Strain LS3 Research Articles

Screening, Identification, and Pigment Characteristics of Actinomycin D-Producing Actinomycetes from Purple Soil in the Sichuan Basin

Background: Natural pigments from microbial sources are a class of compounds with various structures and a wide range of uses, which have become an important source of antibiotic production. Objectives: This study aimed to screen and identify a new type of pigment-producing microorganism from purple soil in the Sichuan Basin. At the same time, this study aimed to purify and identify the produced pigment, preliminarily optimize its fermentation conditions, and characterize its antibacterial activity. Methods: Through morphology, physiology, biochemistry, and molecular sequencing, the strain LS-2 was identified. The pigment was purified by column chromatography, and its antibacterial activity was characterized by a disc diffusion assay. Through the analysis of the ultraviolet-visible (UV-vis) absorption spectrum, infrared (IR) absorption spectrum, and liquid chromatography-mass spectrometry (LC-MS), the yellow pigment was identified. Results: An actinomycin D-producing Streptomyces parvulus was isolated from the purple soil in the Sichuan Basin. Its optimal fermentation conditions were culture at 34°C on Gause’s synthetic medium with pH 6.5, and the yield reached 540 mg/L after 48 hours. The actinomycin D produced by the strain has excellent antibacterial activity against gram-positive (Staphylococcus aureus) and gram-negative (Escherichia coli). Conclusions: A new actinomycin D-producing strain of Streptomyces parvulus LS-2 was isolated and identified. The strain has a high production of actinomycin D, which has excellent antibacterial activity.

Biodegradation mechanism of chlortetracycline by a novel fungal Aspergillus sp. LS-1

Chlortetracycline (CTC), a widely used typical tetracycline antibiotic, has raised increasing concerns due to its potential health and environmental risks. Biodegradation is considered an effective method to reduce CTC in environment. In this study, a strain Aspergillus sp. LS-1, which can efficiently degrade CTC, was isolated from CTC-rich activated sludge. Under optimal conditions, the maximum removal efficiency of CTC could reach 95.41%. Temperature was the most significant factor affecting the degradation efficiency of LS-1. The 19 products were identified in the CTC degradation by strain LS-1, and three degradation pathways were proposed. All the degradation pathways for CTC exhibited ring-cleaving, which may accelerate the mineralization of CTC. To gain more comprehensive insights into this strain, we obtained the genome of LS-1, which had high GC content (50.1%) and completeness (99.3%). The gene annotation revealed that LS-1 contains some vital enzymes and resistance genes that may carry functional genes involved in the CTC degradation. In addition, other antibiotic resistance genes were found in the genome of LS-1, indicating that LS-1 has the potential to degrade other antibiotics. This study provides a more theoretical basis for the investigation of CTC degradation by fungi and new insights into the biodegradation of CTC.

Comprehensive Genome Analysis of Cellulose and Xylan-Active CAZymes from the Genus Paenibacillus: Special Emphasis on the Novel Xylanolytic Paenibacillus sp. LS1.

Xylan is the most abundant hemicellulose in hardwood and graminaceous plants. It is a heteropolysaccharide comprising different moieties appended to the xylose units. Complete degradation of xylan requires an arsenal of xylanolytic enzymes that can remove the substitutions and mediate internal hydrolysis of the xylan backbone. Here, we describe the xylan degradation potential and underlying enzyme machinery of the strain, Paenibacillus sp. LS1. The strain LS1 was able to utilize both beechwood and corncob xylan as the sole source of carbon, with the former being the preferred substrate. Genome analysis revealed an extensive xylan-active CAZyme repertoire capable of mediating efficient degradation of the complex polymer. In addition to this, a putative xylooligosaccharide ABC transporter and homologues of the enzymes involved in the xylose isomerase pathway were identified. Further, we have validated the expression of selected xylan-active CAZymes, transporters, and metabolic enzymes during growth of the LS1 on xylan substrates using qRT-PCR. The genome comparison and genomic index (average nucleotide identity [ANI] and digital DNA-DNA hybridization) values revealed that strain LS1 is a novel species of the genus Paenibacillus. Lastly, comparative genome analysis of 238 genomes revealed the prevalence of xylan-active CAZymes over cellulose across the Paenibacillus genus. Taken together, our results indicate that Paenibacillus sp. LS1 is an efficient degrader of xylan polymers, with potential implications in the production of biofuels and other beneficial by-products from lignocellulosic biomass. IMPORTANCE Xylan is the most abundant hemicellulose in the lignocellulosic (plant) biomass that requires cooperative deconstruction by an arsenal of different xylanolytic enzymes to produce xylose and xylooligosaccharides. Microbial (particularly, bacterial) candidates that encode such enzymes are an asset to the biorefineries to mediate efficient and eco-friendly deconstruction of xylan to generate products of value. Although xylan degradation by a few Paenibacillus spp. is reported, a complete genus-wide understanding of the said trait is unavailable till date. Through comparative genome analysis, we showed the prevalence of xylan-active CAZymes across Paenibacillus spp., therefore making them an attractive option towards efficient xylan degradation. Additionally, we deciphered the xylan degradation potential of the strain Paenibacillus sp. LS1 through genome analysis, expression profiling, and biochemical studies. The ability of Paenibacillus sp. LS1 to degrade different xylan types obtained from different plant species, emphasizes its potential implication in lignocellulosic biorefineries.

A novel strategy for enhancing bioremediation of polychlorinated biphenyl-contaminated soil with resuscitation promoting factor and resuscitated strain

PCBs bioremediation is largely impeded by the reduced metabolic activity and degradation ability of indigenous and exogenous microorganisms. Resuscitation promoting factor (Rpf) of Micrococcus luteus, has been reported to resuscitate and stimulate the growth of PCB-degrading bacterial populations, and the resuscitated strains exhibited excellent PCB-degrading performances. Therefore, this study was conducted to assess the feasibility of supplementing Rpf (SR) or resuscitated strain LS1 (SL), or both (SRL) for enhanced bioremediation of PCB-contaminated soil. The results indicated that Rpf and/or LS1 amended soil microcosms achieved more rapid PCBs degradation, which were 1.1–3.2 times faster than control microcosms. Although soil-inoculated LS1 maintained the PCB-degrading activity, higher PCBs degradation was observed in Rpf-amended soil microcosms compared with SL. The order of enhancement effect on PCBs bioremediation was SRL > SR > SL. PCBs degradation in soil microcosms was via HOPDA-benzoate-catechol/protocatechuate pathways. The improved PCBs degradation in Rpf-amended soil microcosms was attributed to the enhanced abundances of PCB-degrading populations which were mainly belonged to Proteobacteria and Actinobacteria. These results suggest that Rpf and resuscitated strains serve as effective additive and bio-inoculant for enhanced bioremediation, providing new approaches to realizing large scale applications of in situ bioremediation.

High PCBs mineralization capability of a resuscitated strain Bacillus sp. LS1 and its survival in PCB-contaminated soil

Polychlorinated biphenyl (PCB)-degrading strains resuscitated by resuscitation promoting factor (Rpf) enlarged pure degraders to screen effective bio-inoculants for soil bioaugmentation. In this study, whole-genome analysis and PCB-degrading performance of a resuscitated strain LS1 were investigated. Importantly, the persistence and the physiological response of soil-inoculated LS1 were checked. The results indicate that the Bacillus sp. strain LS1 possessed the potential to degrade polycyclic aromatic compounds. LS1 exhibited better performance in degrading PCBs 18 and 52, but lower PCB 77 degradation capability. At PCBs concentration of 10 mg/L, the degradation efficiencies of PCBs 18, 52 and 77 within 96 h were 62.8 %, 59.6 % and 39.8 %, respectively. Combined the bph genes and metabolites detected, as well as the genes found in the genome, the abilities of LS1 for oxidative dehalogenation and mineralization of PCBs via HOPDA-benzoate-protocatechuate-β-ketoadipate pathway were determined. Notably, LS1 can still maintain survival and culturable state after inoculation into PCB-contaminated soil for 70 days. This is the first report to demonstrate the fate of resuscitated strain when used as soil bio-inoculant, which revealed the necessity and feasibility of using resuscitated strains to enhance bioremediation of PCB-contaminated soils.

Natronococcus pandeyae sp. nov., a Novel Haloarchaeon from Sambhar Salt Lake

A halophilic archaeon, designated strain LS1_42T, was isolated from Sambhar Salt Lake, Rajasthan, India. Cells were non-motile, coccoid, Gram-stain-variable and present in irregular clusters with light pink pigmented colonies. The strain was strictly aerobic and able to grow without Mg2+. Growth of the strain LS1_42T was observed at 25-45°C, pH 7.0-11.0 and NaCl concentrations of 10-35% (w/v). The nearest phylogenetic neighbor of strain LS1_42T was Natronococcus amylolyticus Ah-36T based on 16S rRNA and rpoB' genes with similarity of 95.4% and 91.9%, respectively. Phylogenetic analysis based on 16S rRNA gene, rpoB' gene and whole-genome sequences indicate that the strain LS1_42T belongs to the genus Natronococcus and is closely related to N. amylolyticus. The genome size was 5.38Mb with 98.9% completeness. The DNA G + C content of the strain LS1_42T was 63.0mol%. The average nucleotide identity, average amino acid identity and DNA-DNA hybridization values between LS1_42T and N. amylolyticus Ah-36T were 81.3%, 77.7% and 24.8%, respectively. The major polar lipids detected were phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. On the basis of phenotypic, chemotaxonomic and genome-based analysis, strain LS1_42T represents a novel species within the genus Natronococcus, for which the name Natronococcus pandeyae sp. nov. is proposed. The type strain is LS1_42T (MCC 3654T = JCM 33003T = KCTC 4280T = CGMCC 1.16738T).

The native acyltransferase-coding genes DGA1 and DGA2 affect lipid accumulation in Blastobotrys raffinosifermentans differently when overexpressed.

Blastobotrys raffinosifermentans is an ascomycetous yeast with biotechnological applications, recently shown to be an oleaginous yeast accumulating lipids under nitrogen limitation. Diacylglycerol acyltransferases (DGATs) act in the lipid storage pathway, in the last step of triacylglycerol biosynthesis. Two DGAT families are widespread in eukaryotes. We first checked that B. raffinosifermentans strain LS3 possessed both types of DGAT, and we then overexpressed the native DGAT-encoding genes, DGA1 and DGA2, separately or together. DGA2 (from the DGAT1 family) overexpression was sufficient to increase lipid content significantly in LS3, to up to 26.5% of dry cell weight (DCW), 1.6 times the lipid content of the parental strain (16.90% of DCW) in glucose medium under nitrogen limitation. By contrast, DGA1 (of the DGAT2 type) overexpression led to a large increase (up to 140-fold) in the amount of the corresponding transcript, but had no effect on overall lipid content relative to the parental strain. Analysis of the expression of the native genes over time in the parental strain revealed that DGA2 transcript levels quadrupled between 8 and 24h in the N-limited lipogenic medium, whereas DGA1 transcript levels remained stable. This survey highlights the predominant role of the DGAT1 family in lipid accumulation and demonstrates the suitability of B. raffinosifermentans for engineering for lipid production.

Bacillus cereus LS2 from Apostichopus japonicus antagonizes Vibrio splendidus growth

In this study, a bacterium identified as Bacillus cereus LS2 was isolated from healthy sea cucumbers and possessed strong antagonistic activity toward Vibrio splendidus, an important pathogen to Apostichopus japonicus. The antagonistic activity of strain LS2 to the growth of V. splendidus was 86.83% ± 1.47%. The antagonistic substance, with molecular weight less than 3 kDa, was sensitive to trypsin but stable at high temperatures. The antagonistic substances could be precipitated by acid and dissolved in anhydrous methanol. Further, the in-situ hydrolysis and ninhydrin staining assay showed that the antagonistic substance was a peptide. On the basis of these characteristics, the antagonistic substance was postulated to be a kind of lipopeptide. The analysis of differentially expressed proteins revealed that the expression of dihydrolipoamide dehydrogenase 1 (DLDH1) in V. splendidus could be upregulated in the presence of the LS2 supernatant. Furthermore, the overexpression of DLDH1 reduced the growth of V. splendidus by 12.5% compared with that of the wild-type strain. Our findings suggest that LS2 could be used as a potential bacterial antagonist to control V. splendidus infections by upregulating the DLDH1 expression in V. splendidus.

Blastobotrys adeninivorans and B. raffinosifermentans, two sibling yeast species which accumulate lipids at elevated temperatures and from diverse sugars

BackgroundIn the context of sustainable development, yeast are one class of microorganisms foreseen for the production of oil from diverse renewable feedstocks, in particular those that do not compete with the food supply. However, their use in bulk production, such as for the production of biodiesel, is still not cost effective, partly due to the possible poor use of desired substrates or poor robustness in the practical bioconversion process. We investigated the natural capacity of Blastobotrys adeninivorans, a yeast already used in biotechnology, to store lipids under different conditions.ResultsThe genotyping of seven strains showed the species to actually be composed of two different groups, one that (including the well-known strain LS3) could be reassigned to Blastobotrys raffinosifermentans. We showed that, under nitrogen limitation, strains of both species can synthesize lipids to over 20% of their dry-cell weight during shake-flask cultivation in glucose or xylose medium for 96 h. In addition, organic acids were excreted into the medium. LS3, our best lipid-producing strain, could also accumulate lipids from exogenous oleic acid, up to 38.1 ± 1.6% of its dry-cell weight, and synthesize lipids from various sugar substrates, up to 36.6 ± 0.5% when growing in cellobiose. Both species, represented by LS3 and CBS 8244T, could grow with little filamentation in the lipogenic medium from 28 to 45 °C and reached lipid titers ranging from 1.76 ± 0.28 to 3.08 ± 0.49 g/L in flasks. Under these conditions, the maximum bioconversion yield (YFA/S = 0.093 ± 0.017) was obtained with LS3 at 37 °C. The presence of genes for predicted subunits of an ATP citrate lyase in the genome of LS3 reinforces its oleaginous character.ConclusionsBlastobotrys adeninivorans and B. raffinosifermentans, which are known to be xerotolerant and genetically-tractable, are promising biotechnological yeasts of the Saccharomycotina that could be further developed through genetic engineering for the production of microbial oil. To our knowledge, this is the first report of efficient lipid storage in yeast when cultivated at a temperature above 40 °C. This paves the way to help reducing costs through consolidated bioprocessing.

Draft Genome Sequence of Deoxynivalenol-Degrading Actinomycete Nocardioides sp. Strain LS1, Isolated from Wheat Leaves in Japan.

Actinomycete Nocardioides sp. strain LS1, isolated from wheat leaf, is a bacterium that degrades and assimilates the mycotoxin deoxynivalenol (DON) as the carbon source. This is the first study of the genome sequence of the DON-degrading genus Nocardioides, and it facilitates the study of genes encoding the DON-degrading pathway.

Integration of biological and chemical control of brown rot of stone fruits to reduce disease incidence on fruits and minimize fungicide residues in juice

Brown rot is a major disease of stone fruits caused by Monilinia spp. It can reach high incidence that leads to considerable losses during storage. Our work aimed at the evaluation of innovative biological and integrated approaches to control brown rot of apricots and peaches, and of their influence on the presence of fungicide residues both in the harvested fruits and derived peach juices. In this work, we report the results of a two-year field investigation carried out in 5 different farms in Southern Italy. Plant health management strategy was based on two treatments performed in the last thirty days before harvest. Two biocontrol agents (BCAs), the yeast Rhodotorula kratochvilovae strain LS11 and the commercial biofungicide Serenade Max® (based on Bacillus subtilis strain QST 713), were applied alone (biocontrol) or in combination with low doses of the fungicides (25% of full dosage, integrated control) cyprodinil (30 days before harvest), and boscalid (7 days before harvest). The highest protection was recorded in conventional (fungicides applied at full dosage) and integrated control treatments, both on apricots and peaches. In the integrated control, residues of fungicides in fruits and in peach juice were significantly lower compared to those of the conventional control in both fruit species. Our data show that biological and integrated control based on two key treatments at thirty and seven days before harvest can be considered as effective and safer control strategies of brown rot of stone fruits. Furthermore, the applied strategies can dramatically reduce and even set to zero the level of fungicide residues in derived fruit juices.

Pathogenomics of Virulence Traits of Plesiomonas shigelloides That Were Deemed Inconclusive by Traditional Experimental Approaches.

One of the major challenges of modern medicine includes the failure of conventional protocols to characterize the pathogenicity of emerging pathogens. This is particularly apparent in the case of Plesiomonas shigelloides. Although a number of infections have been linked to this microorganism, experimental evidence of its virulence factors (VFs), obtained by traditional approaches, is somewhat inconclusive. Hence, it remains unclear whether P. shigelloides is a true or opportunistic one. In the current study, four publicly available whole-genome sequences of P. shigelloides (GN7, NCTC10360, 302-73, and LS1) were profiled using bioinformatics platforms to determine the putative candidate VFs to characterize the bacterial pathogenicity. Overall, 134 unique open reading frames (ORFs) were identified that were homologous or orthologous to virulence genes identified in other pathogens. Of these, 52.24% (70/134) were jointly shared by the strains. The numbers of strain-specific virulence traits were 4 in LS1; 7 in NCTC10360; 10 in 302-73; and 15 in GN7. The pathogenicity islands (PAIs) common to all the strains accounted for 24.07% ORFs. The numbers of PAIs exclusive to each strain were 8 in 302-73; 11 in NCTC10360; 14 in GN7; and 18 in LS1. A PAI encoding Vibrio cholerae ToxR-activated gene d protein was specific to 302-73, GN7, and NCTC10360 strains. Out of 33 antibiotic multi-resistance genes identified, 16 (48.48%) genes were intrinsic to all strains. Further, 17 (22.08%) of 77 antibiotic resistance islands were found in all the strains. Out of 23 identified distinct insertion sequences, 13 were only harbored by strain LS1. The number of intact prophages identified in the strains was 1 in GN7; 2 in 302-73; and 2 in NCTC10360. Further, 1 CRISPR element was identified in LS1; 2 in NCTC10360; and 8 in 302-73. Fifteen (78.95%) of 19 secretion systems and secretion effector variants were identified in all the strains. In conclusion, certain P. shigelloides strains might possess VFs associated with gastroenteritis and extraintestinal infections. However, the role of host factors in the onset of infections should not be undermined.

Isotopic Labeling Studies Reveal the Patulin Detoxification Pathway by the Biocontrol Yeast Rhodotorula kratochvilovae LS11.

Patulin (1) is a mycotoxin contaminant in fruit and vegetable products worldwide. Biocontrol agents, such as the yeast Rhodotorula kratochvilovae strain LS11, can reduce patulin (1) contamination in food. R. kratochvilovae LS11 converts patulin (1) into desoxypatulinic acid (DPA) (5), which is less cytotoxic than the mycotoxin (1) to in vitro human lymphocytes. In the present study, we report our investigations into the pathway of degradation of patulin (1) to DPA (5) by R. kratochvilovae. Isotopic labeling experiments revealed that 5 derives from patulin (1) through the hydrolysis of the γ-lactone ring and subsequent enzymatic modifications. The ability of patulin (1) and DPA (5) to cause genetic damage was also investigated by the cytokinesis-block micronucleus cytome assay on in vitro human lymphocytes. Patulin (1) was demonstrated to cause much higher chromosomal damage than DPA (5).

Draft Genome Sequence of Pseudomonas sp. LS-2, Isolated from a Diseased Gastrodia elata Plant.

We report here the draft genome sequence of Pseudomonas sp. LS-2, isolated from the decaying aerial stem of a Gastrodia elata plant. This genome harbored 96 potential genes implicated in bacterium-plant interactions, which may facilitate the adaptation of strain LS-2 to plant environments.

In vitro screening of putative probiotics and their dual beneficial effects: To white shrimp (Litopenaeus vannamei) postlarvae and to the rearing water

Shrimp aquaculture has been severely threatened by vibriosis. Traditional methods to combat Vibrio diseases with antibiotics and chemotherapeutics have been discouraged due to their potential negative consequences. The aim of this study was: firstly screen potential probiotics using in vitro assays; then evaluate the beneficial effects of the screened probiotics in Litopenamei vannamei postlarvae by in vivo feeding experiments. Pre-screening of 12 candidate probiotics based on criteria such as extracellular enzyme production, haemolytic activity, tolerance to bile salt, tolerance to gastrointestinal stress, inhibitory activity against Vibrio pathogens, cell surface hydrophobicity and autoaggregation resulted in two potential probiotic isolates: LS-1 and LD-1. Both isolates showed good probiotic characteristics on all criteria above. Biochemical and 16S rRNA sequencing analysis identified LS-1 and LD-1 as Bacillus licheniformis and Bacillus flexus, respectively. In vivo feeding experiments with LS-1, or LD-1, or LS-1 + LD-1 as dietary supplementation demonstrated that both strains could effectively enhance the growth, innate immune enzyme activities, digestive enzyme activities, stress tolerance and disease resistance of L. vannamei. In addition, both strains also illustrated water quality improving effects in the probiotic supplement feeding experiments. This is one of the few reports of Bacillus probiotics that display dual beneficial effects: both to the host and to the rearing water. Results from this study demonstrated that Bacillus licheniformis strain LS-1 and Bacillus flexus strain LD-1 are promising probiotic candidates to provide multiple benefits for shrimp rearing.

Bicarbonate induces high-level resistance to the human antimicrobial peptide LL-37 in Staphylococcus aureus small colony variants.

Objectives Staphylococcus aureus small colony variants (SCVs) cause persistent infections and are resistant to cationic antibiotics. Antimicrobial peptides (AMPs) have been suggested as promising alternatives for treating antibiotic-resistant bacteria. We investigated the capacity of the human cationic AMP LL-37 to kill SCVs in the presence of physiological concentrations of bicarbonate, which are reported to alter bacterial membrane permeability and change resistance of bacteria to AMPs.MethodsMBCs of LL-37 for S. aureus SCVs with mutations in different genes in the presence and absence of bicarbonate were determined.ResultsIn the absence of bicarbonate, SCVs of S. aureus strains LS-1 and 8325-4 had the same level of resistance to LL-37 as the parental strain (8 mg/L). In the presence of bicarbonate, hemB, menD and aroD SCVs of LS-1 had high-level resistance to LL-37 (≥128 mg/L) compared with the parental strain (16 mg/L). However, only the aroD SCV of strain 8324-5 showed high-level resistance. 8325-4 harbours mutations in two genes, tcaR and rsbU, which are involved in antimicrobial sensing and the stress response, respectively. When rsbU was repaired in 8325-4 it displayed high-level resistance to LL-37 in the presence of bicarbonate. This phenotype was lost when tcaR was also repaired, demonstrating that RsbU and TcaR are involved in LL-37 resistance in the presence of bicarbonateConclusions S. aureus SCVs would be resistant to high concentrations of LL-37 in niches where there are physiological concentrations of bicarbonate and therefore this AMP may not be effective in combating SCVs.

Biocontrol Agents Increase the Specific Rate of Patulin Production by Penicillium expansum but Decrease the Disease and Total Patulin Contamination of Apples

Synthetic fungicides are commonly employed for the control of postharvest diseases of fruits. However, due to health concerns about the use of these chemicals, alternative control methods including biocontrol based on antagonistic yeasts are gaining in popularity. In this study, we investigated the effects of two biocontrol yeasts, Rhodotorula mucilaginosa strain 3617 and Rhodotorula kratochvilovae strain LS11, on blue mold and patulin (PAT) contamination caused by Penicillium expansum strains PY and FS7 in artificially inoculated Fuji apples stored at 20°C for 9 days. To correlate the development of the P. expansum strains in yeast-treated and untreated apples with PAT production, we quantified their biomass in the infected fruits using a recently published quantitative real-time polymerase chain reaction method based on specific primers for patF, a gene from P. expansum that is involved in PAT biosynthesis. Both yeasts significantly reduced the disease incidence caused by the two strains of P. expansum up to 5–7 days of incubation, and lowered their biomass and the progression of symptoms up to 9 days. Interestingly, both yeasts strains increased the rate of PAT production (expressed as ng patulin/μg fungal DNA) by the two pathogenic strains. Nevertheless, both biocontrol agents reduced the total PAT contamination, especially in the case of P. expansum strain FS7, the higher PAT producer of the two tested P. expansum strains. Comparing between the yeast strains, R. kratochvilovae LS11 was more effective than R. mucilaginosa 3617 for the control of P. expansum.

Isolation, Identification and Genomic Analysis of Plesiomonas shigelloides Isolated from Diseased Percocypris pingi (Tchang, 1930)

Recently, the outbreak of a serious infectious disease of unknown etiology was noted in Percocypris pingi (Tchang, 1930) farms in Yunnan province. Due to currently limited information, we aimed to identify the pathogen isolates, determine the susceptibility of the isolates, evaluate the pathogenicity and analyze the genome of the representative strain. Ten strains of Gram-negative rods were isolated from diseased P. pingi and the isolates were identified as Plesiomonas shigelloides based on biochemical characteristics, 16S rRNA gene sequencing and species-specific PCR detection. The results of susceptibility analysis showed that two selected strains LS1 and LL2 were resistant to ampicillin, penicillin G, trimethoprim/sulfamethoxazole, tetracycline, enrofloxacin, nalidixic acid and enoxacin. A virulence assay indicated that the pathogen was virulent to zebrafish. Genomic analysis revealed that the LS1 isolate was closely related to strain GN7, which was isolated from animal farms. To the best of our knowledge, this is the first report of P. shigelloides as a pathogen of P. pingi. This study will provide a rational framework for exploration of epidemiological analysis of P. shigelloides in fish diseases and would further benefit conservation of the species.

Transcriptomic responses of the basidiomycete yeast Sporobolomyces sp. to the mycotoxin patulin.

BackgroundPatulin is a mycotoxin produced by Penicillium expansum, the causal agent of blue mold of stored pome fruits, and several other species of filamentous fungi. This mycotoxin has genotoxic, teratogenic and immunotoxic effects in mammals, and its presence in pome fruits and derived products represents a serious health hazard. Biocontrol agents in the Pucciniomycotina, such as the yeasts Sporobolomyces sp. strain IAM 13481 and Rhodosporidium kratochvilovae strain LS11, are able to resist patulin and degrade it into the less toxic compounds desoxypatulinic acid and ascladiol.ResultsIn this investigation we applied a transcriptomic approach based on RNAseq to annotate the genome of Sporobolomyces sp. IAM 13481 and then study the changes of gene expression in Sporobolomyces sp. exposed to patulin. Patulin treatment leads to ROS production and oxidative stress that result in the activation of stress response mechanisms controlled by transcription factors. Upregulated Sporobolomyces genes were those involved in oxidation-reduction and transport processes, suggesting the activation of defense mechanisms to resist patulin toxicity and expel the mycotoxin out of the cells. Other upregulated genes encoded proteins involved in metabolic processes such as those of the glutathione and thioredoxin systems, which are essential to restore the cellular redox homeostasis. Conversely, patulin treatment decreased the expression of genes involved in the processes of protein synthesis and modification, such as transcription, RNA processing, translation, protein phosphorylation and biosynthesis of amino acids. Also, genes encoding proteins involved in transport of ions, cell division and cell cycle were downregulated. This indicates a reduction of metabolic activity, probably due to the high energy requirement by the cells or metabolic arrest while recovering from the insult caused by patulin toxicity.ConclusionsComplex mechanisms are activated in a biocontrol yeast in response to patulin. The genes identified in this study can pave the way to develop i) a biodetoxification process of patulin in juices and ii) a biosensor for the rapid and cost-effective detection of this mycotoxin.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2550-4) contains supplementary material, which is available to authorized users.

Fermentative production of dextran using Leuconostoc spp. isolated from fermented food products

Leuconostoc spp. (LS1and LI1) isolated from sauerkraut and idli batter was selected for dextran production. To enhance the yield of dextran, effects of various parameters such as sucrose concentration, pH, temperature, incubation and inoculum percentage were analyzed. The optimum sucrose concentration for the Leuconostoc spp. (LS1 and LI1) was found to be 15% and 25% respectively. Isolates produced maximum dextran after 20 h of incubation at 29° C and the optimum pH was found between 8 and 8.5. The inoculum concentration of 7.5% was more favorable for the production of dextran by Leuconostoc spp. (LS1 and LI1). The growth kinetic parameters were studied and compared for the strains LS1 and LI1. Mass production of dextran was carried out using a stirred tank batch reactor. FTIR analysis was done to determine the functional groups of dextran. sephadex is prepared by cross linking dextran using epichlorohydrin and the functional groups are determined by FTIR analysis.