DCiPatho: deep cross-fusion networks for genome scale identification of pathogens.

Pathogen detection from biological and environmental samples is important for global disease control. Despite advances in pathogen detection using deep learning, current algorithms have limitations in processing long genomic sequences. Through the deep cross-fusion of cross, residual and deep neural networks, we developed DCiPatho for accurate pathogen detection based on the integrated frequency features of 3-to-7 k-mers. Compared with the existing state-of-the-art algorithms, DCiPatho can be used to accurately identify distinct pathogenic bacteria infecting humans, animals and plants. We evaluated DCiPatho on both learned and unlearned pathogen species using both genomics and metagenomics datasets. DCiPatho is an effective tool for the genomic-scale identification of pathogens by integrating the frequency of k-mers into deep cross-fusion networks. The source code is publicly available at https://github.com/LorMeBioAI/DCiPatho.

Preparation and characterization of a novel blue-TiO2/PbO2-carbon nanotube electrode and its application for degradation of phenol.

In this study, we fabricated a blue-TiO2/PbO2-carbon nanotube (CNT) electrode in which blue TiO2 nanotube arrays (blue-TNA) served as the substrate for PbO2-CNT eletrodeposition. Scanning electron microscope (SEM) showed compact surface structure of the electrode. The ß-PbO2 crystal structure was detected by X-ray diffraction (XRD). The distribution of Pb, O, C, and Na elements on the electrode surface have been confirmed by X-ray photoelectron spectroscopy (XPS). Blue-TiO2/PbO2-CNT electrode had higher response current (213.12 mA), larger active surface area and lower charge transfer resistance (2.22 Ω/cm2) than conventional TiO2/PbO2-CNT electrode. The influences of current density, initial phenol concentration, initial solution pH, and Na2SO4 concentration on the electrochemical oxidation of phenol have been analyzed. The results showed that the 100 mg/L phenol could be destroyed completely after 210 min, and chemical oxygen demand (COD) removal rate was 89.3% within 240 min. Additionally, the electrode showed long actual lifetime (5468.80 hr) and low energy consumption (0.08 kWh/gCOD). A phenol degradation mechanism was proposed by analyzing the intermediate products with high-performance liquid chromatography-mass spectrometry (HPLC-MS). Importantly, the blue-TiO2/PbO2-CNT electrode exhibited superior stability and high degradation efficiency after 15 times reuse, demonstrating its promising application potential on phenol-containing wastewater treatment.

Resource availability drives bacteria community resistance to pathogen invasion via altering bacterial pairwise interactions.

Microbial interactions within resident communities are a major determinant of resistance to pathogen invasion. Yet, interactions vary with environmental conditions, raising the question of how community composition and environments interactively shape invasion resistance. Here, we use resource availability (RA) as a model parameter altering the resistance of model bacterial communities to invasion by the plant pathogenic bacterium Ralstonia solanacearum. We found that at high RA, interactions between resident bacterial species were mainly driven by the direct antagonism, in terms of the means of invader inhibition. Consequently, the competitive resident communities with a higher production of antibacterial were invaded to a lesser degree than facilitative communities. At low RA, bacteria produced little direct antagonist potential, but facilitative communities reached a relatively higher community productivity, which showed higher resistance to pathogen invasion than competitive communities with lower productivities. This framework may lay the basis to understand complex microbial interactions and biological invasion as modulated by the dynamic changes of environmental resource availability.

Introduction of probiotic bacterial consortia promotes plant growth via impacts on the resident rhizosphere microbiome.

Plant growth depends on a range of functions provided by their associated rhizosphere microbiome, including nutrient mineralization, hormone co-regulation and pathogen suppression. Improving the ability of plant-associated microbiomes to deliver these functions is thus important for developing robust and sustainable crop production. However, it is yet unclear how beneficial effects of probiotic microbial inoculants can be optimized and how their effects are mediated. Here, we sought to enhance tomato plant growth by targeted introduction of probiotic bacterial consortia consisting of up to eight plant-associated Pseudomonas strains. We found that the effect of probiotic consortium inoculation was richness-dependent: consortia that contained more Pseudomonas strains reached higher densities in the tomato rhizosphere and had clearer beneficial effects on multiple plant growth characteristics. Crucially, these effects were best explained by changes in the resident community diversity, composition and increase in the relative abundance of initially rare taxa, instead of introduction of plant-beneficial traits into the existing community along with probiotic consortia. Together, our results suggest that beneficial effects of microbial introductions can be driven indirectly through effects on the diversity and composition of the resident plant rhizosphere microbiome.

SELE Downregulation Suppresses Mast Cell Accumulation to Protect against Inflammatory Response in Chronic Idiopathic Urticaria.

BACKGROUND: Chronic idiopathic urticaria (CIU) represents a common skin disorder often characterized by mast cell activation and secretion of histamine and other proinflammatory factors. E-selectin (SELE) has been implicated in the pathogenesis of common inflammatory cutaneous disorders, while the role of SELE in CIU is yet to be fully understood. Thus, we aimed to investigate the mechanism by which SELE influences CIU in connection with the involvement of mast cells. METHODS: SELE expression was measured in blood samples obtained from CIU patients and normal individuals. A CIU mouse model was subsequently established by intradermally injecting a normal saline solution with ovalbumin IgE antiserum into the mice. Loss- and gain-of-function investigations were conducted on the mouse models. The number of degranulated mast cells and the amount of histamine release in vitro were determined. The levels of SELE, tumor necrosis factor (TNF)-α, homologous restriction factor (HRF), and interleukin (IL)-6 levels were determined. RESULTS: The CIU clinical samples exhibited upregulated SELE, while the CIU mice showed increased mast cell degranulation and an increased rate of histamine directional release, as well as an elevated expression of SELE, TNF-α, HRF, and IL-6. SELE silencing was found to decrease the number of degranulated mast cells and reduce the rate of histamine directional release, along with suppressed TNF-α, HRF, and IL-6 expression, in the serum of CIU mice. Ketotifen was observed to rescue the increased expression of TNF-α, HRF, and IL-6 caused by SELE overexpression. CONCLUSIONS: This study highlights the potential of SELE downregulation to repress inflammatory factor secretion caused by the accumulation of mast cells, which ultimately inhibits the development of CIU.

Adaboost-Based Machine Learning Improved the Modeling Robust and Estimation Accuracy of Pear Leaf Nitrogen Concentration by In-Field VIS-NIR Spectroscopy.

Different cultivars of pear trees are often planted in one orchard to enhance yield for its gametophytic self-incompatibility. Therefore, an accurate and robust modelling method is needed for the non-destructive determination of leaf nitrogen (N) concentration in pear orchards with mixed cultivars. This study proposes a new technique based on in-field visible-near infrared (VIS-NIR) spectroscopy and the Adaboost algorithm initiated with machine learning methods. The performance was evaluated by estimating leaf N concentration for a total of 1285 samples from different cultivars, growth regions, and tree ages and compared with traditional techniques, including vegetation indices, partial least squares regression, singular support vector regression (SVR) and neural networks (NN). The results demonstrated that the leaf reflectance responded to the leaf nitrogen concentration were more sensitive to the types of cultivars than to the different growing regions and tree ages. Moreover, the AdaBoost.RT-BP had the best accuracy in both the training (R2 = 0.96, root mean relative error (RMSE) = 1.03 g kg-1) and the test datasets (R2 = 0.91, RMSE = 1.29 g kg-1), and was the most robust in repeated experiments. This study provides a new insight for monitoring the status of pear trees by the in-field VIS-NIR spectroscopy for better N managements in heterogeneous pear orchards.

Glutaredoxins Play an Important Role in the Redox Homeostasis and Symbiotic Capacity of Azorhizobium caulinodans ORS571.

Glutaredoxin (GRX) plays an essential role in the control of the cellular redox state and related pathways in many organisms. There is limited information on GRXs from the model nitrogen (N2)-fixing bacterium Azorhizobium caulinodans. In the present work, we identified and performed functional analyses of monothiol and dithiol GRXs in A. caulinodans in the free-living state and during symbiosis with Sesbania rostrata. Our data show that monothiol GRXs may be very important for bacterial growth under normal conditions and in response to oxidative stress due to imbalance of the redox state in grx mutants of A. caulinodans. Functional redundancies were also observed within monothiol and dithiol GRXs in terms of different physiological functions. The changes in catalase activity and iron content in grx mutants were assumed to favor the maintenance of bacterial resistance against oxidants, nodulation, and N2 fixation efficiency in this bacterium. Furthermore, the monothiol GRX12 and dithiol GRX34 play a collective role in symbiotic associations between A. caulinodans and Sesbania rostrata. Our study provided systematic evidence that further investigations are required to understand the importance of glutaredoxins in A. caulinodans and other rhizobia.

Rhizosphere microbiome functional diversity and pathogen invasion resistance build up during plant development.

The rhizosphere microbiome is essential for plant growth and health, and numerous studies have attempted to link microbiome functionality to species and trait composition. However, to date little is known about the actual ecological processes shaping community composition, complicating attempts to steer microbiome functionality. Here, we assess the development of microbial life history and community-level species interaction patterns that emerge during plant development. We use microbial phenotyping to experimentally test the development of niche complementarity and life history traits linked to microbiome performance. We show that the rhizosphere microbiome assembles from pioneer assemblages of species with random resource overlap into high-density, functionally complementary climax communities at later stages. During plant growth, fast-growing species were further replaced by antagonistic and stress-tolerant ones. Using synthetic consortia isolated from different plant growth stages, we demonstrate that the high functional diversity of 'climax' microbiomes leads to a better resistance to bacterial pathogen invasion. By demonstrating that different life-history strategies prevail at different plant growth stages and that community-level processes may supersede the importance of single species, we provide a new toolbox to understand microbiome assembly and steer its functionality at a community level.

LncRNA MEG3 suppressed the progression of ovarian cancer via sponging miR-30e-3p and regulating LAMA4 expression.

BACKGROUND: Ovarian cancer (OC) is a common female reproductive malignancy with a high mortality rate. Although LAMA4 was observed to be downregulated in OC cells, its mechanism in regulating OC metastasis is still unknown. This study aimed to investigate the effect of LAMA4 and its mechanism on OC. METHODS: To achieve this aim, a microarray analysis was performed to screen out the key genes involved in OC pathogenesis. Western-blot and qRT-PCR assays were also carried out to detect protein and mRNA expressions, respectively. A luciferase reporter assay was further used to confirm the direct interaction of miR-30e-3p with MEG3, and the direct interaction of miR-30e-3p with LAMA4 mRNA. Cytological experiments (CCK8, colony formation assay, wound-healing assay etc.) were then performed to explore the roles of miR-30e-3p, MEG3, and LAMA4 in OC cells. RESULTS: After carrying out microarray analysis, LAMA4 was confirmed as a key gene associated with OC pathogenesis. Research results proved that miR-30e-3p was markedly upregulated, while MEG3 and LAMA4 were noticeably downregulated in OC tissues and cells. The overexpression of LAMA4 significantly impaired the proliferation, migration, and invasion of OC cells. However, the upregulation of MEG3 increased the expression of LAMA4 by sponging miR-30e-3p, which alleviated the malignancy of OC cells. CONCLUSIONS: Observations showed that forced LAMA4 overexpression could inhibit OC progression, which was regulated by MEG3 via sponging miR-30e-3p. The findings of this research could provide new insights into the mechanism by which MEG3 and LAMA4 exert their anti-oncogenic roles in OC progression.Trial registration Not applicable.

Transcriptome Analysis of Pyrus betulaefolia Seedling Root Responses to Short-Term Potassium Deficiency.

Potassium (K) plays a crucial role in multiple physiological and developmental processes in plants. Its deficiency is a common abiotic stress that inhibits plant growth and reduces crop productivity. A better understanding of the mechanisms involved in plant responses to low K could help to improve the efficiency of K use in plants. However, such responses remain poorly characterized in fruit tree species such as pears (Pyrus sp). We analyzed the physiological and transcriptome responses of a commonly used pear rootstock, Pyrus betulaefolia, to K-deficiency stress (0 mM). Potassium deprivation resulted in apparent changes in root morphology, with short-term low-K stress resulting in rapidly enhanced root growth. Transcriptome analyses indicated that the root transcriptome was coordinately altered within 6 h after K deprivation, a process that continued until 15 d after treatment. Potassium deprivation resulted in the enhanced expression (up to 5-fold) of a putative high-affinity K+ transporter, PbHAK5 (Pbr037826.1), suggesting the up-regulation of mechanisms associated with K+ acquisition. The enhanced root growth in response to K-deficiency stress was associated with a rapid and sustained decrease in the expression of a transcription factor, PbMYB44 (Pbr015309.1), potentially involved in mediating auxin responses, and the increased expression of multiple genes associated with regulating root growth. The concentrations of several phytohormones including indoleacetic acid (IAA), ABA, ETH, gibberellin (GA3), and jasmonic acid (JA) were higher in response to K deprivation. Furthermore, genes coding for enzymes associated with carbon metabolism such as SORBITOL DEHYDROGENASE (SDH) and SUCROSE SYNTHASE (SUS) displayed greatly enhanced expression in the roots under K deprivation, presumably indicating enhanced metabolism to meet the increased energy demands for growth and K+ acquisition. Together, these data suggest that K deprivation in P. betulaefolia results in the rapid re-programming of the transcriptome to enhance root growth and K+ acquisition. These data provide key insights into the molecular basis for understanding low-K-tolerance mechanisms in pears and in other related fruit trees and identifying potential candidates that warrant further analyses.

Facilitation promotes invasions in plant-associated microbial communities.

While several studies have established a positive correlation between community diversity and invasion resistance, it is less clear how species interactions within resident communities shape this process. Here, we experimentally tested how antagonistic and facilitative pairwise interactions within resident model microbial communities predict invasion by the plant-pathogenic bacterium Ralstonia solanacearum. We found that facilitative resident community interactions promoted and antagonistic interactions suppressed invasions both in the lab and in the tomato plant rhizosphere. Crucially, pairwise interactions reliably explained observed invasion outcomes also in multispecies communities, and mechanistically, this was linked to direct inhibition of the invader by antagonistic communities (antibiosis), and to a lesser degree by resource competition between members of the resident community and the invader. Together, our findings suggest that the type and strength of pairwise interactions can reliably predict the outcome of invasions in more complex multispecies communities.

Simultaneous dermatophytosis and keratomycosis caused by Trichophyton interdigitale infection: a case report and literature review.

BACKGROUND: Dermatophytosis is a fungal infectious disease caused by dermatophytes, which produce protease and keratinase to digest keratin, leading to the colonization, invasion, and infection of the stratum corneum of the skin, hair shafts, and nails. Trichophyton interdigitale belongs to Trichophyton mentagrophytes complex, which is the common pathogen causing dermatophytosis. Fungal keratitis, also called keratomycosis, is an infectious disease of cornea. CASE PRESENTATION: Here, we report a case of simultaneous dermatophytosis and keratomycosis caused by Trichophyton interdigitale. A 67-year-old man presented with extensive erythema all over the body since 4 years ago, fungal infection of left eye for 2 years, and loss of vision in the eye. These symptoms had become aggravated in the last month. Dermatological examinations showed extensive erythematous plaques with clear borders and scales, scattered red papules with ulceration, and scabs throughout the body. Onychomycosis was observed on the nails of left hand, conjunctival infection with secretion and loss of vision were noted in left eye. Hyaline septate hyphae were observed under direct microscopic examination, fungal culture and internal transcribed spacer sequencing revealed T. interdigitale. Histopathological examination suggested infectious granuloma. A diagnosis of dermatophytosis and keratomycosis caused by T. interdigitale with loss of vision in left eye was made. The patient was treated with luliconazole cream (two applications per day) and itraconazole (100 mg, BID, PO). Complete clinical remission was achieved after 1 month. Subsequently, the patient underwent left eye enucleation in the ophthalmology department. CONCLUSIONS: In the present study, we reported a case of simultaneous dermatophytosis and keratomycosis caused by T. interdigitale, and reviewed the literature on corneal infection caused by Trichophyton. A total of 10 articles with 45 patients were published between 1973 and 2018. The pathogen of 27 patient were identified to species level. There were T. schoenleinii (17), T. mentagrophytes (4), T. verrucosum (3), T. rubrum (1), T. erinacei (1), and T. interdigitale (1). Five patients had corneal trauma, one had contact lens use history. Direct microscopic examination, fungal culture, and analysis of physiological characteristics were the main methods of identification. Early diagnosis and prompt treatment may help improve the management and outcomes.

Resource stoichiometry shapes community invasion resistance via productivity-mediated species identity effects.

Diversity-invasion resistance relationships are often variable and sensitive to environmental conditions such as resource availability. Resource stoichiometry, the relative concentration of different elements in the environment, has been shown to have strong effects on the physiology and interactions between different species. Yet, its role for diversity-invasion resistance relationships is still poorly understood. Here, we explored how the ratio of nitrogen (N) and phosphorus affects the productivity and invasion resistance of constructed microbial communities by a plant pathogenic bacterium, Ralstonia solanacearum. We found that resource stoichiometry and species identity effects affected the invasion resistance of communities. Both high N concentration and resident community diversity constrained invasions, and two resident species, in particular, had strong negative effects on the relative density of the invader and the resident community productivity. While resource stoichiometry did not affect the mean productivity of the resident community, it favoured the growth of two species that strongly constrained invasions turning the slope of productivity-invasion resistance relationship more negative. Together our findings suggest that alterations in resource stoichiometry can change the community resistance to invasions by having disproportionate effects on species growth, potentially explaining changes in microbial community composition under eutrophication.

Resource availability modulates biodiversity-invasion relationships by altering competitive interactions.

Community diversity affects the survival of newly introduced species via resource competition. Competitive interactions can be modulated by resource availability and we hypothesized that this may alter biodiversity-invasion relationships. To study this, we assessed the growth of a bacterial invader, Ralstonia solanacearum, when introduced into communities comprised of one to five closely related resident species under different resource concentrations. The invader growth was then examined as a function of resident community richness, species composition and resource availability. We found that the relative density of the invader was reduced by increasing resident community richness and resource availability. Mechanistically, this could be explained by changes in the competitive interactions between the resident species and the invader along the resource availability gradient. At low resource availability, resident species with a high catabolic similarity with the invader efficiently reduced the invader relative density, while at high resource availability, fast-growing resident species became more important for the invader suppression. These results indicate that the relative importance of different resident community species can change dynamically along to resource availability gradient. Diverse communities could be thus more robust to invasions by providing a set of significant species that can take suppressive roles across different environments.

Success evaluation of the biological control of Fusarium wilts of cucumber, banana, and tomato since 2000 and future research strategies.

The Fusarium wilt caused by Fusarium oxysporum strains is the most devastating disease of cucumber, banana, and tomato. The biological control of this disease has become an attractive alternative to the chemical fungicides and other conventional control methods. In this review, the research trends and biological control efficiencies (BCE) of different microbial strains since 2000 are reviewed in detail, considering types of microbial genera, inoculum application methods, plant growth medium and conditions, inoculum application with amendments, and co-inoculation of different microbial strains and how those affect the BCE of Fusarium wilt. The data evaluation showed that the BCE of biocontrol agents was higher against the Fusarium wilt of cucumber compared to the Fusarium wilts of banana and tomato. Several biocontrol agents mainly Bacillus, Trichoderma, Pseudomonas, nonpathogenic Fusarium, and Penicillium strains were evaluated to control Fusarium wilt, but still this lethal disease could not be controlled completely. We have discussed different reasons of inconsistent results and recommendations for the betterment of BCE in the future. This review provides knowledge of the biotechnology of biological control of Fusarium wilt of cucumber, banana, and tomato in a nut shell that will provide researchers a beginning line to start and to organize and plan research for the future studies.

Non-Destructive Evaluation of the Leaf Nitrogen Concentration by In-Field Visible/Near-Infrared Spectroscopy in Pear Orchards.

Non-destructive and timely determination of leaf nitrogen (N) concentration is urgently needed for N management in pear orchards. A two-year field experiment was conducted in a commercial pear orchard with five N application rates: 0 (N0), 165 (N1), 330 (N2), 660 (N3), and 990 (N4) kg·N·ha-1. The mid-portion leaves on the year's shoot were selected for the spectral measurement first and then N concentration determination in the laboratory at 50 and 80 days after full bloom (DAB). Three methods of in-field spectral measurement (25° bare fibre under solar conditions, black background attached to plant probe, and white background attached to plant probe) were compared. We also investigated the modelling performances of four chemometric techniques (principal components regression, PCR; partial least squares regression, PLSR; stepwise multiple linear regression, SMLR; and back propagation neural network, BPNN) and three vegetation indices (difference spectral index, normalized difference spectral index, and ratio spectral index). Due to the low correlation of reflectance obtained by the 25° field of view method, all of the modelling was performed on two spectral datasets-both acquired by a plant probe. Results showed that the best modelling and prediction accuracy were found in the model established by PLSR and spectra measured with a black background. The randomly-separated subsets of calibration (n = 1000) and validation (n = 420) of this model resulted in high R² values of 0.86 and 0.85, respectively, as well as a low mean relative error (<6%). Furthermore, a higher coefficient of determination between the leaf N concentration and fruit yield was found at 50 DAB samplings in both 2015 (R² = 0.77) and 2014 (R² = 0.59). Thus, the leaf N concentration was suggested to be determined at 50 DAB by visible/near-infrared spectroscopy and the threshold should be 24-27 g/kg.

Genome-wide transcriptomic analysis of a superior biomass-degrading strain of A. fumigatus revealed active lignocellulose-degrading genes.

BACKGROUND: Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural materials on earth. It consists of complex carbohydrates and aromatic polymers found in the plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was isolated from compost heaps and showed highly efficient plant biomass-degradation capability. RESULTS: The 29-million base-pair genome of Z5 was sequenced and 9540 protein-coding genes were predicted and annotated. Genome analysis revealed an impressive array of genes encoding cellulases, hemicellulases and pectinases involved in lignocellulosic biomass degradation. Transcriptional responses of A. fumigatus Z5 induced by sucrose, oat spelt xylan, Avicel PH-101 and rice straw were compared. There were 444, 1711 and 1386 significantly differently expressed genes in xylan, cellulose and rice straw, respectively, when compared to sucrose as a control condition. CONCLUSIONS: Combined analysis of the genomic and transcriptomic data provides a comprehensive understanding of the responding mechanisms to the most abundant natural polysaccharides in A. fumigatus. This study provides a basis for further analysis of genes shown to be highly induced in the presence of polysaccharide substrates and also the information which could prove useful for biomass degradation and heterologous protein expression.

A new acidophilic thermostable endo-1,4-ß-mannanase from Penicillium oxalicum GZ-2: cloning, characterization and functional expression in Pichia pastoris.

BACKGROUND: Endo-1,4-ß-mannanase is an enzyme that can catalyze the random hydrolysis of ß-1, 4-mannosidic linkages in the main chain of mannans, glucomannans and galactomannans and has a number of applications in different biotechnology industries. Penicillium oxalicum is a powerful hemicellulase-producing fungus (Bioresour Technol 123:117-124, 2012); however, few previous studies have focused on the cloning and expression of the endo-1,4-ß-mannanase gene from Penicillium oxalicum. RESULTS: A gene encoding an acidophilic thermostable endo-1,4-ß-mannanase (E.C. 3.2.1.78) from Penicillium oxalicum GZ-2, which belongs to glycoside hydrolase family 5, was cloned and successfully expressed in Pichia pastoris GS115. A high enzyme activity (84.4 U mL(-1)) was detected in the culture supernatant. The recombinant endo-1,4-ß-mannanase (rPoMan5A) was tagged with 6 × His at its C-terminus and purified using a Ni-NTA Sepharose column to apparent homogeneity. The purified rPoMan5A showed a single band on SDS-PAGE with a molecular mass of approximately 61.6 kDa. The specific activity of the purified rPoMan5A was 420.9 U mg(-1) using locust bean gum as substrate. The optimal catalytic temperature (10 min assay) and pH value for rPoMan5A are 80 °C and pH 4.0, respectively. The rPoMan5A is highly thermostable with a half-life of approximately 58 h at 60 °C at pH 4.0. The K m and V max values for locust bean gum, konjac mannan, and guar gum are 7.6 mg mL(-1) and 1425.5 µmol min(-1) mg(-1), 2.1 mg mL(-1) and 154.8 µmol min(-1) mg(-1), and 2.3 mg mL(-1) and 18.9 µmol min(-1) mg(-1), respectively. The enzymatic activity of rPoMan5A was not significantly affected by an array of metal ions, but was inhibited by Fe(3+) and Hg(2+). Analytical results of hydrolytic products showed that rPoMan5A could hydrolyze various types of mannan polymers and released various mannose and manno-oligosaccharides, with the main products being mannobiose, mannotriose, and mannopentaose. CONCLUSION: Our study demonstrated that the high-efficient expression and secretion of acid stable and thermostable recombinant endo-1, 4-ß-mannanase in Pichia pastoris is suitable for various biotechnology applications.

Pyrosequencing reveals contrasting soil bacterial diversity and community structure of two main winter wheat cropping systems in China.

Microbes are key components of the soil environment, playing an important role in maintaining soil health, sustainability, and productivity. The composition and structure of soil bacterial communities were examined in winter wheat-rice (WR) and winter wheat-maize (WM) cropping systems derived from five locations in the Low-Middle Yangtze River plain and the Huang-Huai-Hai plain by pyrosequencing of the 16S ribosomal RNA gene amplicons. A total of 102,367 high quality sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as crop rotations, soil properties, and locations. The most abundant phyla across all soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Similar patterns of bacterial diversity and community structure were observed within the same cropping systems, and a higher relative abundance of anaerobic bacteria was found in WR compared to WM cropping systems. Variance partitioning analysis revealed complex relationships between bacterial community and environmental variables. The effect of crop rotations was low but significant, and interactions among soil properties, locations, and crop rotations accounted for most of the explained variation in the structure of bacterial communities. Soil properties such as pH, available P, and available K showed higher correlations (positive or negative) with the majority of the abundant taxa. Bacterial diversity (the Shannon index) and richness (Chao1 and ACE) were higher under WR than WM cropping systems.

A new acidophilic endo-ß-1,4-xylanase from Penicillium oxalicum: cloning, purification, and insights into the influence of metal ions on xylanase activity.

A new acidophilic xylanase (XYN11A) from Penicillium oxalicum GZ-2 has been purified, identified and characterized. Synchronized fluorescence spectroscopy was used for the first time to evaluate the influence of metal ions on xylanase activity. The purified enzyme was identified by MALDI TOF/TOF mass spectrometry, and its gene (xyn11A) was identified as an open reading frame of 706 bp with a 68 bp intron. This gene encodes a mature protein of 196 residues with a predicted molecular weight of 21.3 kDa that has the 100 % identity with the putative xylanase from the P. oxalicum 114-2. The enzyme shows a structure comprising a catalytic module family 10 (GH10) and no carbohydrate-binding module family. The specific activities were 150.2, 60.2, and 72.6 U/mg for beechwood xylan, birchwood xylan, and oat spelt xylan, respectively. XYN11A exhibited optimal activity at pH 4.0 and remarkable pH stability under extremely acidic condition (pH 3). The specific activity, K m and V max values were 150.2 U/mg, 30.7 mg/mL, and 403.9 µmol/min/mg for beechwood xylan, respectively. XYN11A is a endo-ß-1,4-xylanase since it release xylobiose and xylotriose as the main products by hydrolyzing xylans. The activity of XYN11A was enhanced 155 % by 1 mM Fe(2+) ions, but was inhibited strongly by Fe(3+). The reason of enhancing the xylanase activity of XYN11A with 1 mM Fe(2+) treatment may be responsible for the change of microenvironment of tryptophan residues studied by synchronous fluorescence spectrophotometry. Inhibition of the xylanase activity by Fe(3+) was first time demonstrated to associate tryptophan fluorescence quenching.