Transformation of the endochitinase gene Chi67-1 in Clonostachys rosea 67-1 increases its biocontrol activity against Sclerotinia sclerotiorum

Harnessing the chromium reduction potential of Pseudomonas aeruginosa JRHM33: A comprehensive study on bioinformatics, phenotype microarray, and CCD-RSM optimization

Large amounts of wastewater are generated due to overpopulation and industrialization, The bioavailability, toxicity, and permanence of metals make heavy metal contamination a big environmental hazard. In order to maximize chromium (Cr+6) removal efficiency, the current investigation was carried out from industrial wastewater using Pseudomonas aeruginosa JRHM33.35 bacterial strains were discovered based on their physical, and biochemical properties and resistance towards chromium (Cr+6) heavy metal. The most significant bacterial strain JRHM33 found the highest-level of 1000 mg/L of chromium (Cr+6) resistance. The bacterial strain JRHM33, which has 99 % similarity to Pseudomonas aeruginosa, was found using 16 S rRNA sequencing and is employed in subsequent steps. Sequencing and study of conserved domains indicate that JRHM33 contains the laccase gene and belongs to the multicopper oxidase superfamily, which is known for its ability to reduce metal ions. Analysing phenotype microarray (PM) technology sheds light on Pseudomonas aeruginosa JRHM33 metabolic profile of microbial cells. Additionally, a series of process parameter optimizations were tried using the central composite design of response surface methodology (CCD-RSM) in an effort to reduce the amount of chromium (Cr+6) in the effluent as much as possible. At 6.8 pH, 90 min of incubation, inoculum size is 3.8 ml, and agitation is 104 rpm, a maximum 71 % Cr+6 reduction was attained. The model constructed has an R2 score of 0.983 indicates a very statistically significant outcome from the analysis of variance. The experimental outcomes and the predicted results were remarkably similar, according to the validation experiment. Studies have revealed that bacterial strains obtained from effluent containing high levels of metals utilize their inherent capability to change harmful heavy metals into less dangerous or harmless forms.

Factors affecting biofilm formation by bacteria on fabrics

Fabrics act as fomites for microorganisms, thereby playing a significant role in infection transmission, especially in the healthcare and hospitality sectors. This study aimed to examine the biofilm formation ability of four nosocomial infection-causing bacteria (Acinetobacter calcoaceticus, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus) on cotton, polyester, polyester-cotton blend, silk, wool, viscose, and nylon, used frequently in the healthcare sector, by qualitative and quantitative methods. The impact of temperature, pH, and relative humidity (RH) on biofilm formation was also assessed. P. aeruginosa and S. aureus were strong biofilm producers, while E. coli produced weak biofilm. Wool (maximum roughness) showed the highest bacterial load, while silk (lowest roughness) showed the least. P. aeruginosa exhibited a higher load on all fabrics, than other test bacteria. Extracellular polymeric substances were characterized by infrared spectroscopy. Roughness of biofilms was assessed by atomic force microscopy. For biofilm formation, optimum temperature, pH, and RH were 30 °C, 7.0, and 62%, respectively. MgCl2 and CaCl2 were the most effective in removing bacterial biofilm. In conclusion, biofilm formation was observed to be influenced by the type of fabric, bacteria, and environmental conditions. Implementing recommended guidelines for the effective disinfection of fabrics is crucial to curb the risk of nosocomial infections. In addition, designing modified healthcare fabrics that inhibit pathogen load could be an effective method to mitigate the transmission of infections.

Endophytic fungi: A future prospect for breast cancer therapeutics and drug development

Globally, breast cancer is a primary contributor to cancer-related fatalities and illnesses among women. Consequently, there is a pressing need for safe and effective treatments for breast cancer. Bioactive compounds from endophytic fungi that live in symbiosis with medicinal plants have garnered significant interest in pharmaceutical research due to their extensive chemical composition and prospective medicinal attributes. This review underscores the potentiality of fungal endophytes as a promising resource for the development of innovative anticancer agents specifically tailored for breast cancer therapy. The diversity of endophytic fungi residing in medicinal plants, success stories of key endophytic bioactive metabolites tested against breast cancer and the current progress with regards to in vivo studies and clinical trials on endophytic fungal metabolites in breast cancer research forms the underlying theme of this article. A thorough compilation of putative anticancer compounds sourced from endophytic fungi that have demonstrated therapeutic potential against breast cancer, spanning the period from 1990 to 2022, has been presented. This review article also outlines the latest trends in endophyte-based drug discovery, including the use of artificial intelligence, machine learning, multi-omics approaches, and high-throughput strategies. The challenges and future prospects associated with fungal endophytes as substitutive sources for developing anticancer drugs targeting breast cancer are also being highlighted.

Biocontrol Methods for the Management of Sclerotinia sclerotiorum in Legumes: A Review

Sclerotinia sclerotiorum is an economically damaging fungal pathogen that causes Sclerotinia stem rot in legumes, producing enormous yield losses. This pathogen is difficult to control due to its wide host spectrum and ability to produce sclerotia, which are resistant bodies that can remain active for long periods under harsh environmental conditions. Here, the biocontrol methods for the management of S. sclerotiorum in legumes are reviewed. Bacillus strains, which synthesized lipopeptides and volatile organic compounds, showed high efficacies in soybean plants, whereas the highest efficacies for the control of the pathogen in alfalfa and common bean were observed when using Coniothyrium minitans and Streptomyces spp., respectively. The biocontrol efficacies in fields were under 65%, highlighting the lack of strategies to achieve a complete control. Overall, although most studies involved extensive screenings using different biocontrol agent concentrations and application conditions, there is a lack of knowledge regarding the specific antifungal mechanisms, which limits the optimization of the reported methods.

A review on mycogenic metallic nanoparticles and their potential role as antioxidant, antibiofilm and quorum quenching agents

The emergence of antimicrobial resistance among biofilm forming pathogens aimed to search for the efficient and novel alternative strategies. Metallic nanoparticles have drawn a considerable attention because of their significant applications in various fields. Numerous methods are developed for the generation of these nanoparticles however, mycogenic (fungal-mediated) synthesis is attractive due to high yields, easier handling, eco-friendly and being energy efficient when compared with conventional physico-chemical methods. Moreover, mycogenic synthesis provides fungal derived biomolecules that coat the nanoparticles thus improving their stability. The process of mycogenic synthesis can be extracellular or intracellular depending on the fungal genera used and various factors such as temperature, pH, biomass concentration and cultivation time may influence the synthesis process. This review focuses on the synthesis of metallic nanoparticles by using fungal mycelium, mechanism of synthesis, factors affecting the mycosynthesis and also describes their potential applications as antioxidants and antibiofilm agents. Moreover, the utilization of mycogenic nanoparticles as quorum quenching agent in hampering the bacterial cell-cell communication (quorum sensing) has also been discussed.

Study on diazinon toxicity reduction by electro-Fenton process: A bioassay using daphnia magna

The realm of diazinon reduction from polluted water has witnessed a surge in the significance of advanced oxidation processes (AOPs) in recent times. However, there is a dearth of research focusing on the mitigation of its toxicity through AOPs. Thus, the primary objective of this study was to evaluate the effectiveness of the Electro-Fenton process (EFP) in the eradication and detoxification of diazinon in aqueous solutions. Synthetic wastewater samples with concentrations of 2, 2.5 and 3 mg/L were prepared. A total of 27 samples were determined using Box Behnken Design. Reaction time, pH and iron to hydrogen peroxide ratio (Fe2+/H2O2) were examined as operational parameters under a constant current of 5.4 amps. The quantification of diazinon concentration was performed using High-Performance Liquid Chromatography (HPLC). To evaluate the detoxification of diazinon, the Daphnia magna bioassay was employed as a methodology in this study. According to the results, the EFP could reduce the diazinon to zero and the LC50 values are increased by applying the process. The LC50 values for diazinon were determined using the Daphnia magna bioassay, considering initial concentrations of 2, 2.5, and 3 mg/L at a pH of 5, a reaction time of 15 min, and an iron to hydrogen peroxide molar ratio of 2. The recorded LC50 values were 3.039, 3.076, and 3.106, respectively, indicating the lowest frequency of cumulative death in Daphnia magna. In this case, after 96 h, only 3 cases (30%) of Daphnia magna death were observed. However, for all the mentioned concentrations of diazinon, after 96 h of exposure to samples without applying the Daphnia Magna death process, it was observed between 60 and 100%. Reducing the diazinon concentration and increasing the 96-h LC50 showed that the EFP can reduce the toxicity of diazinon on Daphnia Magna at the same time. Therefore, EFP can be considered a superior method with low ecotoxicity.

Insect-based agri-food waste valorization: Agricultural applications and roles of insect gut microbiota

Meeting the demands of the growing population requires increased food and feed production, leading to higher levels of agri-food waste. As this type of waste seriously threatens public health and the environment, novel approaches to waste management should be developed. Insects have been proposed as efficient agents for biorefining waste, producing biomass that can be used for commercial products. However, challenges in achieving optimal outcomes and maximizing beneficial results remain. Microbial symbionts associated with insects are known to have a critical role in the development, fitness, and versatility of insects, and as such, they can be utilized as targets for the optimization of agri-food waste insect-based biorefinery systems. This review discusses insect-based biorefineries, focusing on the agricultural applications of edible insects, mainly as animal feed and organic fertilizers. We also describe the interplay between agri-food waste-utilizing insects and associated microbiota and the microbial contribution in enhancing insect growth, development, and involvement in organic waste bioconversion processes. The potential contribution of insect gut microbiota in eliminating pathogens, toxins, and pollutants and microbe-mediated approaches for enhancing insect growth and the bioconversion of organic waste are also discussed. The present review outlines the benefits of using insects in agri-food and organic waste biorefinery systems, describes the roles of insect-associated microbial symbionts in waste bioconversion processes, and highlights the potential of such biorefinery systems in addressing the current agri-food waste-related challenges.

Resistance of aerobic granular sludge microbiomes to periodic loss of biomass

Granular sludge is a biofilm process used for wastewater treatment which is currently being implemented worldwide. It is important to understand how disturbances affect the microbial community and performance of reactors. Here, two acetate-fed replicate reactors were inoculated with acclimatized sludge and the reactor performance, and the granular sludge microbial community succession were studied for 149 days. During this time, the microbial community was challenged by periodically removing half of the reactor biomass, subsequently increasing the food-to-microorganism (F/M) ratio. Diversity analysis together with null models show that overall, the microbial communities were resistant to the disturbances, observing some minor effects on polyphosphate-accumulating and denitrifying microbial communities and their associated reactor functions. Community turnover was driven by drift and random granule loss, and stochasticity was the governing ecological process for community assembly. These results evidence the aerobic granular sludge process as a robust system for wastewater treatment.

Serine protease CrKP43 interacts with MAPK and regulates fungal development and mycoparasitism in Clonostachys chloroleuca

IMPORTANCE

Mycoparasites play important roles in the biocontrol of plant fungal diseases, during which they secret multiple hydrolases such as serine proteases to degrade their fungal hosts. In this study, we demonstrated that the serine protease CrKP43 was involved in C. chloroleuca development and mycoparasitism with the regulation of Crmapk. To the best of our knowledge, it is the first report on the functions and regulatory mechanisms of serine proteases in C. chloroleuca. Our findings will provide new insight into the regulatory mechanisms of serine proteases in mycoparasites and contribute to clarifying the mechanisms underlying mycoparasitism of C. chloroleuca, which will facilitate the development of highly efficient fungal biocontrol agents as well.

The Adenylate Cyclase-Encoding Gene crac Is Involved in Clonostachys rosea Mycoparasitism

Clonostachys rosea is an excellent biocontrol fungus against numerous fungal plant pathogens. The cAMP signaling pathway is a crucial signal transduction pathway in fungi. To date, the role of the cAMP signaling pathway in C. rosea mycoparasitism remains unknown. An adenylate cyclase-encoding gene, crac (an important component of the cAMP signaling pathway), was previously screened from C. rosea 67-1, and its expression level was dramatically upregulated during the C. rosea mycoparasitization of the sclerotia of Sclerotinia sclerotiorum. In this study, the function of crac in C. rosea mycoparasitism was explored through gene knockout and complementation. The obtained results show that the deletion of crac influenced the growth rate and colony morphology of C. rosea, as well as the tolerance to NaCl and H2O2 stress. The mycoparasitic effects on the sclerotia of S. sclerotiorum and the biocontrol capacity on soybean Sclerotinia stem rot in ∆crac-6 and ∆crac-13 were both attenuated compared with that of the wild-type strain and complementation transformants. To understand the regulatory mechanism of crac during C. rosea mycoparasitism, transcriptomic analysis was conducted between the wild-type strain and knockout mutant. A number of biocontrol-related genes, including genes encoding cell wall-degrading enzymes and transporters, were significantly differentially expressed during C. rosea mycoparasitism, suggesting that crac may be involved in C. rosea mycoparasitism by regulating the expression of these DEGs. These findings provide insight for further exploring the molecular mechanism of C. rosea mycoparasitism.

Production and characterization of lipopeptide biosurfactant from a new strain of Pseudomonas antarctica 28E using crude glycerol as a carbon source

Pseudomonas is a cosmopolitan genus of bacteria found in soil, water, organic matter, plants and animals and known for the production of glycolipid and lipopeptide biosurfactants. In this study bacteria (laboratory collection number 28E) isolated from soil collected in Spitsbergen were used for biosurfactant production. 16S rRNA sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) revealed that this isolate belongs to the species Pseudomonas antarctica. In the present study, crude glycerol, a raw material obtained from several industrial processes, was evaluated as a potential low-cost carbon source to reduce the costs of lipopeptide production. Among several tested glycerols, a waste product of stearin production, rich in nitrogen, iron and calcium, ensured optimal conditions for bacterial growth. Biosurfactant production was evidenced by a reduction of surface tension (ST) and an increase in the emulsification index (E24%). According to Fourier-transform infrared spectroscopy (FTIR) and electrospray ionization mass spectrometry (ESI-MS), the biosurfactant was identified as viscosin. The critical micelle concentration (CMC) of lipopeptide was determined to be 20 mg L-1. Interestingly, viscosin production has been reported previously for Pseudomonas viscosa, Pseudomonas fluorescens and Pseudomonas libanensis. To the best of our knowledge, this is the first report on viscosin production by a P. antarctica 28E. The results indicated the potential of crude glycerol as a low-cost substrate to produce a lipopeptide biosurfactant with promising tensioactive and emulsifying properties.

Transcriptomic Response of Clonostachys rosea Mycoparasitizing Rhizoctonia solani

Clonostachys rosea is an important mycoparasitism biocontrol agent that exhibits excellent control efficacy against numerous fungal plant pathogens. Transcriptomic sequencing may be used to preliminarily screen mycoparasitism-related genes of C. rosea against fungal pathogens. The present study sequenced and analyzed the transcriptome of C. rosea mycoparasitizing a Basidiomycota (phylum) fungal pathogen, Rhizoctonia solani, under three touch stages: the pre-touch stage, touch stage and after-touch stage. The results showed that a number of genes were differentially expressed during C. rosea mycoparasitization of R. solani. At the pre-touch stage, 154 and 315 genes were up- and down-regulated, respectively. At the touch stage, the numbers of up- and down-regulated differentially expressed genes (DEGs) were 163 and 188, respectively. The after-touch stage obtained the highest number of DEGs, with 412 and 326 DEGs being up- and down-regulated, respectively. Among these DEGs, ABC transporter-, glucanase- and chitinase-encoding genes were selected as potential mycoparasitic genes according to a phylogenetic analysis. A comparative transcriptomic analysis between C. rosea mycoparasitizing R. solani and Sclerotinia sclerotiorum showed that several DEGs, including the tartrate transporter, SDR family oxidoreductase, metallophosphoesterase, gluconate 5-dehydrogenase and pyruvate carboxylase, were uniquely expressed in C. rosea mycoparasitizing R. solani. These results significantly expand our knowledge of mycoparasitism-related genes in C. rosea and elucidate the mycoparasitism mechanism of C. rosea.

Glucose-6-phosphate 1-Epimerase CrGlu6 Contributes to Development and Biocontrol Efficiency in Clonostachys chloroleuca

Clonostachys chloroleuca (formerly classified as C. rosea) is an important mycoparasite active against various plant fungal pathogens. Mitogen-activated protein kinase (MAPK) signaling pathways are vital in mycoparasitic interactions; they participate in responses to diverse stresses and mediate fungal development. In previous studies, the MAPK-encoding gene Crmapk has been proven to be involved in mycoparasitism and the biocontrol processes of C. chloroleuca, but its regulatory mechanisms remain unclear. Aldose 1-epimerases are key enzymes in filamentous fungi that generate energy for fungal growth and development. By protein-protein interaction assays, the glucose-6-phosphate 1-epimerase CrGlu6 was found to interact with Crmapk, and expression of the CrGlu6 gene was significantly upregulated when C. chloroleuca colonized Sclerotinia sclerotiorum sclerotia. Gene deletion and complementation analyses showed that CrGlu6 deficiency caused abnormal morphology of hyphae and cells, and greatly reduced conidiation. Moreover, deletion mutants presented much lower antifungal activities and mycoparasitic ability, and control efficiency against sclerotinia stem rot was markedly decreased. When the CrGlu6 gene was reinserted, all biological characteristics and biocontrol activities were recovered. These findings provide new insight into the mechanisms of glucose-6-phosphate 1-epimerase in mycoparasitism and help to further reveal the regulation of MAPK and its interacting proteins in the biocontrol of C. chloroleuca.

Genetic Basis and Expression Pattern Indicate the Biocontrol Potential and Soil Adaption of Lysobacter capsici CK09

Lysobacter species have attracted increasing attention in recent years due to their capacities to produce diverse secondary metabolites against phytopathogens. In this research, we analyzed the genomic and transcriptomic patterns of Lysobacter capsici CK09. Our data showed that L. capsici CK09 harbored various contact-independent biocontrol traits, such as fungal cell wall lytic enzymes and HSAF/WAP-8294A2 biosynthesis, as well as several contact-dependent machineries, including type 2/4/6 secretion systems. Additionally, a variety of hydrolytic enzymes, particularly extracellular enzymes, were found in the L. capsici CK09 genome and predicted to improve its adaption in soil. Furthermore, several systems, including type 4 pili, type 3 secretion system and polysaccharide biosynthesis, can provide a selective advantage to L. capsici CK09, enabling the species to live on the surface in soil. The expression of these genes was then confirmed via transcriptomic analysis, indicating the activities of these genes. Collectively, our research provides a comprehensive understanding of the biocontrol potential and soil adaption of L. capsici CK09 and implies the potential of this strain for application in the future.

Natto: A medicinal and edible food with health function

Natto is a soybean product fermented by natto bacteria. It is rich in a variety of amino acids, vitamins, proteins and active enzymes. It has a number of biological activities, such as thrombolysis, prevention of osteoporosis, antibacterial, anticancer, antioxidant and so on. It is widely used in medicine, health-care food, biocatalysis and other fields. Natto is rich in many pharmacological active substances and has significant medicinal research value. This paper summarizes the pharmacological activities and applications of natto in and outside China, so as to provide references for further research and development of natto.

Revising Clonostachys and allied genera in Bionectriaceae

Clonostachys (Bionectriaceae, Hypocreales) species are common soil-borne fungi, endophytes, epiphytes, and saprotrophs. Sexual morphs of Clonostachys spp. were placed in the genus Bionectria, which was further segregated into the six subgenera Astromata, Bionectria, Epiphloea, Myronectria, Uniparietina, and Zebrinella. However, with the end of dual nomenclature, Clonostachys became the single depository for sexual and asexual morph-typified species. Species of Clonostachys are typically characterised by penicillate, sporodochial, and, in many cases, dimorphic conidiophores (primary and secondary conidiophores). Primary conidiophores are mononematous, either verticillium-like or narrowly penicillate. The secondary conidiophores generally form imbricate conidial chains that can collapse to slimy masses, particularly on sporodochia. In the present study, we investigated the species diversity within a collection of 420 strains of Clonostachys from the culture collection of, and personal collections at, the Westerdijk Fungal Biodiversity Institute in Utrecht, the Netherlands. Strains were analysed based on their morphological characters and molecular phylogeny. The latter used DNA sequence data of the nuclear ribosomal internal transcribed spacer regions and intervening 5.8S nrDNA (ITS) and partial 28S large subunit (LSU) nrDNA and partial protein encoding genes including the RNA polymerase II second largest subunit (RPB2), translation elongation factor 1-alpha (TEF1) and β-tubulin (TUB2). Based on these results, the subgenera Astromata, Bionectria, Myronectria and Zebrinella are supported within Clonostachys. Furthermore, the genus Sesquicillium is resurrected to accommodate the former subgenera Epiphloea and Uniparietina. The close relationship of Clonostachys and Sesquicillium is strongly supported as both are inferred phylogenetically as sister-genera. New taxa include 24 new species and 10 new combinations. Recognition of Sesquicillium distinguishes species typically forming a reduced perithecial stroma superficially on plant tissue from species in Clonostachys often forming well-developed, through bark erumpent stromata. The patterns of observed perithecial wall anatomies, perithecial wall and stroma interfaces, and asexual morph diversifications described in a previously compiled monograph are used for interpreting ancestral state reconstructions. It is inferred that the common ancestor of Clonostachys and Sesquicillium may have formed perithecia superficially on leaves, possessed a perithecial wall consisting of a single region, and formed intercalary phialides in penicilli of conidiophores. Character interpretation may also allow hypothesising that diversification of morphs occurred then in the two genera independently and that the frequently stroma-linked Clonostachys morphs evolved together with the occupation of woody host niches and mycoparasitism. Taxonomic novelties: New species: Clonostachys aurantiaca L. Zhao & Crous, Clonostachys australiana L. Zhao & Crous, Clonostachys bambusae L. Zhao & Crous, Clonostachys buxicola L. Zhao & Crous, Clonostachys cylindrica L. Zhao & Crous, Clonostachys ellipsoidea L. Zhao & Crous, Clonostachys flava L. Zhao, Crous & Schroers, Clonostachys fujianensis L. Zhao & Crous, Clonostachys fusca L. Zhao, Crous & Schroers, Clonostachys garysamuelsii L. Zhao & Crous, Clonostachys hongkongensis L. Zhao & Crous, Clonostachys longiphialidica L. Zhao, Crous & Schroers, Clonostachys obovatispora, L. Zhao & Crous, Clonostachys palmae L. Zhao, Crous & Schroers, Clonostachys parasporodochialis L. Zhao & Crous, Clonostachys penicillata L. Zhao, Crous & Schroers, Clonostachys reniformis L. Zhao & Crous, Clonostachys vacuolata L. Zhao, Crous & Schroers, Clonostachys venezuelae L. Zhao, Crous & Schroers, Mycocitrus synnematus L. Zhao & Crous, Nectriopsis didymii L. Zhao & Crous, Sesquicillium intermediophialidicum L. Zhao & Crous, Sesquicillium neerlandicum L. Zhao & Crous, Sesquicillium symmetricum L. Zhao & Crous. New combinations: Mycocitrus coccicola (J.A. Stev.) L. Zhao & Crous, Mycocitrus coxeniae (Y.P. Tan et al.) L. Zhao & Crous, Sesquicillium essexcoheniae (Y.P. Tan et al.) L. Zhao & Crous, Sesquicillium lasiacidis (Samuels) L. Zhao, Crous & Schroers, Sesquicillium phyllophilum (Schroers) L. Zhao, Crous & Schroers, Sesquicillium rossmaniae (Schroers) L. Zhao, Crous & Schroers, Sesquicillium saulense (Lechat & J. Fourn.) L. Zhao & Crous, Sesquicillium sesquicillii (Samuels) L. Zhao, Crous & Schroers, Sesquicillium spinulosisporum (Lechat & J. Fourn.) L. Zhao & Crous, Sesquicillium tornatum (Höhn.) Schroers. New synonyms: Clonostachys aranearum W.H. Chen et al., Clonostachys chuyangsinensis H. Yu & Y. Wang, Clonostachys eriocamporesiana R.H. Perera & K.D. Hyde, Clonostachys granuligera (Starbäck) Forin & Vizzini, Clonostachys indica Prasher & R. Chauhan, Clonostachys spinulosa R.H. Perera et al., Clonostachys squamuligera (Sacc.) Forin & Vizzini, Clonostachys wenpingii (J. Luo & W.Y. Zhuang) Z.Q. Zeng & W.Y. Zhuang. Epitypes (basionyms): Fusidium buxi J.C. Schmidt ex Link, Verticillium candelabrum Bonord. Citation: Zhao L, Groenewald JZ, Hernández-Restrepo M, Schroers H-J, Crous PW (2023). Revising Clonostachys and allied genera in Bionectriaceae. Studies in Mycology 105: 205-266. doi: 10.3114/sim.2023.105.03.

In vitro assessment for the probiotic potential of Pichia kudriavzevii

It is of interest to isolate the probiotic yeast Pichia kudriavzevii based on its probiotic characteristics and enzyme production. The isolate was able to withstand high acid, bile concentration and showed a high viability. Additionally, it showed auto aggregation ability that increases with time and hydrophobicity with xylene. It was resistant to different antibiotics and showed no hemolytic activity. The isolate was also capable of producing phytase that can break down phytate. Overall, the characteristics of P. kudriavzevii suggest that it could potentially have probiotic properties, and its ability to produce phytase could also make it useful in feed and animal industries.

Autodisplay of streptococcal protein G for construction of an orientation-controlled immunoaffinity layer

An immunoaffinity layer with orientation-controlled antibodies was constructed to express streptococcal protein G in Escherichia coli cells using autodisplay technology. The sequence of protein G, a specific IgG-binding protein, was inserted into the autodisplay vector using recombinant technology and the constructed plasmid vector was transformed into E. coli cells. Protein G was confirmed to be autodisplayed with a high density of 2 × 10⁵ copies per cell by SDS-PAGE analysis, and its IgG-binding affinity was confirmed by fluorescence microscopy. Autodisplayed protein G showed higher affinity than the IgG-binding Z-domain for goat IgG. Immunoassays based on E. coli cells were established to detect horseradish peroxidase (HRP) and C-reactive protein (CRP). Protein G autodisplaying E. coli cells were utilized as a solid support and immunoassays showed improved sensitivity by orientation control of autodisplayed protein G. The outer membrane (OM) of protein G autodisplaying E. coli was isolated and layered to construct an immunoaffinity layer. The OM was coated on a microplate to perform the immunoassays, which showed limits of detection of 5 and 0.2 ng mL^-1 for HRP and CRP, respectively. An OM layer with autodisplayed protein G was applied as the immunoaffinity layer of a surface plasmon resonance (SPR) biosensor. After CRP detection, the SPR responses showed good linearity, with an R² value of 0.99. The immunoaffinity layer with orientation control by autodisplayed protein G was confirmed to be applicable in immunoassays and immunosensors to improve sensitivity.

First Report of Clonostachys rosea as a Mycoparasite on Sclerotinia sclerotiorum Causing Head Rot of Cabbage in India

Clonostachys rosea, an ascomycetous, omnipresent, cellulose-decaying soil fungus, has been reported to be a well-known mycoparasitic biological control agent. In this study, we isolated C. rosea, a mycoparasitic fungus for the first time in India from sclerotia of the notorious plant pathogen Sclerotinia sclerotiorum, causing head rot disease in cabbage. A total of five mycoparasitic fungi were isolated from the sclerotial bodies of S. sclerotiorum (TNAU-CR 01, 02, 03, 04 and 05). All the isolates were tested under morpho-molecular characterization. Among them, TNAU-CR 02 showed the greatest mycelial inhibition of 79.63% over the control. Similarly, the SEM imaging of effective C. rosea isolates indicated the presence of numerous conidia destroying the outer cortex layers of sclerotia. Metabolite fingerprinting of C. rosea TNAU-CR 02 identified 18 chemical compounds using GC-MS analysis. The crude antibiotics of C. rosea TNAU-CR 02 were verified for their antifungal activity against S. sclerotiorum and the results revealed 97.17% mycelial inhibition compared with the control. Similarly, foliar application of TNAU-CR 02 at 5 mL/litre on 30, 45 and 60 days after transplanting showed the lowest disease incidence of 15.1 PDI compared to the control. This discovery expands our understanding of the biology and the dissemination of C. rosea, providing a way for the exploitation of C. rosea against cabbage head rot pathogens.

Insights into the ecological generalist lifestyle of Clonostachys fungi through analysis of their predicted secretomes

Introduction

The fungal secretome comprise diverse proteins that are involved in various aspects of fungal lifestyles, including adaptation to ecological niches and environmental interactions. The aim of this study was to investigate the composition and activity of fungal secretomes in mycoparasitic and beneficial fungal-plant interactions.

Methods

We used six Clonostachys spp. that exhibit saprotrophic, mycotrophic and plant endophytic lifestyles. Genome-wide analyses was performed to investigate the composition, diversity, evolution and gene expression of Clonostachys secretomes in relation to their potential role in mycoparasitic and endophytic lifestyles.

Results and discussion

Our analyses showed that the predicted secretomes of the analyzed species comprised between 7 and 8% of the respective proteomes. Mining of transcriptome data collected during previous studies showed that 18% of the genes encoding predicted secreted proteins were upregulated during the interactions with the mycohosts Fusarium graminearum and Helminthosporium solani. Functional annotation of the predicted secretomes revealed that the most represented protease family was subclass S8A (11-14% of the total), which include members that are shown to be involved in the response to nematodes and mycohosts. Conversely, the most numerous lipases and carbohydrate-active enzyme (CAZyme) groups appeared to be potentially involved in eliciting defense responses in the plants. For example, analysis of gene family evolution identified nine CAZyme orthogroups evolving for gene gains (p ≤ 0.05), predicted to be involved in hemicellulose degradation, potentially producing plant defense-inducing oligomers. Moreover, 8-10% of the secretomes was composed of cysteine-enriched proteins, including hydrophobins, important for root colonization. Effectors were more numerous, comprising 35-37% of the secretomes, where certain members belonged to seven orthogroups evolving for gene gains and were induced during the C. rosea response to F. graminearum or H. solani. Furthermore, the considered Clonostachys spp. possessed high numbers of proteins containing Common in Fungal Extracellular Membranes (CFEM) modules, known for their role in fungal virulence. Overall, this study improves our understanding of Clonostachys spp. adaptation to diverse ecological niches and establishes a basis for future investigation aiming at sustainable biocontrol of plant diseases.

Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer (Cervus albirostris)

The gut microbiota has key physiological functions in host adaptation, although little is known about the seasonal changes in the composition and diversity of the gut microbiota in deer. In this study, seasonal variations (grassy and withering season) in the gut microbiota of white-lipped deer (Cervus albirostris), which lives in alpine environments, were explored through 16S rRNA high-throughput sequencing based on sixteen fecal samples collected from Gansu Qilian Mountain National Nature Reserve in China. At the phylum level, Firmicutes, Bacteroidota, and Actinobacteriota dominated the grassy season, while Firmicutes, Proteobacteria, and Actinobacteriota dominated the withering season. At the genus level, Carnobacterium dominated the grassy season, while Arthrobacter and Acinetobacter dominated the withering season. Alpha diversity results (Shannon: P = 0.01, ACE: P = 0.00, Chao1: P = 0.00) indicated that there was a difference in the diversity and richness of the gut microbiota between the two seasons, with higher diversity in the grassy season than in the withering season. Beta diversity results further indicated that there was a significant difference in the community structure between the two seasons (P = 0.001). In summary, the composition, diversity, and community structure of the gut microbiota showed significant seasonal variations, which could be explained by variations in the seasonal food availability, composition, diversity, and nutrition due to phenological alternations. The results of this study indicate that the gut microbiota can adapt to changes in the environment and provide the scientific basis for health assessment of white-lipped deer.

Potential Bioactive Compounds from Marine Streptomyces sp. and Their In Vitro Antibiofilm and Antibacterial Activities Against Antimicrobial-Resistant Clinical Pathogens

Antimicrobial resistance issues have risen dramatically in recent years, posing a severe concern to humans worldwide. The urgent need to find novel compounds for pharmaceutical applications prompts the research of under-explored environments such as marine ecosystems. The present study was designed to discover novel secondary metabolites, and we have isolated about 30 actinomycetes from the marine soil samples collected in Thondi (Ramanathapuram, Tamil Nadu, India), where most isolates are associated with the genus Streptomyces. Out of 30, one potentially active strain (Streptomyces sp. SRMA3) was identified using primary and secondary screening methods against the drug-resistant clinical pathogens. The active metabolites extracted from the selected active isolate were subjected to partial purification and characterization using Fourier transform infrared spectrophotometer (FTIR) and gas chromatography-mass spectroscopy (GC-MS) analysis. The minimum inhibitory concentration (MIC) value was determined for the active metabolite. Further, the partially purified active fraction was revealed for its antibacterial and antibiofilm activity against drug-resistant clinical pathogens. Light and fluorescence microscopy detected the viability and adhesion of the biofilm-forming drug-resistant pathogens. Growth curve analysis showed that the active metabolite has the potential to inhibit drug-resistant pathogens. The synergistic effect of active metabolite with commercial antibiotics also revealed that it could enhance the activity of antibiotics in antimicrobial resistance pathogens. This study shows that the isolated Streptomyces sp. SRMA3 is a potentially active strain, and the metabolite derived from this strain has a good antibacterial and antibiofilm activity against antimicrobially resistant clinical pathogens and could be used for various biotechnological applications.

The Effect of Pimpinella Anisum and Origanum Vulgare Extracts Against Streptococcus Sanguinis, Streptococcus Mutans, and Streptococcus Salivarius

Statement of the Problem

There are global efforts for introducing a new herbal antimicrobial agent with minimal side effects. There are some reports about the antimicrobial properties of Pimpinella anisum and Oregano Vulgare.

Purpose

In this study, the antimicrobial properties of Pimpinella anisum and Oregano Vulgare have been assessed.

Material and Method

In this experimental in vitro study, the dental plaque samples were collected from children aged 3 to 5 years old who were referred to a private dental office with diagnosis of dental caries. After determination of the bacterial colonies of Streptococcus sanguinis, Streptococcus mutans and Streptococcus salivarius, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of ethanolic and methanolic extracts of Pimpinella anisum and Oregano vulgare were measured by macrodilution and microdilution methods.

Results

The mean MIC and MBC of Pimpinella anisum extract and Oregano vulgare extract and their combination against Streptococcus mutans, Streptococcus sanguinis, and Streptococcus salivarius were statistically different (p< 0.001). The combination of these extracts showed the lowest MIC and MBC.

Conclusion

Hydroalcoholic extracts of the Pimpinella anisum and Oregano Vulgare were effective antibacterial agent against Streptococcus mutans, Streptococcus salivarius, and Streptococcus sanguinis so the combination of these two extracts showed the highest antibacterial properties on all the bacteria evaluated.

Comprehensive Review on Applications of Surfactants in Vaccine Formulation, Therapeutic and Cosmetic Pharmacy and Prevention of Pulmonary Failure due to COVID-19

Our world is under serious threat of environmental degradation, climate change and in association with this the out breaks of diseases as pandemics. The devastating impact of the very recent COVID-19, The sharp increase in cases of Cancer, Pulmonary failure, Heart health has triggered questions for the sustainable development of pharmaceutical and medical sciences. In the search of inclusive and effective strategies to meet today’s demand, improvised methodologies and alternative green chemical, bio-based precursors are being introduced by scientists around the globe. In this extensive review we have presented the potentiality and Realtime applications of both synthetic and bio-based surfactants in bio-medical and pharmaceutical fields. For their excellent unique amphoteric nature and ability to solubilise in both organic and inorganic drugs, surfactants are one of the most potential candidates for bio-medicinal fields such as dermatology, drug delivery, anticancer treatment, surfactant therapy, vaccine formulation, personal hygiene care and many more. The self-assembly property of surfactants is a very powerful function for drug delivery systems that increases the bio-availability of the poorly aqueous soluble pharmaceutical products by influencing their solubility. Over the decades many researchers have reported the antimicrobial, anti-adhesive, antibiofilm, anti-inflammatory, antioxidant activities of surfactants regarding its utility in medicinal purposes. In some reports surfactants are found to have spermicidal and laxative activity too. This comprehensive report is targeted to enlighten the versatile applications of Surfactants in drug delivery, vaccine formulation, Cancer Treatment, Therapeutic and cosmetic Pharmaceutical Sciences and prevention of pulmonary failure due to COVID-19.

Monitoring Mycoparasitism of Clonostachys rosea against Botrytis cinerea Using GFP

Clonostachys rosea is an important mycoparasite, with great potential for controlling numerous plant fungal diseases. Understanding the mechanisms and modes of action will assist the development and application of this biocontrol fungus. In this study, the highly efficient C. rosea 67-1 strain was marked with the green fluorescent protein (GFP), and the transformant possessed the same biological characteristics as the wild-type strain. Fungal interactions with Botrytis cinerea during co-culture and encounter on tomato leaves were assessed by fluorescence confocal and electron microscopy. The results indicated that once the two fungi met, the hyphae of C. rosea grew alongside those of B. cinerea, then attached tightly to the host and developed special structures, via which the biocontrol fungus penetrated the host and absorbed nutrients, eventually disintegrating the cells of the pathogen. Mycoparasitism to B. cinerea was also observed on tomato leaves, suggesting that C. rosea can colonize on plants and act following the invasion of the pathogenic fungus.

Influence of cerium oxide nanoparticles on dairy effluent nitrate and phosphate bioremediation

This study investigated, for the first time, the role of cerium oxide nanoparticles (CeO2 NPs) on dairy effluent nitrate and phosphate bioremediation using different inoculum sources. Two inoculum sources (wastewater and sludge) were obtained from the dairy wastewater treatment plant unit. A culture was prepared to be tested in the treatment of nitrate and phosphate effluent, and the role of CeO2 NPs was checked to be completely efficient after 5 days of incubation. The reduction efficiency of nitrate using sludge as inoculum source was improved up to 89.01% and 68.12% for phosphate compared to control. In the case of using wastewater as an inoculum source, the nitrate reduction was improved up to 83.30% and 87.75% for phosphate compared to control. The bacterial richness showed a significant variance (higher richness) between control and other samples. The optimal concentration of CeO2 NPs for inoculum richness and nitrate and phosphate reduction was (sludge: 1 × 10-10 ppm) and (wastewater: 1 × 10-12 ppm). The results revealed that CeO2 NPs could enhance the microbial growth of different inoculum sources that have a key role in dairy effluent nitrate and phosphate bioremediation.

Altering the fatty acid profile of Yarrowia lipolytica to mimic cocoa butter by genetic engineering of desaturases

Background

Demand for Cocoa butter is steadily increasing, but the supply of cocoa beans is naturally limited and under threat from global warming. One route to meeting the future demand for cocoa butter equivalent (CBE) could be to utilize microbial cell factories such as the oleaginous yeast Yarrowia lipolytica.

Results

The main goal was to achieve triacyl-glycerol (TAG) storage lipids in Y. lipolytica mimicking cocoa butter. This was accomplished by replacing the native Δ9 fatty acid desaturase (Ole1p) with homologs from other species and changing the expression of both Ole1p and the Δ12 fatty acid desaturase (Fad2p). We thereby abolished the palmitoleic acid and reduced the linoleic acid content in TAG, while the oleic acid content was reduced to approximately 40 percent of the total fatty acids. The proportion of fatty acids in TAG changed dramatically over time during growth, and the fatty acid composition of TAG, free fatty acids and phospholipids was found to be very different.

Conclusions

We show that the fatty acid profile in the TAG of Y. lipolytica can be altered to mimic cocoa butter. We also demonstrate that a wide range of fatty acid profiles can be achieved while maintaining good growth and high lipid accumulation, which, together with the ability of Y. lipolytica to utilize a wide variety of carbon sources, opens up the path toward sustainable production of CBE and other food oils.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01748-x.

A survey of Methylobacterium species and strains reveals widespread production and varying profiles of cytokinin phytohormones

Background

Symbiotic Methylobacterium strains comprise a significant part of plant microbiomes. Their presence enhances plant productivity and stress resistance, prompting classification of these strains as plant growth-promoting bacteria (PGPB). Methylobacteria can synthesize unusually high levels of plant hormones, called cytokinins (CKs), including the most active form, trans-Zeatin (tZ).

Results

This study provides a comprehensive inventory of 46 representatives of Methylobacterium genus with respect to phytohormone production in vitro, including 16 CK forms, abscisic acid (ABA) and indole-3-acetic acid (IAA). High performance-liquid chromatography—tandem mass spectrometry (HPLC–MS/MS) analyses revealed varying abilities of Methylobacterium strains to secrete phytohormones that ranged from 5.09 to 191.47 pmol mL⁻¹ for total CKs, and 0.46 to 82.16 pmol mL⁻¹ for tZ. Results indicate that reduced methanol availability, the sole carbon source for bacteria in the medium, stimulates CK secretion by Methylobacterium. Additionally, select strains were able to transform L-tryptophan into IAA while no ABA production was detected.

Conclusions

To better understand features of CKs in plants, this study uncovers CK profiles of Methylobacterium that are instrumental in microbe selection for effective biofertilizer formulations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02454-9.

Influence of selected factors on the Firmicutes, Bacteroidetes phyla and the Lactobacillaceae family in the digestive tract of sheep

In this study, we used 10 healthy sheep, which gave birth to healthy twins. Stool samples were collected from mothers and their offspring 3 times during the study (0, 28 and 56 day postpartum). Milk samples were taken from the mothers at the same time. RT PCR analysis of faeces and milk was performed in order to assess the level of bacteria from the Firmicutes and Bacteroidetes phyla including the family Lactobacillaceae (phylum Firmicutes). The composition of mother's milk was also analyzed and their BCS. The data were compiled statistically. The obtained results showed that the level of the studied groups of bacteria may change due to the change of diet. Additionally, there were significant differences between lambs and mothers in the levels of the studied groups of bacteria. Analysis also shown that in the digestive system of mothers was a smaller disproportion in the level of the studied bacterial phyla than in lambs. The results also indicated the occurrence of differences in the bacterial composition at the individual level, both in ewes and their offspring. Additionally, in the conducted experiment, there were differences in the level of Firmicutes and Bacteroidetes groups depending on the sex.

State of the art of urine treatment technologies: A critical review

Over the last 15 years, urine treatment technologies have developed from lab studies of a few pioneers to an interesting innovation, attracting attention from a growing number of process engineers. In this broad review, we present literature from more than a decade on biological, physical-chemical and electrochemical urine treatment processes. Like in the first review on urine treatment from 2006, we categorize the technologies according to the following objectives: stabilization, volume reduction, targeted N-recovery, targeted P-recovery, nutrient removal, sanitization, and handling of organic micropollutants. We add energy recovery as a new objective, because extensive work has been done on electrochemical energy harvesting, especially with bio-electrochemical systems. Our review reveals that biological processes are a good choice for urine stabilization. They have the advantage of little demand for chemicals and energy. Due to instabilities, however, they are not suited for bathroom applications and they cannot provide the desired volume reduction on their own. A number of physical-chemical treatment technologies are applicable at bathroom scale and can provide the necessary volume reduction, but only with a steady supply of chemicals and often with high demand for energy and maintenance. Electrochemical processes is a recent, but rapidly growing field, which could give rise to exciting technologies at bathroom scale, although energy production might only be interesting for niche applications. The review includes a qualitative assessment of all unit processes. A quantitative comparison of treatment performance was not the goal of the study and could anyway only be done for complete treatment trains. An important next step in urine technology research and development will be the combination of unit processes to set up and test robust treatment trains. We hope that the present review will help guide these efforts to accelerate the development towards a mature technology with pilot scale and eventually full-scale implementations.

Biodegradation of waste cooking oil and simultaneous production of rhamnolipid biosurfactant by Pseudomonas aeruginosa P7815 in batch and fed-batch bioreactor

Biosurfactants are non-toxic, surface-active biomolecules capable of reducing surface tension (ST) and emulsifying interface at a comparably lower concentration than commercial surfactants. Yet, poor yield, costlier substrates, and complex cultivation processes limit their commercial applications. This study focuses on producing biosurfactants by Pseudomonas aeruginosa P7815 in batch and fed-batch bioreactor systems using waste cooking oil (WCO) as the sole carbon source. The batch study showed a 92% of WCO biodegradation ability of P. aeruginosa producing 11 g L^-1 of biosurfactant. To enhance this biosurfactant production, a fed-batch oil feeding strategy was opted to extend the stationary phase of the bacterium and minimize the effects of substrate deprivation. An enhanced biosurfactant production of 16 g L^-1 (i.e. 1.5 times of batch study) was achieved at a feed rate of 5.7 g L^-1d^-1 with almost 94% of WCO biodegradation activity. The biosurfactant was characterized as rhamnolipid using Fourier transform infrared spectroscopy (FTIR), and its interfacial characterization showed ST reduction to 29 ± 1 mN m^-1 and effective emulsification stability at pH value of 4, temperature up to 40 °C and salinity up to 40 g L^-1. The biosurfactant exhibited antibacterial activity with minimum inhibitory concentration (MIC) values of 100 µg mL^-1 and 150 µg mL^-1 for pathogenic E. hirae and E. coli, respectively. These findings suggest that biodegradation of WCO by P. aeruginosa in a fed-batch cultivation strategy is a potential alternative for the economical production of biosurfactants, which can be further explored for biomedical, cosmetics, and oil washing/recovery applications.

Biosynthesis of polyunsaturated fatty acids by two newly cold-adapted Egyptian marine yeast

The widespread awareness of polyunsaturated fatty acids (PUFAs) benefits for human health has increased the need for their commercial production. Two oleaginous yeast were isolated from the Mediterranean Sea fish and Red Sea fish Epinephelus aeneus and E. areolatus, respectively. These marine candidates were identified by MALDI-TOF/MS biotyper^® as Lodderomyces elongisporus and Rhodotorula mucilaginosa. The effect of incubation temperature (7, 15, and 26 °C) and glucose concentration (3% and 8%) on their lipids content were investigated using Sulfo-Phospho-Vanillin (SPV) assay. Their intercellular lipids were visualized by fluorescence microscope using Nile-Red dye. L. elongisporus and R. mucilaginosa produced 20.04% and 26.79% of Linoleic acid, respectively, on normal Basal-Defatted Medium (BDM). Linoleic acid (21.4-22.7%) and α-Linolenic acid (7.5-10.8%) were produced by R. mucilaginosa and L. elongisporus, on normal BDM at 15 °C. High-Glucose BDM induced a positive effect on the total lipids production that reached its maximum of 48% and 54% by R. mucilaginosa and L. elongisporus, respectively, grown at 15 °C. Remarkably, 12.12% of long-chain 15-Docosenoic acid (C_22:1) and 21.49% of Tricosanoic acid (C_23:0) were detected in the FAs profile of L. elongisporus, when grown on normal BDM at 26 °C. The present study is the first one reporting the FAs profile of the Egyptian Marine L. elongisporus, and its capability to accumulate high amounts of lipids under appropriate fermentation conditions; thus, it could be considered for scaling up production.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03010-4.

Valorization of date juice by the production of lipopeptide biosurfactants by a Bacillus mojavensis BI2 strain: bioprocess optimization by response surface methodology and study of surface activities

Lipopeptides biosurfactants (BioS) are natural surface-active compounds produced by a variety of microorganisms. They have great interest in environmental, biomedical and agro-industrial fields. However their large-scale application and production is limited by the cost of culture media and the low yield of production. Therefore, the improvement of the production yields and the development of efficient and cost-effective bioprocess became of a great interest. In this aim, we applied the response surface method to optimize an economic BioS production by a newly isolated strain Bacillus mojavensis BI2 on date Juice called "Luegmi" as unique carbon and nitrogen source. Using a Box-Bhenken design, we studied the effect of three independent variables on lipopeptide production; Leugmi concentration, Na₂HPO₄ and incubation time. The results of this study showed that Leugmi concentration at 25%, Na₂HPO₄ at 0.1% and incubation time of 24 h were optimal conditions for BioS  production, with a maximum Surface Tension (ST) decreasing capacity of 55% corresponding to 27 mN/m and an Oil Dispersing Activity (ODA) of 30 cm² corresponding to a diameter of 6 cm. Preliminary characterization of the BioS produced on Luegmi by UV-Spectra and Thin Layer Chromatography showed its lipopeptide nature. Physic-chemical characterization of the produced lipopeptide on Leugmi showed its great surface activities and stabilities at different pH, temperature and salts concentration. The results of this study suggested that Leugmi, an agricultural byproducts can be used as a low-cost substrate to enhance the yield of lipopeptide BioS with great surface activities for potential environmental application.

Rhodosporidium sp. DR37: a novel strain for production of squalene in optimized cultivation conditions

BACKGROUND

Rhodosporidium strain, a well-known oleaginous yeast, has been widely used as a platform for lipid and carotenoid production. However, the production of squalene for application in lipid-based biofuels is not reported in this strain. Here, a new strain of Rhodosporidium sp. was isolated and identified, and its potential was investigated for production of squalene under various cultivation conditions.

RESULTS

In the present study, Rhodosporidium sp. DR37 was isolated from mangrove ecosystem and its potential for squalene production was assessed. When Rhodosporidium sp. DR37 was cultivated on modified YEPD medium (20 g/L glucose, 5 g/L peptone, 5 g/L YE, seawater (50% v/v), pH 7, 30 °C), 64 mg/L of squalene was produced. Also, squalene content was obtained as 13.9% of total lipid. Significantly, use of optimized medium (20 g/L sucrose, 5 g/L peptone, seawater (20% v/v), pH 7, 25 °C) allowed highest squalene accumulation (619 mg/L) and content (21.6% of total lipid) in Rhodosporidium sp. DR37. Moreover, kinetic parameters including maximum specific cell growth rate (μ_max, h^-1), specific lipid accumulation rate (q_p, h^-1), specific squalene accumulation rate (q_sq, h^-1) and specific sucrose consumption rate (q_s, h^-1) were determined in optimized medium as 0.092, 0.226, 0.036 and 0.010, respectively.

CONCLUSIONS

This study is the first report to employ marine oleaginous Rhodosporidium sp. DR37 for accumulation of squalene in optimized medium. These findings provide the potential of Rhodosporidium sp. DR37 for production of squalene as well as lipid and carotenoids for biofuel applications in large scale.

Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota, Hypocreales)

Various strains of the mycoparasitic fungal species Clonostachys rosea are used commercially as biological control agents for the control of fungal plant diseases in agricultural crop production. Further improvements of the use and efficacy of C. rosea in biocontrol require a mechanistic understanding of the factors that determines the outcome of the interaction between C. rosea and plant pathogenic fungi. Here, we determined the genome sequences of 11 Clonostachys strains, representing five species in Clonostachys subgenus Bionectria, and performed a comparative genomic analysis with the aim to identify gene families evolving under selection for gene gains or losses. Several gene families predicted to encode proteins involved in biosynthesis of secondary metabolites, including polyketide synthases, nonribosomal peptide syntethases and cytochrome P450s, evolved under selection for gene gains (p ≤ .05) in the Bionectria subgenus lineage. This was accompanied with gene copy number increases (p ≤ .05) in ATP-binding cassette (ABC) transporters and major facilitator superfamily (MFS) transporters predicted to contribute to drug efflux. Most Clonostachys species were also characterized by high numbers of auxiliary activity (AA) family 9 lytic polysaccharide monooxygenases, AA3 glucose-methanol-choline oxidoreductases and additional carbohydrate-active enzyme gene families with putative activity (or binding) towards xylan and rhamnose/pectin substrates. Particular features of the C. rosea genome included expansions (p ≤ .05) of the ABC-B4 multidrug resistance transporters, the ABC-C5 multidrug resistance-related transporters and the 2.A.1.3 drug:H + antiporter-2 MFS drug resistance transporters. The ABC-G1 pleiotropic drug resistance transporter gene abcG6 in C. rosea was induced (p ≤ .009) by exposure to the antifungal Fusarium mycotoxin zearalenone (1121-fold) and various fungicides. Deletion of abcG6 resulted in mutants with reduced (p < .001) growth rates on media containing the fungicides boscalid, fenhexamid and iprodione. Our results emphasize the role of biosynthesis of, and protection against, secondary metabolites in Clonostachys subgenus Bionectria.

Design and characterization of a SYBR Green I-based melting curve method for investigation of HER2I655V polymorphism in breast cancer

Background

Breast cancer is a disease in which cell grows rapidly forming a mass in the breast. HER2 polymorphisms Ile655Val have been studied as biomarkers for breast cancer and may comprise a risk factor of cardiac toxicity for breast cancer-consuming trastuzumab. Aim of work: In this study, we developed a simple, low cost, and rapid test to detect polymorphism at HER2 gene using SYBR Green I-based melting curve method.

Subjects and methods

In this report, we performed allelic discrimination with real-time temperature melting (Tm) Shift SYBR Green I-based melting curve method. The melting profiles of amplified DNA HER-2 Ile655Val and its characteristics were analyzed.

Result

Tm value of HER2 GG and AA alleles were 85 ± 0.14 °C and 82.5 ± 0.23 °C, respectively, while cycle threshold (Ct) value of GG, AG, and AA alleles were 19.6 ± 0.27, 22.5 ± 0.23, 18.6 ± 0.22 correspondingly; furthermore, no template control has shown consisting Ct value at 31.18 ± 0.27. The developed methods’ characteristics were optimum annealing at 62 °C and Kappa coefficient value 1 with the mean almost consistent with PCR-sequencing. The coefficient of variability for intra-assay of GG, AG, and AA was in the range of 0.2–1%, while the coefficient of variability for inter-assay for each were in the range 0.7–1%. Further, based on PCR, shelf-life assay has shown stability for 3 months of storage observation.

Conclusion

This approach may be considered as simple, rapid, and low cost supporting the rapid study of HER2 epidemiology. Furthermore, the developed methods potentially facilitate clinicians in dealing with breast cancer patients, especially in considering about the cardiotoxicity effect of trastuzumab.

Cell Wall Biogenesis Protein Phosphatase CrSsd1 Is Required for Conidiation, Cell Wall Integrity, and Mycoparasitism in Clonostachys rosea

Cell wall biogenesis protein phosphatases play important roles in various cellular processes in fungi. However, their functions in the widely distributed mycoparasitic fungus Clonostachys rosea remain unclear, as do their potential for controlling plant fungal diseases. Herein, the function of cell wall biogenesis protein phosphatase CrSsd1 in C. rosea 67-1 was investigated using gene disruption and complementation approaches. The gene-deficient mutant ΔCrSsd1 exhibited much lower conidiation, hyphal growth, mycoparasitic ability, and biocontrol efficacy than the wild-type (WT) strain, and it was more sensitive to sorbitol and Congo red. The results indicate that CrSsd1 is involved in fungal conidiation, osmotic stress adaptation, cell wall integrity, and mycoparasitism in C. rosea.

Geobiochemistry characteristics of rare earth elements in soil and ground water: a case study in Baotou, China

The distribution of rare earth elements and the microbial community in nearby ground water and soil were influenced by tailings ponds. Accordingly, the behaviors of rare earth elements in ground water and soil around the tailings pond, and the changes of microbial communities were both investigated in this study. The results showed that rare earth elements accumulated in ground water and soil around the tailings pond appeared as light rare earth elements enrichment. Through the normalization of rare earth elements, different extents of anomaly (from negative to positive) were observed for Ce and Eu in the distribution patterns of REEs in groundwater, however, Ce and Eu were negatively anomaly in soil. According to the correlation analysis, Mn²⁺, SO₄^2-, Cl^-, ammonia nitrogen and Ca²⁺ are significantly correlated with the distribution of rare earth elements. Meanwhile, there were the same dominant bacteria in ground water and soil including Actinobateria, Proteobacteria and Acidobacteria at the phylum level. This microbial community composition is similar to that reported in arid lands around the world. On the other hand, Bacillus and Blastococcus showed significant correlation with rare earth elements at the genus level. This study might provide an important basis for the risk assessment of REEs in the environment.

Utilization of brewery wastes in food industry

Beer is the most popular low-alcohol beverage consumed in large amounts in many countries each year. The brewing industry is an important global business with huge annual revenues. It is profitable and important for the economies of many countries around the world. The brewing process involves several steps, which lead to fermentation of sugars contained in malt and conversion thereof into alcohol and carbon dioxide by yeasts. Beer brewing generates substantial amounts of by-products. The three main brewing industry wastes include brewer's spent grain, hot trub, and residual brewer's yeast. Proper management of these wastes may bring economical benefits and help to protect the environment from pollution caused by their excessive accumulation. The disposal of these wastes is cumbersome for the producers, however they are suitable for reuse in the food industry. Given their composition, they can serve as a low-cost and highly nutritional source of feed and food additives. They also have a potential to be a cheap material for extraction of compounds valuable for the food industry and a component of media used in biotechnological processes aimed at production of compounds and enzymes relevant for the food industry.

The Mitogen-Activated Protein Kinase Gene Crmapk Is Involved in Clonostachys chloroleuca Mycoparasitism

Clonostachys chloroleuca is a mycoparasite used for biocontrol of numerous fungal plant pathogens. Sequencing of the transcriptome of C. chloroleuca following mycoparasitization of the sclerotia of Sclerotinia sclerotiorum revealed significant upregulation of a mitogen-activated protein kinase (MAPK)-encoding gene, crmapk. Although MAPKs are known to regulate fungal growth and development, the function of crmapk in C. chloroleuca mycoparasitism is unclear. In this study, we investigated the role of crmapk in C. chloroleuca mycoparasitism through gene knockout and complementation. Deletion of crmapk had no influence on the C. chloroleuca morphological characteristics but could significantly reduce the mycoparasitic ability to sclerotia and biocontrol capacity to soybean Sclerotinia stem rot; crmapk complementation restored these abilities. Transcriptome analysis between Δcrmapk and the wild-type strain revealed numerous genes were significantly down-regulated after crmapk deletion, including cytochrome P450, transporters, and cell wall-degrading enzymes (CWDEs). Our findings indicate that crmapk influences C. chloroleuca mycoparasitism by regulation of genes controlling the activity of CWDEs or antibiotic production. This study provides a basis for further studies of the molecular mechanism of C. chloroleuca mycoparasitism.

Transcriptomic and Exometabolomic Profiling Reveals Antagonistic and Defensive Modes of Clonostachys rosea Action Against Fusarium graminearum

The mycoparasite Clonostachys rosea ACM941 is under development as a biocontrol organism against Fusarium graminearum, the causative agent of Fusarium head blight in cereals. To identify molecular factors associated with this interaction, the transcriptomic and exometabolomic profiles of C. rosea and F. graminearum GZ3639 were compared during coculture. Prior to physical contact, the antagonistic activity of C. rosea correlated with a response heavily dominated by upregulation of polyketide synthase gene clusters, consistent with the detected accumulation of corresponding secondary metabolite products. Similarly, prior to contact, trichothecene gene clusters were upregulated in F. graminearum, while those responsible for fusarielin and fusarin biosynthesis were downregulated, correlating with an accumulation of trichothecene products in the interaction zone over time. A concomitant increase in 15-acetyl deoxynivalenol-3-glucoside in the interaction zone was also detected, with C. rosea established as the source of this detoxified mycotoxin. After hyphal contact, C. rosea was found to predominantly transcribe genes encoding cell wall-degradation enzymes, major facilitator superfamily sugar transporters, anion:cation symporters, as well as alternative carbon source utilization pathways, together indicative of a transition to necrotropism at this stage. F. graminearum notably activated the transcription of phosphate starvation pathway signature genes at this time. Overall, a number of signature molecular mechanisms likely contributing to antagonistic activity by C. rosea against F. graminearum, as well as its mycotoxin tolerance, are identified in this report, yielding several new testable hypotheses toward understanding the basis of C. rosea as a biocontrol agent for continued agronomic development and application.

LysM Proteins Regulate Fungal Development and Contribute to Hyphal Protection and Biocontrol Traits in Clonostachys rosea

Lysin motif (LysM) modules are approximately 50 amino acids long and bind to peptidoglycan, chitin and its derivatives. Certain LysM proteins in plant pathogenic and entomopathogenic fungi are shown to scavenge chitin oligosaccharides and thereby dampen host defense reactions. Other LysM proteins can protect the fungal cell wall against hydrolytic enzymes. In this study, we investigated the biological function of LysM proteins in the mycoparasitic fungus Clonostachys rosea. The C. rosea genome contained three genes coding for LysM-containing proteins and gene expression analysis revealed that lysm1 and lysm2 were induced during mycoparasitic interaction with Fusarium graminearum and during colonization of wheat roots. Lysm1 was suppressed in germinating conidia, while lysm2 was induced during growth in chitin or peptidoglycan-containing medium. Deletion of lysm1 and lysm2 resulted in mutants with increased levels of conidiation and conidial germination, but reduced ability to control plant diseases caused by F. graminearum and Botrytis cinerea. The Δlysm2 strain showed a distinct, accelerated mycelial disintegration phenotype accompanied by reduced biomass production and hyphal protection against hydrolytic enzymes including chitinases, suggesting a role of LYSM2 in hyphal protection against chitinases. The Δlysm2 and Δlysm1Δlysm2 strains displayed reduced ability to colonize wheat roots, while only Δlysm1Δlysm2 failed to suppress expression of the wheat defense response genes PR1 and PR4. Based on our data, we propose a role of LYSM1 as a regulator of fungal development and of LYSM2 in cell wall protection against endogenous hydrolytic enzymes, while both are required to suppress plant defense responses. Our findings expand the understanding of the role of LysM proteins in fungal-fungal interactions and biocontrol.

Biology and applications of Clonostachys rosea

Clonostachys rosea is a promising saprophytic filamentous fungus that belongs to phylum Ascomycota. Clonostachys rosea is widespread around the world and exists in many kinds of habitats, with the highest frequency in soil. As an excellent mycoparasite, C. rosea exhibits strong biological control ability against numerous fungal plant pathogens, nematodes and insects. These behaviours are based on the activation of multiple mechanisms such as secreted cell-wall-degrading enzymes, production of antifungal secondary metabolites and induction of plant defence systems. Besides having significant biocontrol activity, C. rosea also functions in the biodegradation of plastic waste, biotransformation of bioactive compounds, as a bioenergy sources and in fermentation. This mini review summarizes information about the biology and various applications of C. rosea and expands on its possible uses.

A Novel Totivirus Naturally Occurring in Two Different Fungal Genera

Mycoviruses are widely distributed across different phyla of the fungal kingdom. Viruses that share significant sequence similarities have been reported in different fungi, suggesting descent from a common ancestor. In this study, two fungal genera isolated from the same sample, Trichoderma koningiopsis isolate Mg10 and Clonostachys rosea isolate Mg06, were reported to have identical double-stranded RNA (dsRNA) profiles that consist of two virus-like, dsRNA elements (dsRNA-L and dsRNA-S). The complete sequence and genome organization of dsRNA-L from isolate Mg10 was determined. It is 4712 nucleotides (nt) long and contains two non-overlapping open reading frames (ORFs) that code for proteins with similarities to totiviruses. Consequently the virus was given the proposed name Trichoderma koningiopsis totivirus 1 (TkTV1/Mg10). The TkTV1/Mg10 genome structure resembles that of yeast totiviruses in which the region preceding the stop codon of ORF1 contains the elements required for -1 ribosomal frameshifting which may induce the expression of an ORF1–ORF2 (CP-RdRp) fusion protein. Sequence analyses of viral dsRNA-L from C. rosea isolate Mg06 revealed that it is nearly identical with that of TkTV1/Mg10. This relatedness was confirmed by northern blot hybridization and indicates very recent natural horizontal transmission of this virus between unrelated fungi. TkTV1 purified isometric virions were ∼38–40 nm in diameter and were able to transfect T. koningiopsis and C. rosea protoplasts. This is another report of a mycovirus present naturally in two taxonomically distinct fungi.

Antifungal, Plant Growth-Promoting, and Genomic Properties of an Endophytic Actinobacterium Streptomyces sp. NEAU-S7GS2

Diseases caused by Sclerotinia sclerotiorum have caused severe losses of many economically important crops worldwide. Due to the long-term persistence of sclerotia in soil and the production of air-borne ascospores, synthetic fungicides play limited roles in controlling the diseases. The application of antagonistic microorganisms can effectively reduce the number of sclerotia and eventually eradicate S. sclerotiorum from soil, and therefore considerable interest has been focused on biological control. Streptomyces sp. NEAU-S7GS2 was isolated from the root of Glycine max and its rhizosphere soil. It showed significant inhibitory activity against the mycelial growth of S. sclerotiorum (99.1%) and completely inhibited sclerotia germination. Compared to the control, in the pot experiment the application of NEAU-S7GS2 not only demonstrated excellent potential to control sclerotinia stem rot of soybean with 77 and 38% decrease in disease incidence and disease index, respectively, but could promote the growth of soybean. The light microscopy and scanning electron microscopy showed that co-culture of NEAU-S7GS2 with S. sclerotiorum on potato dextrose agar could lead to contorted and fragmented mycelia of S. sclerotiorum, which was associated with the secretion of hydrolytic glucanase and cellulase and the production of active secondary metabolites by NEAU-S7GS2. The plant growth promoting activity of NEAU-S7GS2 was related to the solubilization of inorganic phosphate, and production of 1-aminocyclopropane-1-carboxylate (ACC) deaminase and indole acetic acid (IAA). To further explore the plant growth promoting and antifungal mechanisms, the complete genome of strain NEAU-S7GS2 was sequenced. Several genes associated with ammonia assimilation, phosphate solubilization and IAA synthesis, together with genes encoding ACC deaminase, glucanase and α-amylase, were identified. AntiSMASH analysis led to the identification of four gene clusters responsible for the biosynthesis of siderophores including desferrioxamine B and enterobactin. Moreover, the biosynthetic gene clusters of lydicamycins, phenazines, and a glycosylated polyol macrolide showing 88% gene similarity to PM100117/PM100118 were identified. These results suggested that strain NEAU-S7GS2 may be a potential biocontrol agent and biofertilizer used in agriculture.

The heat shock protein 70 gene is involved for colony morphology, sporulation and mycoparasitism of Clonostachys rosea

Heat shock protein 70 (HSP70) is an evolutionarily conserved chaperone protein. However, the role of HSP70 in mycoparasitism is unclear. Clonostachys rosea shows great potential against plant fungal pathogens. An HSP70 encoding gene, crhsp, from C. rosea 67-1 was significantly upregulated during C. rosea parasitization of the sclerotia of Sclerotinia sclerotiorum. In the present study, we investigated the role of crhsp in mycoparasitism using gene knockout experiments. The results showed that disruption of crhsp had remarkabe effects on the morphological characteristics of C. rosea. In addition, the ability of C. rosea to parasitize sclerotia and control soybean Sclerotinia stem rot in the greenhouse was significantly reduced in the Δcrhsp mutant. The results indicated that crhsp is involved in C. rosea mycoparasitism and provide the basis for further study of the molecular mechanism of C. rosea mycoparasitism. This is the first report to demonstrate the involvement of the HSP70 gene in C. rosea mycoparasitism.

Co-culture of Bacillus amyloliquefaciens ACCC11060 and Trichoderma asperellum GDFS1009 enhanced pathogen-inhibition and amino acid yield

Background

Bacillus spp. are a genus of biocontrol bacteria widely used for antibiosis, while Trichoderma spp. are biocontrol fungi that are abundantly explored. In this study, a liquid co-cultivation of these two organisms was tried firstly.

Results and discussion

Through liquid chromatography-mass spectrometry/mass spectrometry (LC–MS/MS), it was discovered that with an inoculation in the ratio of 1.9:1, the antimicrobial effect of the co-cultured fermentation liquor of Bacillus amyloliquefaciens ACCC11060 and Trichoderma asperellum GDFS1009 was found to be significantly higher than that of pure-cultivation. A raise in the synthesis of antimicrobial substances contributed to this significant increase. Additionally, a co-culture with the inoculation of the two organisms in the ratio of 1:1 was found to enhance the production of specific amino acids. This technique could be further explored for either a large scale production of amino acids or could serve as a theoretical base for the generation of certain rare amino acids.

Conclusions

This work clearly demonstrated that co-cultivation of B. amyloliquefaciens ACCC11060 and T. asperellum GDFS1009 could produce more specific biocontrol substances and amino acids.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-1004-x) contains supplementary material, which is available to authorized users.