetic Bacterial Consortium "The Great Five" with Antagonistic Activity Against Plant-Pathogenic Pectobacterium spp. and Dickeya spp.

Complete Genome Sequences of Five Gram-Negative Bacterial Strains Comprising Synthetic Bacterial Consortium "The Great Five" with Antagonistic Activity Against Plant-Pathogenic Pectobacterium spp. and Dickeya spp.

Hybrid Catalysts from Copper Biosorbing Bacterial Strains and Their Recycling for Catalytic Application in the Asymmetric Addition Reaction of B2(pin)2 on α,β-Unsaturated Chalcones

The recycling of heavy metal contaminants from wastewater as a source of valuable products perfectly fits with the principles of a Circular Economy system in view of restoring pollutants back into the system endowed with new social and economic benefits. Heavy metals are often present in such a low concentration that it makes the removal efficiency difficult to realize through the conventional physicochemical methods with high selectivity. Biosorption, conversely, by EPSs (extracellular polymeric substances) produced by several bacterial cells’ strains, is gaining a great deal of attention as an economic, efficient and sustainable depolluting process of wastewater from metal cations such as copper. Metal coordination to EPS components was thus deeply investigated by 1H NMR titration experiments. The 1,10–Phenanthroline–copper complex was exploited for quantifying the ability of different strains to sequester copper by a practical UV-Vis spectrophotometric method. The obtained data distinguished Serratia plymuthica strain SC5II as the bacterial strain displaying copper-adsorbing properties higher than any other, with Stenotrophomonas sp. strain 13a resulting in the worst one. Different analytical techniques, i.e., Dynamic Light Scattering (DLS), FT-IR analysis and SEM spectroscopy were thus employed to rationalize these results. Finally, the obtained copper chelates were successfully employed as hybrid catalysts in the asymmetric boron addition to α,β-unsaturated chalcones for the synthesis of valuable pharmaceutical intermediates, thus placing waste management in a new circular perspective.

Potential of Serratia plymuthica IV-11-34 strain for biodegradation of polylactide and poly(ethylene terephthalate)

Serratia plymuthica strain IV-11-34 belongs to the plant growth promoting bacteria (PGPR). In the sequenced genome of S. plymuthica IV-11-34, we have identified the genes involved in biodegradation and metabolisms of xenobiotics. The potential of S. plymuthica IV-11-34 for the degradation of biodegradable aliphatic polyester polylactide (PLA) and resistant to biodegradation – poly(ethylene terephthalate) (PET) was assessed by biochemical oxygen consumption (BOD) and carbon dioxide methods. After seven days of growth, the bacteria strain showed more than 80% and 60% increase in respiratory activity in the presence of PLA and PET, respectively. We assume that during biodegradation, S. plymuthica IV-11-34 colonise the surface of PLA and PET, since the formation of a biofilm on the surface of polymers was shown by the LIVE/DEAD method. We have demonstrated for the relA gene, which is an alarmone synthetase, a 1.2-fold increase in expression in the presence of PLA, and a 4-fold decrease in expression in the presence of PET for the spoT gene, which is a hydrolase of alarmones. Research has shown that the bacterium has the ability to biodegrade PLA and PET, and the first stage of this process involves bacterial stringent response genes responsible for survival under extreme conditions.

Antifungal abilities of Serratia plymuthica UBCF_13 produced in different types of media and culture time

Serratia plymuthica strain UBCF_13 is a potential biocontrol agent to inhibit pathogen causing anthracnose disease in plants, Colletotrichum gloesporioedes. The production of bacterial antifungal compounds is affected by nutrition and the growth phase of bacteria. This study is aimed to determine the optimal medium and duration of culture for the production of antifungal compounds. This study used three types of liquid media culture for UBCF_13 [King’s B, Potato Dextrose, and tryptic Soy] and six variations in duration culture [8, 16, 24, 32, 40, and 48 hours]. Extracellular that has been produced was used for antifungal activity assay against C. gloeosporioides. The results showed that the extracellular produced in the PDB with 48 hours culture duration could inhibit 18%. C. gloeosporioides growth. Different nutritional compositions for UBCF_13 cultures show affect the metabolism and compound produced as well. This was indicated by differences in protein profiles of the intracellular and extracellular. Further studies are necessary to be carried out, particularly to see the mechanism of the nutrient medium that could affect the metabolism of UBCF_13 in the synthesis of antifungal compounds.

Cloning of gyrB housekeeping gene from Serratia plymuthica UBCF_13

Serratia plymuthica strain UBCF_13 is a biocontrol agent that has the potential to inhibit pathogenic fungi. S. plymuthica has housekeeping genes, one of which is the gyrB gene. The housekeeping gene was cloned to be used as a template for standard curve creation regarding the correlation of gene copy number and Ct value in absolute quantification data. This study was conducted to provide the plasmid housekeeping gene gyrB from S. plymuthica which will be used as a template for standard curve creation in absolute quantification. The method used in this study were DNA genome isolation, PCR, ligation, and transformation. The result showed that the housekeeping gene gyrB has been successfully cloning based on the size of the estimated amplicon, which is 114 bp.

Different pH levels medium effects in IAA production of phylloplane bacterium Serratia plymuthica strain UBCF_13

Indole-3-acetic acid [IAA] is the main source of auxin in plants that plays a major role in controlling various physiological processes. The ability of bacterium in IAA biosynthesis depends on several environmental factors, usually triggered by acidic stresses. This study was aimed to optimize the IAA production by phylloplane bacterium Serratiaplymuthica strain UBCF_13 with various pH levels. Optimization was carried out by using 0.2% L-Tryptophan in Luria Bertani[LB] media with various pH levels namely pH 4.0; 4.5; 5.0; 5.5; 6.0; 6.5; 7.0 and 9.0. UBCF_13 showed the best IAA production at pH 6.0 and 0.2% L-Tryptophan exhibited IAA concentration in the amount of 24.13 ppm. The UBCF_13 extracellular protein profile analysis showed that at pH 6.0 induced L-Tryptophan 0.2% produced protein bands of 60.8 kDa and 45 kDa in size. These protein bands are assumed to be ipdC and nitrilase proteins which are involved in the IAA biosynthesis. The application of IAA was carried out using chili peppers [Capsicum annuum L.] germination of the Lotanbar genotype. The application was using supernatant produced from media of pH 6.0 and 0.2% L-Tryptophan. The results show that root and hypocotyl lengths were 4.10 cm and 2.90 cm, respectively. Meanwhile, root and hypocotyl lengths in the control sample only 2.78 cm and 1.88 cm. The results indicated that the IAA production of UBCF_13 can promote the growth of chili seedling. A further detailed study on the visualization of protein profiles at the optimum treatment needs to be done. Two-DimensionalElectrophoresis is recommended to be applied so that protein bands can be accurately separated to identify detailed proteins involved in the IAA biosynthesis.

RNA-sequencing for transcriptomic analysis of chili peppers induced by Serratia plymuthica strain UBCF_13

Non-pathogenic bacteria are used as biocontrol agents in plants because of their capability to induce the plant’s resistance system through the ISR [Induction Systemic Resistance] mechanism. Rhizobacteria are known for their ability to signal the biosynthesis of jasmonic acid and ethylene, also stimulate an increased expression level of resistance genes and auxin in plants. RNA-sequencing can be used to analyze the transcriptomic profile of plants. In this study, we used the bacteria Serratia plymuthica strain UBCF_13 to induce the resistance system of chili plants. This study aimed to obtain information on the transcriptome level of chili after being induced by the bacteria. This study is expected to be a useful reference for generating transcriptome data of bacteria UBCF_13 as a biocontrol agent. For RNA sequencing, we used two different plants, namely plants without and with the induction of bacteria UBCF_13. The bacteria UBCF_13 [OD600 1] was applied 12 days after planting in the root area. Total RNA was isolated from plant roots after 14 days of treatment. Differential gene expression, GO enrichment, and KEGG analysis showed that the resistance genes expression increases. Genes involved in hormone signal transduction like tryptophan metabolism is affected by the induction of bacteria UBCF_13. The AUX1 [Auxin Influx Carrier], SAUR [Small Auxin Up RNA], and GH3 [Gretchen Hagen 3] genes family in the tryptophan metabolism become upregulated.

Safety evaluation of the food enzyme preparation isomaltulose synthase from Serratia plymuthica strain Z12A

The food enzyme isomaltulose synthase (sucrose glucosylmutase; EC 5.4.99.11) is produced with Serratia plymuthica strain Z12A by BENEO‐Palatinit GmbH. The food enzyme is used only in the form of an immobilised preparation of non‐viable cells for the production of isomaltulose. Residual amounts of total organic solids (TOS) are removed by the purification steps applied during the production of isomaltulose consequently, dietary exposure was not calculated. Genotoxicity tests did not indicate safety concern. The systemic toxicity was assessed by means of a repeated dose 90‐day oral toxicity study in rats. The Panel identified a no observed adverse effect level of 1,011 mg TOS/kg body weight (bw) per day, the highest dose tested. Similarity of the amino acid sequence of the enzyme to those of known allergens was searched and no match was found. The Panel considered that, under the intended conditions of use, the risk of allergic sensitisation and elicitation reactions by dietary exposure cannot be excluded, but the likelihood of such reactions to occur is considered to be low. Based on the data provided, the use of an immobilised food enzyme and the removal of TOS during the production of isomaltulose the Panel concluded that this food enzyme preparation does not give rise to safety concerns under the intended conditions of use.

Crystal Structure of a Phospholipase D from the Plant-Associated Bacteria Serratia plymuthica Strain AS9 Reveals a Unique Arrangement of Catalytic Pocket.

Phospholipases D (PLDs) play important roles in different organisms and in vitro phospholipid modifications, which attract strong interests for investigation. However, the lack of PLD structural information has seriously hampered both the understanding of their structure–function relationships and the structure-based bioengineering of this enzyme. Herein, we presented the crystal structure of a PLD from the plant-associated bacteria Serratia plymuthica strain AS9 (SpPLD) at a resolution of 1.79 Å. Two classical HxKxxxxD (HKD) motifs were found in SpPLD and have shown high structural consistence with several PLDs in the same family. While comparing the structure of SpPLD with the previous resolved PLDs from the same family, several unique conformations on the C-terminus of the HKD motif were demonstrated to participate in the arrangement of the catalytic pocket of SpPLD. In SpPLD, an extented loop conformation between β9 and α9 (aa228–246) was found. Moreover, electrostatic surface potential showed that this loop region in SpPLD was positively charged while the corresponding loops in the two Streptomyces originated PLDs (PDB ID: 1F0I, 2ZE4/2ZE9) were neutral. The shortened loop between α10 and α11 (aa272–275) made the SpPLD unable to form the gate-like structure which existed specically in the two Streptomyces originated PLDs (PDB ID: 1F0I, 2ZE4/2ZE9) and functioned to stabilize the substrates. In contrast, the shortened loop conformation at this corresponding segment was more alike to several nucleases (Nuc, Zuc, mZuc, NucT) within the same family. Moreover, the loop composition between β11 and β12 was also different from the two Streptomyces originated PLDs (PDB ID: 1F0I, 2ZE4/2ZE9), which formed the entrance of the catalytic pocket and were closely related to substrate recognition. So far, SpPLD was the only structurally characterized PLD enzyme from Serratia. The structural information derived here not only helps for the understanding of the biological function of this enzyme in plant protection, but also helps for the understanding of the rational design of the mutant, with potential application in phospholipid modification.

Stability assay of antagonistic activity of Serratia plymuthica strain UBCR_12 under various environmental factors

Serratia plymuthica strain UBCR_12 exhibited promising antifungal activity against Colletotrichum gloeosporioides. The development of this strain for field use requires a certain level of stability towards various environmental exposures that might occur in the natural condition. This study was aimed to evaluate the stability level of antifungal activity produced by the culture supernatants of S. plymuthica strain UBCR_12 under several environmental factors. Antifungal assay of this strain was performed through the application of culture supernatants under several parameters and was performed in five technical replications. Data were confirmed statistically using one-way and two-way ANOVA and significance among treatments were verified through DNMRT with a p<0.05. The antagonistic effect of this strain varied in each environmental parameter tested. The highest suppression was recorded at pH 8.0 [30.32%] after eight days of application indicating that the alkaline condition might trigger its defense mechanism. Other parameters showed quite similar inhibition efficacy, such as 24.06% [100 C for 45 minutes] and 21.15% [CaCl2 addition]. Compared to control, this strain could suppress anthracnose-causing fungi up to 24.06% suggesting that its antifungal activity was considered as quite stable over the presence of heat and calcium.

The Great Five\u2014an artificial bacterial consortium with antagonistic activity towards Pectobacterium spp. and Dickeya spp.: formulation, shelf life, and the ability to prevent soft rot of potato in storage

“The Great Five” (GF) is an artificial bacterial consortium developed to protect potato tubers from soft rot caused by Pectobacterium spp. and Dickeya spp. To investigate the commercialization potential of the GF, we developed liquid and powder formulations of the consortium and of each of the comprising strains (Serratia plymuthica strain A294, Enterobacter amnigenus strain A167, Rahnella aquatilis strain H145, Serratia rubidaea strain H440, and S. rubidaea strain H469). To form powders, the cells were lyophilized using a newly developed lyoprotectant: Reagent PS. The shelf life of the formulations stored at 8 and 22 °C was monitored for a period of 12 months. The longest shelf life was obtained for formulations stored at 8 °C; however, the viability of all formulations was negatively affected at 22 °C. For the consortium, a 2.5 log10 cfu (colony forming units) drop in cell number was recorded for the liquid formulation after 6 months, while in case of powders, the drop remained below 1 log10 cfu following 12 months. The ability of the powder formulations to preserve biocontrol activity of the consortium was tested on potato tubers treated with the formulations and a mixture of the soft rot pathogens. The inoculated tubers were stored for 6 months at 8 °C to mimic commercial storage conditions. Soft rot severity and incidence on potato tubers treated with formulations were significantly reduced (62–75% and 48–61%, respectively) in comparison to positive control with pathogens alone. The potential use of the newly developed formulations of “The Great Five” for the biocontrol of soft rot is discussed.Key Points• An innovative reagent to protect bacterial cells during lyophilization was developed.• Powder formulations of “The Great Five” prolonged its shelf life.• The powder-formulated “The Great Five” was active against soft rot bacteria on potato tubers.

Antibacterial 3,6-Disubstituted 4-Hydroxy-5,6-dihydro-2H-pyran-2-ones from Serratia plymuthica MF371-2.

Bioassay-guided fractionation of culture extracts of Serratia plymuthica strain MF371-2 resulted in the isolation of two new antibacterial compounds with potent activity against Gram-positive bacteria, including Staphylococcus aureus LMG 15975 (MRSA). A spectroscopic investigation, in combination with synthesis, enabled the characterization of the compounds as 3-butyryl-4-hydroxy-6-heptyl-5,6-dihydro-2H-pyran-2-one (plymuthipyranone A, 1) and 3-butyryl-4-hydroxy-6-nonyl-5,6-dihydro-2H-pyran-2-one (plymuthipyranone B, 2). The MIC values for 1 and 2 against S. aureus LMG 15975 were determined to be 1-2 μg mL-1 and 0.8 μg mL-1, respectively. Compound 2 was found to have potent activity against many strains of S. aureus, including several mupirocin-resistant strains, other species of Staphylococcus, and vancomycin-resistant enterococci. Compound 2 was slightly cytotoxic for human cells, with CC50 values between 4.7 and 40 μg mL-1, but the CC50/MIC ratio was ≥10 for many tested combinations of human cells and bacteria, suggesting its possible use as an antibacterial agent. Several analogues were synthesized with different alkyl groups in the 3- and 6-positions (6-13), and their biological properties were evaluated. It was concluded that the activity of the compounds increased with the lengths of the alkyl and acyl substituents.

Genome Sequence of Serratia plymuthica Strain S13, an Endophyte with Germination- and Plant-Growth-Promoting Activity from the Flower of Styrian Oil Pumpkin

The bacterium Serratia plymuthica strain S13 was demonstrated to colonize various plant-associated microhabitats and to suppress damping-off diseases. The completed genome sequence has a size of 5.5 Mb, containing 4,957 putative protein-encoding regions, and will be used to identify genetic determinants enabling the bacterium to escort a plant’s entire life cycle.

A PKS/NRPS/FAS Hybrid Gene Cluster from Serratia plymuthica RVH1 Encoding the Biosynthesis of Three Broad Spectrum, Zeamine-Related Antibiotics

Serratia plymuthica strain RVH1, initially isolated from an industrial food processing environment, displays potent antimicrobial activity towards a broad spectrum of Gram-positive and Gram-negative bacterial pathogens. Isolation and subsequent structure determination of bioactive molecules led to the identification of two polyamino antibiotics with the same molecular structure as zeamine and zeamine II as well as a third, closely related analogue, designated zeamine I. The gene cluster encoding the biosynthesis of the zeamine antibiotics was cloned and sequenced and shown to encode FAS, PKS as well as NRPS related enzymes in addition to putative tailoring and export enzymes. Interestingly, several genes show strong homology to the pfa cluster of genes involved in the biosynthesis of long chain polyunsaturated fatty acids in marine bacteria. We postulate that a mixed FAS/PKS and a hybrid NRPS/PKS assembly line each synthesize parts of the backbone that are linked together post-assembly in the case of zeamine and zeamine I. This interaction reflects a unique interplay between secondary lipid and secondary metabolite biosynthesis. Most likely, the zeamine antibiotics are produced as prodrugs that undergo activation in which a nonribosomal peptide sequence is cleaved off.

Complete genome sequence of the plant-associated Serratia plymuthica strain AS13.

Serratia plymuthica AS13 is a plant-associated Gammaproteobacteria, isolated from rapeseed roots. It is of special interest because of its ability to inhibit fungal pathogens of rapeseed and to promote plant growth. The complete genome of S. plymuthica AS13 consists of a 5,442,549 bp circular chromosome. The chromosome contains 4,951 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced as part of the project entitled “Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens” within the 2010 DOE-JGI Community Sequencing Program (CSP2010).

Draft Genome Sequence of the Antagonistic Rhizosphere Bacterium Serratia plymuthica Strain PRI-2C

Serratia plymuthica strain PRI-2C is a rhizosphere bacterial strain with antagonistic activity against different plant pathogens. Here we present the 5.39-Mb (G+C content, 55.67%) draft genome sequence of S. plymuthica strain PRI-2C with the aim of providing insight into the genomic basis of its antagonistic activity.

Biocontrol of Rhizoctonia solani: complex interaction of biocontrol strains, pathogen and indigenous microbial community in the rhizosphere of lettuce shown by molecular methods

Background and aims Co-inoculation of biocontrol agents with different modes of action is assumed to improve biocontrol activity. The present study aimed to investigate the effects of single or co-inoculation of Trichoderma viride strain GB7 and Serratia plymuthica strain 3Re4-18 on microbial communities in the rhizosphere of lettuce and their ability to suppress Rhizoctonia solani AG1-IB.

Complete genome sequence of Serratia plymuthica strain AS12.

A plant-associated member of the family Enterobacteriaceae, Serratia plymuthica strain AS12 was isolated from rapeseed roots. It is of scientific interest because it promotes plant growth and inhibits plant pathogens. The genome of S. plymuthica AS12 comprises a 5,443,009 bp long circular chromosome, which consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced within the 2010 DOE-JGI Community Sequencing Program (CSP2010) as part of the project entitled “Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens”.