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Journal of Applied Microbiology
Wiley-Blackwell
Journal of Applied Microbiology

Wiley-Blackwell

1364-5072

Journal of Applied Microbiology/Journal Journal of Applied MicrobiologyISTPSCIEI
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    2页

    Genetic sequence data evidence that human faecal‐associated HF183 sequences are on human skin and in urine

    Dong LiLaurie C. Van De WerfhorstPatricia A. Holden
    9页
    查看更多>>摘要:Abstract Aims The DNA marker HF183 is a partial 16S rRNA gene sequence highly specific to human‐associated Bacteroides including Bacteroides dorei. While HF183 is used to assess human faecal contamination in aquatic environments worldwide, little is known about the existence of HF183 and B. dorei in human microbiomes outside of the human gastrointestinal tract and faeces. Methods and Results Previously published human skin and urine microbiome data sets from five independent human body skin studies, the Human Microbiome Project (HMP) and three independent human urine studies were analysed. The HF183 gene sequence was detected in all skin data sets, with the ratios of positive samples ranging from 0.5% to 36.3%. Popliteal fossa (knee), volar forearm and inguinal (groin) creases were identified as hot spots. HF183 was detected in two of three urine data sets, with ratios of positive samples ranging from 0% to 37.5%. All HF183‐containing sequences from these data sets were classified as associated with B. dorei. Conclusions HF183 is widespread on human skin and present in urine. Significance and Impact of Study Skin and urine microbiomes could be sources of HF183 to environmental waters. Such non‐faecal sources of HF183 might explain low concentrations of HF183 in recreational waters when swimmers are present.

    Meta‐analysis of the antifungal activities of three essential oils as alternative therapies in dermatophytosis infections

    Julia Villar RodríguezAna María Pérez‐PicoEsther Mingorance‐álvarezRaquel Mayordomo Acevedo...
    13页
    查看更多>>摘要:Abstract Aims This work examines the available scientific evidence about the efficiency of essential oils (EO) as an alternative therapy to traditional treatment of fungal infections, including onychomycosis, assessing the effect of the three EO most frequently studied for their antifungal activity (thyme, cinnamon and tea tree EO) against three causative agents of fungal diseases in humans: Trichophyton rubrum, Trichophyton mentagrophytes complex and Candida albicans. Methods and Results The PRISMA statement protocol was followed to conduct a bibliographical search and 54 articles that met all the inclusion criteria were retrieved. Differences were observed in the MIC and MFC values depending on the micro‐organism strain and the EO used. The lowest MIC were observed with Cinnamomum zeylanicum EO (0.013–1120?μl?ml?1) against the three micro‐organisms. For MFC, the lowest value was found for Thymus vulgaris EO (4.2?μl?ml?1) against Trichophyton rubrum. Conclusions The antifungal effects of EO could be a very promising solution to overcome the therapeutic shortcomings of antimycotic medication. More experiments are needed to examine the properties of these oils to devise effective and nonaggressive therapies for treatment of dermatophytosis. Significance and Impact of Study The results indicate that EO remain good candidates for future treatments and could provide a solution for failed medications and/or adverse reactions to current pharmacological treatments.

    Management of abiotic stresses by microbiome‐based engineering of the rhizosphere

    Rashi TyagiSalila PradhanAnnapurna BhattacharjeeShubham Dubey...
    19页
    查看更多>>摘要:Abstract Abiotic stresses detrimentally affect both plant and soil health, threatening food security in an ever‐increasing world population. Sustainable agriculture is necessary to augment crop yield with simultaneous management of stresses. Limitations of conventional bioinoculants have shifted the focus to more effective alternatives. With the realization of the potential of rhizospheric microbiome engineering in enhancing plant's fitness under stress, efforts have accelerated in this direction. Though still in its infancy, microbiome‐based engineering has gained popularity because of its advantages over the microbe‐based approach. This review briefly presents major abiotic stresses afflicting arable land, followed by an introduction to the conventional approach of microbe‐based enhancement of plant attributes and stress mitigation with its inherent limitations. It then focuses on the significance of the rhizospheric microbiome and possibilities of harnessing its potential by its strategic engineering for stress management. Further, success stories related to two major approaches of microbiome engineering (generation of synthetic microbial community/consortium, and host‐mediated artificial selection) pertaining to stress management have been critically presented. Together with bringing forth the challenges associated with the wide application of rhizospheric microbiome engineering in agriculture, the review proposes the adoption of a combinational scheme for the same, bringing together ecological and reductionist approaches for improvised sustainable agricultural practices.

    Bacterial mandelic acid degradation pathway and its application in biotechnology

    Qingzhuo WangShanshan GengLingru WangZhiqiang Wen...
    14页
    查看更多>>摘要:Abstract Mandelic acid and its derivatives are an important class of chemical synthetic blocks, which is widely used in drug synthesis and stereochemistry research. In nature, mandelic acid degradation pathway has been widely identified and analysed as a representative pathway of aromatic compounds degradation. The most studied mandelic acid degradation pathway from Pseudomonas putida consists of mandelate racemase, S‐mandelate dehydrogenase, benzoylformate decarboxylase, benzaldehyde dehydrogenase and downstream benzoic acid degradation pathways. Because of the ability to catalyse various reactions of aromatic substrates, pathway enzymes have been widely used in biocatalysis, kinetic resolution, chiral compounds synthesis or construction of new metabolic pathways. In this paper, the physiological significance and the existing range of the mandelic acid degradation pathway were introduced first. Then each of the enzymes in the pathway is reviewed one by one, including the researches on enzymatic properties and the applications in biotechnology as well as efforts that have been made to modify the substrate specificity or improving catalytic activity by enzyme engineering to adapt different applications. The composition of the important metabolic pathway of bacterial mandelic acid degradation pathway as well as the researches and applications of pathway enzymes is summarized in this review for the first time.

    Plant‐associated endophytic fungi as potential bio‐factories for extracellular enzymes: Progress, Challenges and Strain improvement with precision approaches

    Anupam JyotiArif Jamal SiddiquiJuhi SaxenaDivyangi Raghav...
    24页
    查看更多>>摘要:Abstract There is an intricate network of relations between endophytic fungi and their hosts that affects the production of various bioactive compounds. Plant‐associated endophytic fungi contain industrially important enzymes and have the potential to fulfil their rapid demand in the international market to boost business in technology. Being safe and metabolically active, they have replaced the usage of toxic and harmful chemicals and hold a credible application in biotransformation, bioremediation and industrial processes. Despite these, there are limited reports on fungal endophytes that can directly cater to the demand and supply of industrially stable enzymes. The underlying reasons include low endogenous production and secretion of enzymes from fungal endophytes which have raised concern for widely accepted applications. Hence, it is imperative to augment the biosynthetic and secretory potential of fungal endophytes. Modern state‐of‐the‐art biotechnological technologies aiming at strain improvement using cell factory engineering as well as precise gene editing like Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and its Associated proteins (Cas) systems which can provide a boost in fungal endophyte enzyme production. Additionally, it is vital to characterize optimum conditions to grow one strain with multiple enzymes (OSME). The present review encompasses various plants‐derived endophytic fungal enzymes and their applications in various sectors. Furthermore, we postulate the feasibility of new precision approaches with an aim for strain improvement and enhanced enzyme production.

    Characterization of nitrilases from Variovorax boronicumulans that functions in insecticide flonicamid degradation and β‐cyano‐L‐alanine detoxification

    Huoyong JiangNengdang JiangLi WangJingjing Guo...
    12页
    查看更多>>摘要:Abstract Aims To characterize the functions of nitrilases of Variovorax boronicumulans CGMCC 4969 and evaluate flonicamid (FLO) degradation and β‐cyano‐L‐alanine (Ala(CN)) detoxification by this bacterium. Methods and Results Variovorax boronicumulans CGMCC 4969 nitrilases (NitA and NitB) were purified, and substrate specificity assay indicated that both of them degraded insecticide FLO to N‐(4‐trifluoromethylnicotinoyl)glycinamide (TFNG‐AM) and 4‐(trifluoromethyl)nicotinol glycine (TFNG). Ala(CN), a plant detoxification intermediate, was hydrolysed by NitB. Escherichia coli overexpressing NitA and NitB degraded 41.2 and 93.8% of FLO (0.87?mmol·L?1) within 1?h, with half‐lives of 1.30 and 0.25?h, respectively. NitB exhibited the highest nitrilase activity towards FLO. FLO was used as a substrate to compare their enzymatic properties. NitB was more tolerant to acidic conditions and organic solvents than NitA. Conversely, NitA was more tolerant to metal ions than NitB. CGMCC 4969 facilitated FLO degradation in soil and surface water and utilized Ala(CN) as a sole nitrogen source for growth. Conclusions CGMCC 4969 efficiently degraded FLO mediated by NitA and NitB; NitB was involved in Ala(CN) detoxification. Significance and Impact of the Study This study promotes our understanding of versatile functions of nitrilases from CGMCC 4969 that is promising for environmental remediation.

    Difference responses of soil fungal communities to cattle and chicken manure composting application

    Junhua ZhangCong ShenTian H. ShangJi L. Liu...
    17页
    查看更多>>摘要:Abstract Aims Cattle and poultry manure composting are often applied on agricultural lands but the fungal community composition before and after application in soils is still unclear. This study describes soil fungal diversity after manure applications contribute to the correct resource use of livestock and poultry manures. Methods and Results Fresh manure samples were obtained from 10 beef cow farms and 12 egg‐laying poultry farms at five distinct phases of rearing. Surface soil samples were collected from vegetable plots within the farms after manure application at 15, 30 and 45?t?hm?2. Using high‐throughput sequencing techniques, the ITS region was used to describe soil fungus populations. The fungal OTUs, Chao1 and ACE of cattle manure were relatively higher in the fattening stage (>12?months), the OTUs and ACE of chicken manure were the highest in the initial laying stage (16–24?weeks). The fungal diversity indices of vegetable soils had no linear change after cow or chicken manure application compared with the control. Ascomycota (84.7% of total sequences), Neocallimastigomycota (9.69%) and Basidiomycota (4.6%) were the dominant phyla in cattle manure. Ascomycota (88.9%) also predominated in chicken manure followed by Basidiomycota (8.9%). Following both cattle and chicken manure applications, the abundance of Ascomycota decreased, whereas Basidiomycota and Chytridiomycota increased in the soils. None of the dominant genus increased or decreased linearly with the increase of cattle and chicken composting application rate. The fungal‐dominant genera of the soils with and without manure composting application were mostly affected by soil pH and EC than manure. Pearson’s correlation analysis revealed that organic matter, Cu and Hg contents were strongly linked to the fungal diversity and the abundance of specific taxa in cattle manure. In chicken manure, OM, TN and Zn were major factors controlling the fungal diversity and community composition. Soil pH, EC and Cu, Zn, Cd, Hg and As content had pronounced effects on the beneficial and pathogenic genus in soil with and without manure composting. Beneficial fungal genus such as Aspergillus, Plectosphaerella, Acremonium, Meyerozyma and fungal pathogenic such as Fusarium, Cladosporium, Verticillium were sensitive to properties (EC, pH, OM) and heavy metals (Cu, Zn, Hg) contents of the environment relatively. This study can serve as an applicable contribution helping in farms management (especially to cattle and poultry breeding) and improving their resource use of livestock and poultry manures. Conclusions Soil heterogeneity rather than manure determines fungal communities in the vegetable fields, but we can encourage the sensible use of cattle and chicken manures in agroecosystems. Significance and Impact of the study This study will help farmers regulate the dosage of feed components which can increase the number of beneficial fungal genus or reduce the number of pathogenic fungal genus, improve their resource use of livestock and poultry manures and encourage the sensible use of cattle and chicken manures in agroecosystems.

    Assessing cross‐laboratory performance for quantifying coliphage using EPA Method 1642

    Amity G. Zimmer‐FaustJohn F. GriffithJoshua A. SteeleTania Chiem...
    9页
    查看更多>>摘要:Abstract Aims Widespread adoption of the new U.S. Environmental Protection Agency (USEPA) Method 1642 for enumeration of coliphage in recreational water requires demonstration that laboratories consistently meet internal method performance goals and yield results that are consistent across laboratories. Methods and Results Here we assess the performance of six laboratories processing a series of blind wastewater‐ and coliphage‐spiked samples along with laboratory blanks. All laboratories met the method‐defined recovery requirements when performance was averaged across samples, with the few failures on individual samples mostly occurring for less‐experienced laboratories on the initial samples processed. Failures that occurred on later samples were generally attributed to easily correctable activities. Failure rates were higher for somatic vs. F+ coliphage, attributable to the more stringent performance criteria associated with somatic coliphage. There was no difference in failure rate between samples prepared in a marine water matrix compared to that in phosphate‐buffered saline. Conclusions Variation among laboratories was similar to that previously reported for enterococci, the current bacterial indicator used for evaluating beach water quality for public health protection. Significance and Impact of the Study These findings suggest that laboratory performance is not an inhibitor to the adoption of coliphage as a new indicator for assessing recreational health risk.

    Predictive growth kinetic parameters and modelled probabilities of deoxynivalenol production by Fusarium graminearum on wheat during simulated storing conditions

    Penggang PeiKe XiongXiaoyi WangBaoguo Sun...
    13页
    查看更多>>摘要:Abstract Aims Mathematical models were employed to predict the growth kinetic parameters of Fusarium graminearum and the accumulation of deoxynivalenol (DON) during wheat storage as a function of different moisture contents (MCs) and temperatures. Methods and results The colony counting method was used to quantify F. graminearum growth under different environmental conditions, and kinetic and probability models were developed to describe the effect of different MCs and temperatures on fungal growth and DON production during wheat storage. Among the employed secondary models (Arrhenius‐Davey, Gibson and Cardinal), the general polynomial best predicted the fungal growth rate under varying temperature and MC during wheat storage. According to the logistic model, DON contamination was correctly predicted in 96.5% of cases. Conclusions The maximum growth rate of fungi was 0.4889?±?0.092?Log?CFU?g?1?day?1 at 25°C and 30% moisture according to the polynomial model. At below 17°C and ≤15% moisture, no fungal growth was observed. The probability model of toxin production showed no toxin production at less than 15% moisture (aw?≤0.76) and below 15°C. Significance and impact of the study This is the first application of a probability model of DON production during wheat storage, providing a reference for preventing fungal growth and mycotoxin accumulation by F. graminearum during wheat storage and guaranteeing food product safety.