Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities.

While functional gene arrays (FGAs) have greatly expanded our understanding of complex microbial systems, specificity, sensitivity, and quantitation challenges remain. We developed a new generation of FGA, GeoChip 5.0, using the Agilent platform. Two formats were created, a smaller format (GeoChip 5.0S), primarily covering carbon-, nitrogen-, sulfur-, and phosphorus-cycling genes and others providing ecological services, and a larger format (GeoChip 5.0M) containing the functional categories involved in biogeochemical cycling of C, N, S, and P and various metals, stress response, microbial defense, electron transport, plant growth promotion, virulence, gyrB, and fungus-, protozoan-, and virus-specific genes. GeoChip 5.0M contains 161,961 oligonucleotide probes covering >365,000 genes of 1,447 gene families from broad, functionally divergent taxonomic groups, including bacteria (2,721 genera), archaea (101 genera), fungi (297 genera), protists (219 genera), and viruses (167 genera), mainly phages. Computational and experimental evaluation indicated that designed probes were highly specific and could detect as little as 0.05 ng of pure culture DNAs within a background of 1 μg community DNA (equivalent to 0.005% of the population). Additionally, strong quantitative linear relationships were observed between signal intensity and amount of pure genomic (∼99% of probes detected; r > 0.9) or soil (∼97%; r > 0.9) DNAs. Application of the GeoChip to a contaminated groundwater microbial community indicated that environmental contaminants (primarily heavy metals) had significant impacts on the biodiversity of the communities. This is the most comprehensive FGA to date, capable of directly linking microbial genes/populations to ecosystem functions.IMPORTANCE The rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding of complex microbial systems. However, because of the ever-expanding number of novel microbial sequences discovered each year, developing a microarray that is representative of real microbial communities, is specific and sensitive, and provides quantitative information remains a challenge. The newly developed GeoChip 5.0 is the most comprehensive microarray available to date for examining the functional capabilities of microbial communities important to biogeochemistry, ecology, environmental sciences, and human health. The GeoChip 5 is highly specific, sensitive, and quantitative based on both computational and experimental assays. Use of the array on a contaminated groundwater sample provided novel insights on the impacts of environmental contaminants on groundwater microbial communities

Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil.

Permafrost soil in high latitude tundra is one of the largest terrestrial carbon (C) stocks and is highly sensitive to climate warming. Understanding microbial responses to warming-induced environmental changes is critical to evaluating their influences on soil biogeochemical cycles. In this study, a functional gene array (i.e., geochip 4.2) was used to analyze the functional capacities of soil microbial communities collected from a naturally degrading permafrost region in Central Alaska. Varied thaw history was reported to be the main driver of soil and plant differences across a gradient of minimally, moderately, and extensively thawed sites. Compared with the minimally thawed site, the number of detected functional gene probes across the 15-65 cm depth profile at the moderately and extensively thawed sites decreased by 25% and 5%, while the community functional gene β-diversity increased by 34% and 45%, respectively, revealing decreased functional gene richness but increased community heterogeneity along the thaw progression. Particularly, the moderately thawed site contained microbial communities with the highest abundances of many genes involved in prokaryotic C degradation, ammonification, and nitrification processes, but lower abundances of fungal C decomposition and anaerobic-related genes. Significant correlations were observed between functional gene abundance and vascular plant primary productivity, suggesting that plant growth and species composition could be co-evolving traits together with microbial community composition. Altogether, this study reveals the complex responses of microbial functional potentials to thaw-related soil and plant changes and provides information on potential microbially mediated biogeochemical cycles in tundra ecosystems

MoIVD-Mediated Leucine Catabolism Is Required for Vegetative Growth, Conidiation and Full Virulence of the Rice Blast Fungus Magnaporthe oryzae

Isovaleryl-CoA dehydrogenase (IVD), a member of the acyl-CoA dehydrogenase (ACAD) family, is a key enzyme catalyzing the conversion of isovaleryl-CoA to β-methylcrotonyl-CoA in the third reaction of the leucine catabolism pathway and simultaneously transfers electrons to the electron-transferring flavoprotein (ETF) for ATP synthesis. We previously identified the ETF ortholog in rice blast fungus Magnaporthe oryzae (MoETF) and showed that MoETF was essential for fungal growth, conidiation and pathogenicity. To further investigate the biological function of electron-transferring proteins and clarify the role of leucine catabolism in growth and pathogenesis, we characterized MoIVD (M. oryzaeisovaleryl-CoA dehydrogenase). MoIvd is highly conserved in fungi and its expression was highly induced by leucine. The Δmoivd mutants showed reduced growth, decreased conidiation and compromised pathogenicity, while the conidial germination and appressorial formation appeared normal. Consistent with a block in leucine degradation, the Δmoivd mutants accumulated isovaleric acid, grew more slowly, fully lacked pigmentation and completely failed to produce conidia on leucine-rich medium. These defects were largely rescued by raising the extracellular pH, suggesting that the accumulation of isovaleric acid contributes to the growth and conidiation defects. However, the reduced virulence of the mutants was probably due to their inability to overcome oxidative stress, since a large amount of ROS (reactive oxygen species) accumulated in infected host cell. In addition, MoIvd is localized to mitochondria and interacted with its electron receptor MoEtfb, the β subunit of MoEtf. Taken together, our results suggest that MoIVD functions in leucine catabolism and is required for the vegetative growth, conidiation and full virulence of M. oryzae, providing the first evidence for IVD-mediated leucine catabolism in the development and pathogenesis of plant fungal pathogens

The regulation of the microstructure, luminescence and lubricity of multi-element doped carbon nanodots with alkylated diquaternary 1, 4-Diazabicyclo[2.2.2]octane derived dicationic ionic liquids inserted in carbon skeleton

The regulation of the microstructure, luminescence and lubricity of multi-element doped carbon nanodots with alkylated diquaternary 1, 4-Diazabicyclo[2.2.2]octane derived dicationic ionic liquids inserted in carbon skeleto

In situ tribochemical sulfurization of polyisobutylene-based molybdenum species for enhanced tribo-performance

In situ tribochemical sulfurization of polyisobutylene-based molybdenum species for enhanced tribo-performanc

Towards synergistic combination of biochar/ultrasonic persulfate enhancing removal of natural humic acids from water

International audienceRemoval of natural organic matter (NOMs) from actual water is a major challenge in the context of worldwide pollution of natural water resources. The removal of humic acids in a system combining biochar adsorption and ultrasonic persulfate oxidation was studied in this paper. The effects of biochar addition, persulfate concentration and initial pH were investigated. A high removal rate of humic acids up to 92.5% was achieved for the combined biochar/ultrasonic/persulfate system, versus 84.0% for combined biochar/persulfate, 52.0% for sole biochar, 50.0% for combined biochar/ultrasonic, 10.0% for combined persulfate/ultrasonic, 4.0% for sole ultrasonic and 1.0% for sole persulfate systems. Ultrasonic treatment increased the removal efficiency of humic acids to 90.0% within 60 min. Mechanisms towards synergistic combination of the biochar/ultrasonic/persulfate system were investigated by gel permeation chromatography, electron paramagnetic resonance and quenching experiments together with the characterization of biochar. Hydroxyl radical and the adsorption of biochar were the major contributors to the proposed synergistic adsorption-oxidation removal mechanism, followed by the sulfate radical SO 4-⋅. The results of three-dimensional fluorescence diagram, fluorescence regional integration and TOC analysis indicated that the system presented promising application prospects to remove NOM pollutants from real water

Covalently attached strategy to modulate surface of carbon quantum dots: Towards effectively multifunctional lubricant additives in polar and apolar base fluids

Covalently attached strategy to modulate surface of carbon quantum dots: Towards effectively multifunctional lubricant additives in polar and apolar base fluid

Removal of humic substances by the synergistic effect of biochar adsorption and activation of persulfate

International audienceCombined adsorption and oxidation using biochar to activate persulfate has been recently applied to remove contaminants, yet most of the experiments are carried out using artificial synthetic water instead of real waters. Here we tested the removal of humic substances which is abundant and affecting water quality in natural waters, by persulfate combined with corn stalk biochar. Results showed that, compared with biochar prepared at 400 °C, 600 °C and 700°C, biochar prepared at 900 °C after modified by hydrochloric acid had greater specific surface of 459.260 m2/g, richer porosity and higher removal of humic acids of more than 80% at pH 5.0-9.0 in pure water. Treatment of real river water showed decrease of 80.4% and 69.7% of total organic carbon (TOC) and UV 254 , respectively. The addition of tert-butyl-alcohol (TBA) and methanol (MeOH) inhibited the removal to a certain extent suggesting the existence of •OH and SO4−•. It was speculated that in addition to the adsorption of biochar, the oxygen-containing functional groups on its surface might act as active sites to promote the production of oxidized species. This work provides a method for corn stalks utilization in accordance with environmental sustainability and resource recovery

Research on the Optimization Design of Solar Energy-Gas-Fired Boiler Systems for Decentralized Heating

Solar energy-gas-fired boiler heating systems attract widespread attention due to their eco-friendly technologies and reasonable prices. In order to promote the application of a solar energy-gas-fired boiler system for decentralized heating, this study proposed a holistic method to optimize the combination of equipment specifications and control strategies of the system. A detailed mathematical model of the hybrid energy system was developed and validated by experiments to simulate various operating conditions and evaluate the optimal design results. A case study was conducted in Tianjin, China, and optimal schemes were obtained. The influence of different factors on the system’s annual comprehensive energy efficiency ratio (AEER) and annual cost (AC) were studied by sensitivity analysis; the results showed that the solar collector area was extremely valuable for the optimization of AEER and AC. The results of this study provide a reference for the optimization design of the solar energy-gas-fired boiler system, which is beneficial to the promotion of the utilization of solar energy

Research Progress in Traditional Applications, Phytochemistry, Pharmacology, and Safety Evaluation of <i>Cynomorium songaricum</i>

Cynomorium songaricum Rupr. (CSR) belongs to the family Cynomoriaceae. It is a perennial succulent parasitic herb with a reddish-brown coloration, predominantly submerged in sand and lacking chlorophyll. Traditionally, it has been used in ethnic medicine to treat various diseases, such as gastric ulcers, indigestion, bowel movements, and improving sexual function. To comprehensively collect CSR data, extensive literature searches were conducted using medical, ecological, and scientific databases such as Google Scholar, PubMed, Science Direct, Web of Science, and China National Knowledge Infrastructure (CNKI). This article summarizes and categorizes research on the uses, phytochemical characteristics, pharmacological activities, and toxicity of ethnic medicine, with the aim of establishing a solid foundation and proposing new avenues for exploring and developing potential applications of CSR. So far, a total of 98 compounds have been isolated and identified from CSR, including flavonoids, terpenes, steroids, and other compounds. It is worth noting that flavonoids and polysaccharides have significant antioxidant and anti-inflammatory properties. In addition, these compounds also show good application prospects in anti-tumor, antioxidant, anti-aging, anti-fatigue, anti-diabetes, and other aspects. Although extensive progress has been made in the basic research of CSR, further research is still needed to enhance the understanding of its mechanism of action and explore more unknown compounds. Our review indicates that CSR has broad prospects and deserves further research