Regulation of plant cell wall degradation by light in Trichoderma

Trichoderma reesei (syn. Hypocrea jecorina) is the model organism for industrial production of plant cell wall degradating enzymes. The integration of light and nutrient signals for adaptation of enzyme production in T. reesei emerged as an important regulatory mechanism to be tackled for strain improvement. Gene regulation specific for cellulase inducing conditions is different in light and darkness with substantial regulation by photoreceptors. Genes regulated by light are clustered in the genome, with several of the clusters overlapping with CAZyme clusters. Major cellulase transcription factor genes and at least 75% of glycoside hydrolase encoding genes show the potential of light dependent regulation. Accordingly, light dependent protein complex formation occurs within the promoters of cellulases and their regulators. Additionally growth on diverse carbon sources is different between light and darkness and dependent on the presence of photoreceptors in several cases. Thereby, also light intensity plays a regulatory role, with cellulase levels dropping at higher light intensities dependent in the strain background. The heterotrimeric G-protein pathway is the most important nutrient signaling pathway in the connection with light response and triggers posttranscriptional regulation of cellulase expression. All G-protein alpha subunits impact cellulase regulation in a light dependent manner. The downstream cAMP pathway is involved in light dependent regulation as well. Connections between the regulatory pathways are mainly established via the photoreceptor ENV1. The effect of photoreceptors on plant cell wall degradation also occurs in the model filamentous fungus Neurospora crassa. In the currently proposed model, T. reesei senses the presence of plant biomass in its environment by detection of building blocks of cellulose and hemicellulose. Interpretation of the respective signals is subsequently adjusted to the requirements in light and darkness (or on the surface versus within the substrate) by an interconnection of nutrient signaling with light response. This review provides an overview on the importance of light, photoreceptors and related signaling pathways for formation of plant cell wall degrading enzymes in T. reesei. Additionally, the relevance of light dependent gene regulation for industrial fermentations with Trichoderma as well as strategies for exploitation of the observed effects are discussed.

Isolation and characterization of diverse microbial representatives from the human skin microbiome

BACKGROUND

The skin micro-environment varies across the body, but all sites are host to microorganisms that can impact skin health. Some of these organisms are true commensals which colonize a unique niche on the skin, while open exposure of the skin to the environment also results in the transient presence of diverse microbes with unknown influences on skin health. Culture-based studies of skin microbiota suggest that skin microbes can affect skin properties, immune responses, pathogen growth, and wound healing.

RESULTS

In this work, we greatly expanded the diversity of available commensal organisms by collecting > 800 organisms from 3 body sites of 17 individuals. Our collection includes > 30 bacterial genera and 14 fungal genera, with Staphylococcus and Micrococcus as the most prevalent isolates. We characterized a subset of skin isolates for the utilization of carbon compounds found on the skin surface. We observed that members of the skin microbiota have the capacity to metabolize amino acids, steroids, lipids, and sugars, as well as compounds originating from personal care products.

CONCLUSIONS

This collection is a resource that will support skin microbiome research with the potential for discovery of novel small molecules, development of novel therapeutics, and insight into the metabolic activities of the skin microbiota. We believe this unique resource will inform skin microbiome management to benefit skin health. Video abstract.

Carbohydrate-related enzymes of important Phytophthora plant pathogens

Carbohydrate-Active enZymes (CAZymes) form particularly interesting targets to study in plant pathogens. Despite the fact that many CAZymes are pathogenicity factors, oomycete CAZymes have received significantly less attention than effectors in the literature. Here we present an analysis of the CAZymes present in the Phytophthora infestans, Ph. ramorum, Ph. sojae and Pythium ultimum genomes compared to growth of these species on a range of different carbon sources. Growth on these carbon sources indicates that the size of enzyme families involved in degradation of cell-wall related substrates like cellulose, xylan and pectin is not always a good predictor of growth on these substrates. While a capacity to degrade xylan and cellulose exists the products are not fully saccharified and used as a carbon source. The Phytophthora genomes encode larger CAZyme sets when compared to Py. ultimum, and encode putative cutinases, GH12 xyloglucanases and GH10 xylanases that are missing in the Py. ultimum genome. Phytophthora spp. also encode a larger number of enzyme families and genes involved in pectin degradation. No loss or gain of complete enzyme families was found between the Phytophthora genomes, but there are some marked differences in the size of some enzyme families.

Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization

Background

Enterohemorrhagic Escherichia coli (E. coli) are intestinal pathogenic bacteria that cause life-threatening disease in humans. Their cardinal virulence factor is Shiga toxin (Stx), which is encoded on lambdoid phages integrated in the chromosome. Stx phages can infect and lysogenize susceptible bacteria, thus either increasing the virulence of already pathogenic bacterial hosts or transforming commensal strains into potential pathogens. There is increasing evidence that Stx phage-encoded factors adaptively regulate bacterial host gene expression. Here, we investigated the effects of Stx phage carriage in E. coli K-12 strain MG1655. We compared the transcriptome and phenotype of naive MG1655 and two lysogens carrying closely related Stx2a phages: ϕO104 from the exceptionally pathogenic 2011 E. coli O104:H4 outbreak strain and ϕPA8 from an E. coli O157:H7 isolate.

Results

Analysis of quantitative RNA sequencing results showed that, in comparison to naive MG1655, genes involved in mixed acid fermentation were upregulated, while genes encoding NADH dehydrogenase I, TCA cycle enzymes and proteins involved in the transport and assimilation of carbon sources were downregulated in MG1655::ϕO104 and MG1655::ϕPA8. The majority of the changes in gene expression were found associated with the corresponding phenotypes. Notably, the Stx2a phage lysogens displayed moderate to severe growth defects in minimal medium supplemented with single carbon sources, e.g. galactose, ribose, L-lactate. In addition, in phenotype microarray assays, the Stx2a phage lysogens were characterized by a significant decrease in the cell respiration with gluconeogenic substrates such as amino acids, nucleosides, carboxylic and dicarboxylic acids. In contrast, MG1655::ϕO104 and MG1655::ϕPA8 displayed enhanced respiration with several sugar components of the intestinal mucus, e.g. arabinose, fucose, N-acetyl-D-glucosamine. We also found that prophage-encoded factors distinct from CI and Cro were responsible for the carbon utilization phenotypes of the Stx2a phage lysogens.

Conclusions

Our study reveals a profound impact of the Stx phage carriage on E. coli carbon source utilization. The Stx2a prophage appears to reprogram the carbon metabolism of its bacterial host by turning down aerobic metabolism in favour of mixed acid fermentation.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5892-x) contains supplementary material, which is available to authorized users.

The mitochondrial protein Mcu1 plays important roles in carbon source utilization, filamentation, and virulence in Candida albicans

The fungus Candida albicans is both a pathogen and a commensal in humans. The ability to utilize different carbon sources available in diverse host niches is vital for both commensalism and pathogenicity. N-acetylglucosamine (GlcNAc) is an important signaling molecule as well as a carbon source in C. albicans. Here, we report the discovery of a novel gene MCU1 essential for GlcNAc utilization. Mcu1 is located in mitochondria and associated with multiple energy- and metabolism-related proteins including Por1, Atp1, Pet9, and Mdh1. Consistently, inactivating Por1 impaired GlcNAc utilization as well. Deletion of MCU1 also caused defects in utilizing non-fermentable carbon sources and amino acids. Furthermore, MCU1 is required for filamentation in several inducing conditions and virulence in a mouse systemic infection model. We also deleted TGL99 and GUP1, two genes adjacent to MCU1, and found that the gup1/gup1 mutant exhibited mild defects in the utilization of several carbon sources including GlcNAc, maltose, galactose, amino acids, and ethanol. Our results indicate that MCU1 exists in a cluster of genes involved in the metabolism of carbon sources. Given its importance in metabolism and lack of a homolog in humans, Mcu1 could be a potential target for developing antifungal agents.

Removal of parabens and their chlorinated by-products by periphyton: influence of light and temperature

The extensive use of parabens as preservatives in food and pharmaceuticals and personal care products results in frequent detection of their residuals in aquatic environment. In this work, the adsorption and removal of four parabens (methyl-, ethyl-, propyl-, and butyl-paraben) and two chlorinated methyl-parabens (CMPs) by periphyton were studied. Characteristics of the periphyton were identified to explore the possible relationship between paraben removal and periphyton properties. Results showed that linear adsorption coefficients (K _d) vary from 554.4 to 808.6 L kg^-1 for the adsorption parabens and CMPs to autoclaved periphyton. The adsorption strength is positively related to the hydrophobicity of these compounds. Removal of parabens from water by periphyton was efficient with half-life (t _1/2) values estimated using first-order kinetic model ranging from 0.49 to 3.29 days, but CMPs were more persistent with t _1/2 ranging from 1.15 to 25.57 days, and t _1/2 increased with the chlorination degree. Higher incubation temperature accelerated the removal of all tested compounds, while a better removal of CMPs was observed in dark condition. Analysis of periphyton properties suggests that bacteria played a more important role in the removal of CMPs, but no specific relationship between periphyton properties and paraben removal ability can be established.

A novel Arabidopsis phyllosphere resident Protomyces species and a re-examination of genus Protomyces based on genome sequence data

Protomyces is an understudied genus of yeast-like fungi currently defined as phytopathogens of only Umbelliferae and Compositae. Species relationships and boundaries remain controversial and molecular data are lacking. Of the 82 named Protomyces, we found few recent studies and six available cultures. We previously isolated Protomyces strains from wild Arabidopsis thaliana, a member of Brassicaceae, a family distant from accepted Protomyces hosts. We previously sequenced the genomes of all available Protomyces species, and P. arabidopsidicola sp. nov. strain C29, from Arabidopsis. Phylogenomics suggests this new species occupied a unique position in the genus. Genomic, morphological, and physiological characteristics distinguished P. arabidopsidicola sp. nov. from other Protomyces. Nuclear gene phylogenetic marker analysis suggests actin1 gene DNA sequences could be used with nuclear ribosomal DNA internal transcribed spacer sequences for rapid identification of Protomyces species. Previous studies demonstrated P. arabidopsidicola sp. nov. could persist on the Arabidopsis phyllosphere and Protomyces sequences were discovered on Arabidopsis at multiple sites in different countries. We conclude that the strain C29 represents a novel Protomyces species and propose the name of P. arabidopsidicola sp. nov. Consequently, we propose that Protomyces is not strictly associated only with the previously recognized host plants.

The novel zinc cluster regulator Tog1 plays important roles in oleate utilization and oxidative stress response in Saccharomyces cerevisiae

Many zinc cluster proteins have been shown to play a role in the transcriptional regulation of glucose-repressible genes during glucose exhaustion and diauxic shift. Here, we studied an additional member of this family called Yer184c (herein called Tog1) for transcriptional regulator of oleate. Our results showed that a Δtog1 strain displays impaired growth with several non-fermentable carbons. Tog1 is also implicated in oxidative stress tolerance. Importantly, during the glucose-oleate shift, combined results from quantitative real time-PCR and chromatin immunoprecipitation (ChIP) experiments showed that Tog1 acts as a direct activator of oleate utilizing genes, encoded key enzymes in β-Oxidation and NADPH regeneration (POX1, FOX2, POT1 and IDP2), the glyoxylate shunt (MLS1 and ICL1), and gluconeogenesis (PCK1 and FBP1). A transmission electron microscopy (TEM) analysis of the Δtog1 strain assayed with oleate also revealed a substantial decrease in peroxisome abundance that is vital for fatty acid oxidation. Overall, our results clearly demonstrated that Tog1 is a newly characterized zinc cluster regulator that functions in the complex network of non-fermentable carbon metabolism in Saccharomyces cerevisiae.

Insights into the simultaneous utilization of glucose and glycerol by Streptomyces albulus M-Z18 for high ε-poly-L-lysine productivity

The simultaneous consumption of glucose and glycerol led to remarkably higher productivity of both biomass and ε-poly-L-lysine (ε-PL), which was of great significance in industrial microbial fermentation. To further understand the superior fermentation performances, transcriptional analysis and exogenous substrates addition were carried out to study the simultaneous utilization of glucose and glycerol by Streptomyces albulus M-Z18. Transcriptome analysis revealed that there was no mutual transcriptional suppression between the utilization of glucose and glycerol, which was quite different from typical "glucose effect". In addition, microorganisms cultivated with single glycerol showed significant demand for ribose-5-phosphate, which resulted in potential demand for glucose and xylitol. The above demand could be relieved by glucose (in the mixed carbon source) or xylitol addition, leading to improvement of biomass production. It indicated that glucose in the mixed carbon source was more important for biomass production. Besides, transcriptional analysis and exogenous citrate addition proved that single carbon sources could not afford enough carbon skeletons for Embden Meyerhof pathway (EMP) while a glucose-glycerol combination could provided sufficient carbon skeletons to saturate the metabolic capability of EMP, which contributed to the replenishment of precursors and energy consumed in ε-PL production. This study offered insight into the simultaneous consumption of glucose and glycerol in the ε-PL batch fermentation, which deepened our comprehension on the high ε-PL productivity in the mixed carbon source.

Absence of the highly expressed small carbohydrate-binding protein Cgt improves the acarbose formation in Actinoplanes sp. SE50/110

Actinoplanes sp. SE50/110 (ATCC 31044) is the wild type of industrial producer strains of acarbose. Acarbose has been used since the early 1990s as an inhibitor of intestinal human α-glucosidases in the medical treatment of type II diabetes mellitus. The small secreted protein Cgt, which consists of a single carbohydrate-binding module (CBM) 20-domain, was found to be highly expressed in Actinoplanes sp. SE50/110 in previous studies, but neither its function nor a possible role in the acarbose formation was explored, yet. Here, we demonstrated the starch-binding function of the Cgt protein in a binding assay. Transcription analysis showed that the cgt gene was strongly repressed in the presence of glucose or lactose. Due to this and its high abundance in the extracellular proteome of Actinoplanes, a functional role within the sugar metabolism or in the environmental stress protection was assumed. However, the gene deletion mutant ∆cgt, constructed by CRISPR/Cas9 technology, displayed no apparent phenotype in screening experiments testing for pH and osmolality stress, limited carbon source starch, and the excess of seven different sugars in liquid culture and further 97 carbon sources in the Omnilog Phenotypic Microarray System of Biolog. Therefore, a protective function as a surface protein or a function within the retainment and the utilization of carbon sources could not be experimentally validated. Remarkably, enhanced production of acarbose was determined yielding into 8–16% higher product titers when grown in maltose-containing medium.

In-situ sludge reduction based on Mn2+-catalytic ozonation conditioning: Feasibility study and microbial mechanisms

To improve the sludge conditioning efficiency without increasing the ozone dose, an in-situ sludge reduction process based on Mn2+-catalytic ozonation conditioning was proposed. Using ozone conditioning alone as a control, a lab-scale sequencing batch reactor coupled with ozonated sludge recycle was evaluated for its operating performance at an ozone dose of 75 mg O3/g VSS and 1.5 mmol/L Mn2+ addition. The results showed a 39.4% reduction in MLSS and an observed sludge yield of 0.236 kg MLSS/kg COD for the O3+Mn2+ group compared to the O3 group (15.3% and 0.292 kg MLSS/kg COD), accompanied by better COD, NH4+-N, TN and TP removal, improved effluent SS and limited impact on excess sludge properties. Subsequently, activity tests, BIOLOG ECO microplates and 16S rRNA sequencing were applied to elucidate the changing mechanisms of Mn2+-catalytic ozonation related to microbial action: (1) Dehydrogenase activity reached a higher peak. (2) Microbial utilization of total carbon sources had an elevated effect, up to approximately 18%, and metabolic levels of six carbon sources were also increased, especially for sugars and amino acids most pronounced. (3) The abundance of Defluviicoccus under the phylum Proteobacteria was enhanced to 12.0% and dominated in the sludge, they had strong hydrolytic activity and metabolic capacity. Denitrifying bacteria of the genus Ferruginibacter also showed an abundance of 7.6%, they contributed to the solubilization and reduction of sludge biomass. These results could guide researchers to further reduce ozonation conditioning costs, improve sludge management and provide theoretical support.

Data on soil microbial carbon source utilization under different carbon input treatments in broadleaf and coniferous plantations

This article presents soil microbial carbon metabolism data under different detritus input and removal treatments (DIRT) in broadleaf and coniferous plantations in the Tashan Forests in Feixian County, Shandong Province, China (35°10′–36°00′N, 117°35′–118°20′E). The local annual air temperature is 13 °C, and the annual precipitation is 700 mm. The soil belongs to Phaeozems. The effects of DIRT on soil microbial carbon (C) metabolism in oak (Quercus variabilis Bl.) plantations and pine (Pinus thunbergii Parl.) plantations were assessed. There were five treatments for each plantation type, including: a control; doubling aboveground litter input; no aboveground litter input; no roots; and no detritus inputs. Soils were sampled after one year and nine months of DIRT. Soil microbial C metabolism was measured by EcoPlate™, which contained 31 different C substrates. The absorbance was measured with a micro-plate reader (Synergy H¹, Biotek, Vermont, USA) at 590 nm every 12 h for 240 h. The data are based on 50 samples (two forest types × five C input treatments × five replicates); three replicates of the samples were taken. Interpretation of the data can be found in “Carbon input manipulations affecting microbial carbon metabolism in temperate forest soils – a comparative study between broadleaf and coniferous plantations” (Wang et al., 2019). The data can be used for studying the roles of aboveground and belowground inputs to soil C stabilization.

Metatranscriptomic profiles reveal the biotransformation potential of azithromycin in river periphyton

Assessment of the interaction between the biotransformation of chemical contaminants and enzyme activity from aquatic microbial communities is critical for improving the micropollutant degradation in river remediation. Here, association mining based on metatranscriptomic analysis was initially applied to determine the genes encoding enzymes involved in the azithromycin (AZI) transformation process and the corresponding microbial hosts in periphyton, followed by revealing the dynamic variation in the community structure and function. In terms of the biotransformation potential, the highly correlated 15 enzymes were suggested to be primarily involved in AZI biotransformation, energy supply, and antibiotic resistance processes, especially aryl-alcohol dehydrogenases (EC: 1.1.1.90), hydroxylamine dehydrogenase (EC: 1.7.2.6), and monooxygenases (EC: 1.14.11.57) that were involved in the biotransformation of AZI. In the matter of community ecological function, the photosystem II (PSII) reaction center in the periphytic photosynthetic process, as indicated by Fv/Fm, was inhibited after AZI exposure, which may be attributed to the down-regulated genes enriched in the photosynthesis - antenna proteins (ko00196), photosynthesis (ko00195), and two-component system (ko02020) pathways. Furthermore, the periphytic utilization capacity for carbohydrates and phenolic acids was enhanced, which was in accordance with all the increased expression of transcripts involved in the corresponding molecular pathways, including aminobenzoate degradation (ko00627), starch and sucrose metabolism (ko00500), ABC transporters (ko02010), phosphotransferase system (ko02060), galactose metabolism (ko00052), amino sugar and nucleotide sugar metabolism (ko00520). Taken together, this study highlighted the critical role of river periphyton in the micropollutant degradation and unraveled the molecular mechanism of antibiotic biotransformation as well as the structural and functional damage in the periphyton.

Effects of tetracycline on the relationship between the microbial community and oxidative stress in earthworms based on canonical correlation analysis

In this study, Eisenia fetida was taken as the test organism and tetracycline was taken as the stress compound. The artificial soil test was conducted to study the utilization intensity of different carbon sources (the Biolog-microplate supplied) by microorganisms under different stress times and stress concentrations. The changes in the in vivo key enzymes activities of earthworms and oxidative stress indicators, such as malondialdehyde (MDA), were explored. The canonical correlation analysis method was the first used to establish a analysis-model to explore the relationship between the functional diversity of microbial community and the oxidative stress in earthworms in vivo under different stress times and concentrations. Research shows: 1) after tetracycline stress, in the earthworm, the CAT, POD, SOD, GPX were related to the microbes that use carbohydrate carbon sources; the GST and AChE were related to the microbes that use polymer carbon sources; the MDA was related to the microbes that use carbon sources: amino acid, carboxylic acid and phenolic acid. 2) Under low concentrations of tetracycline stress, there was no significant relationship between the functional diversity of the microbial communities and the effects of oxidative stress at this concentration. The high concentration of tetracycline can be utilized to screen probiotics that alleviate the effects of oxidative stress. 3) The utilization of carbon sources by microbial community in the earthworm after stress can be used as biomarker of ecotoxicology. It provides a basic theoretical for adding beneficial carbon sources to combat oxidative damage in vivo.

Microbial metabolic flexibility guarantees function resilience in response to starvation disturbance

Starvation disturbance due to nutrient limitation is a common problem in bioreactors. However, an understanding of how microbial systems respond to starvation remains in its infancy. Here the metabolic response mechanism of a biofilm community to starvation was investigated using a well-controlled gaseous toluene treatment biofilter through interruption of its operation. It was found that metabolic characteristics showed significant differences before and after starvation. The dominant carbon source utilization type shifted from amino acids and carboxylic acids to esters and carbohydrates after starvation, which is more conducive to improving energy production. Metagenomic sequencing analysis supported that the changes in the dominant metabolic substrate, enhanced metabolic stability, and flexibility in the mode of energy metabolism could be the main ways to guarantee functional resilience in ecosystems after starvation. The results highlight the microbial metabolic response to starvation, which would be beneficial to the understanding of functional resilience and bioreactor stability.

Metagenomic study of carbon metabolism in black soil microbial communities under lead-lanthanum stress

Pollution of soil environments with heavy metals (HMs) and rare earth elements (REEs) cannot be ignored. We aimed to determine the effects of lead combined with lanthanum (Pb-La) on microbial community structure, carbon metabolism, and differences in carbon source utilization in black soils using EcoPlates™ and a macrogenomic approach. We found that Pb and La contents and the microbial community structure together influence and shape the response of soil carbon metabolism to Pb-La. Compared with controls, microorganisms under pollution stress preferentially use phenolic and carboxylic acids as growth carbon sources. Under Pb-La stress, the relative abundance of Proteobacteria significantly increased, thereby selectively displacing heavy metal-sensitive phyla, such as Chloroflexi, Acidobacteria, and Thaumarchaeota. Altered functional potential of the microbial carbon cycle manifested as differences in carbon metabolism, methane metabolism, and carbon fixation pathways. Furthermore, an appropriate concentration of La can reduce the environmental toxicity of Pb, whereas a high concentration of La has synergistic toxicity with Pb. These findings have important implications for understanding the impact of HM-REE contamination in microbial communities and the functions associated with carbon metabolism in black soils.

Membrane-covered aerobic composting mitigated nitrous oxide emission through improved micro-aerobic state and enhanced carbon source utilization

In this study, the variables related to nitrous oxide (N2O) emissions and their interactions during membrane-covered aerobic composting (MCAC) and conventional aerobic composting were characterized at multiple scales. For the first time, it was quantified that the MCAC-created micro-positive pressure (50-500 Pa) significantly increased compost particles aerobic layer thickness by 24 %-27 % (P < 0.001). Pile-scale results demonstrated that MCAC decreased the abundance of key functional genes (nirS, nirK, cnorB, and nosZ) and microbes (norank_f__A4b, Halomonas, norank_f__norank_o__SBR1031, and norank_f__Xanthomonadaceae) associated with N2O emissions (P < 0.001); MCAC significantly enhanced the microbial metabolic potential for carbohydrate-based, carboxylic acid-based, amino acid-based, lipid-based, organic phosphate-based, and amine-based carbon sources (P < 0.05). Interaction analysis suggested that the improved micro-aerobic state inhibited the N2O generation pathway, while the increased microbial utilization of carbon facilitated the N2O reduction pathway. Consequently, MCAC decreased N2O emissions by 20 %-27 %. These findings offer valuable insights for optimizing MCAC strategies to mitigate N2O emissions.

Isolation of Genes Encoding Carbon Metabolism Pathways from Complex Microbial Communities

The ability to produce high-value products using bacteria will increasingly rely on continued research to make large-scale bacterial fermentation cost-efficient. Engineering bacteria to use alternate carbon sources as feedstock provides an opportunity to reduce production costs. Using inexpensive carbon sources from various forms of waste provides an opportunity to substantially reduce feedstock costs. Functional carbon metabolism pathways can be identified by the introduction of metagenomic libraries into the organism of interest followed by screening for the desired phenotype. We present here a method to transfer metagenomic libraries from E. coli to Pseudomonas alloputida, followed by screening for use of galactose as a sole carbon source.