Deciphering the Enzymatic and Metabolic Functional Potential of Plastisphere Microbiota: Implications for Predictive Bioremediation in Urban Waste Disposal Environments

Isotopic compositions of CH4 and CO2 surface and subsurface gases and groundwater from an urban solid waste disposal site from Gualeguaychu city (Argentina) were measured to detect origin, depth distribution, migration lateral, CH4 oxidation, and dissolution in groundwater. The highest CH4 concentrations (60–88 %) with δ13C-CH4 (between −60 and −45 ‰) and δ2H-CH4 (between −350 and −260 ‰) were attributed to CH4 originated by microbial sources, v. gr. acetate fermentation. The δ13C-CO2 related to this CH4 (between −15 and −5.9 ‰) were compatible with this process. Also, the increase of DIC associated to an increase in δ13C-DIC values (−12.4, −6.4, −5.8, −1.5, +0.1 and +4 ‰) indicated the transport of dissolved gases (from methanogenesis) in the groundwater flow system. High excess deuterium in 3 piezometers suggests that there were hydrogen isotope exchange between CH4 and water too. Evidences for CH4 oxidation were decrease in CH4 concentrations, shift in C and H isotope ratios of CH4 to more enriched in the remaining CH4 (in both, δ13C-CH4 >−50 ‰ and δ2H >−260 ‰) and depletion in 13C of the associated CO2 (<−20 ‰). Since surface CH4 and CO2 concentrations over the covering layer were very low, and the major CH4 concentrations were found between 60m and 90 cm depth, it is very probable USW has been compacted with low permeability materials (e.g., clay) avoiding large emissions to the atmosphere and creating horizontal barriers within the waste that enable lateral gas migration. Horizontally, it can be seen that these gases migrated outside the disposal site following the topography and that CH4 disappeared leading to anomalous concentrations of CO2 whose values are greater than those produced by normal soil respiration. The isotopic value (δ13C) of this CO2 was also different from that of normal soil respiration (~−25 ‰) and reflected effects that generated isotopic depletion by diffusion (~−25 to −32 ‰). The analysis of C isotopes as the main tracer, together H isotopes, has allowed the effective detection of the origin and those secondary processes.

To study the metagenomics of the microbes isolated from the canaliculus of patients with infective canaliculitis. A prospective study was performed on five consecutive canalicular samples obtained for the metagenomic analysis from the patients with infective canaliculitis who underwent non-incisional canalicular curettage at a tertiary care Dacryology service. The canalicular concretions were collected intraoperatively soon after a canalicular curettage and immediately transported on ice to the laboratory. Following DNA extraction and library preparation, a whole shotgun metagenome sequencing was performed on the Illumina™ platform. The downstream processing and bioinformatics of the samples were performed using multiple software packaged in SqueezeMeta™ pipeline or MG-RAST™ pipeline. The taxonomic hit distribution across the samples showed that bacteria were the most common isolates (mean-80.5%), followed by viruses (mean-0.74%), and archaea (0.01%). The five major phyla identified across the samples of infective canaliculitis were, Fusobacteria, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes. The prevalent organisms include Fusobacterium nucelatum, Fusobacterium periodonticum, Parvimonas micra, Prevotella oris, Selonomonas noxia, Pseudopropionobacterium propoinicum, Campylobacter showae, and Streptococcus anginosus, amongst few others. Actinomycetes israelii was noted in all the samples, though it was not the most abundant. The microbial gene mapping and protein prediction demonstrated proteins with known functions to range from 69.91% to 87.09% across the samples. The functional subsystem profiling demonstrated genes associated with carbohydrate, amino acid, and co-enzyme transport and metabolism, cell wall or cell membrane biogenesis, energy production and conversion, transcription, translation, and cellular communications. This is the first whole metagenome sequencing of infective canaliculitis. Infected canaliculi harbor diverse microbial communities, including bacteria, viruses, and archaea. Functional analysis has provided newer insights into the ecosystem dynamics and strategies of microbial communities.

Samples of PM2.5 were collected at three urban sites and one rural site simultaneously in Chongqing, the only megacity in eastern Sichuan Basin, Southwest China, from October 15 to November 13, 2015. Water-soluble ions (WSIs, i.e., F–, Cl–, NO3–, SO42–, K+, Na+, NH4+, Mg2+ and Ca2+) in PM2.5 were measured to investigate their characteristics and formation pathways. The average concentrations of PM2.5 at the urban sites were 55.5–59.0 µg m–3, which was 62.8–73.0% higher than that at rural site. SO42–, NO3–, NH4+ were the dominant ions, contributing to more than 90% of total WSIs. The coefficients of divergence for SO42– between the urban and rural sites were 0.15–0.17, indicating its relatively uniform distribution across Chongqing. Analysis of the formation mechanisms of SO42– and NO3– in PM2.5 suggested that the heterogeneous reaction was responsible for the high concentrations of sulfate among the four sites, whereas nitrate was formed mainly through homogeneous reactions at the urban sites. Furthermore, the results of trajectory clustering showed that the air pollution were mainly from local sources within the basin. Our findings on PM2.5 composition in Chongqing help to advance the knowledge on PM2.5 pollution in Chinese megacities, and to provide more evidence for further pollution mitigation.

Roles of humic substances redox activity on environmental remediation

The science of chemistry has been greatly impacted by environmental degradation, which has led to important breakthroughs and changed educational perspectives. This review highlights the role of chemists in tackling global environmental concerns by examining the diverse effects of environmental contamination on the study of chemistry. Green chemistry principles, which attempt to design safer chemicals and processes that limit waste and lessen detrimental environmental impacts, have been motivated by pollution. Environmental chemistry, which focuses on the behavior, consequences, and mitigation of pollutants, has emerged as a crucial sub-discipline as a result of the pressing need to address pollution. In addition, pollution has made it necessary to integrate interdisciplinary techniques, bringing together the fields of chemistry, biology, environmental science, and engineering to provide novel ways to pollution treatment and control. Educational curricula have evolved to incorporate these trends, emphasizing sustainable practices and the environmental implications of chemical processes. This review highlights how the growing awareness of environmental pollution continues to drive innovation and shape the future of chemical education and research, underscoring the importance of chemists in developing sustainable solutions to protect our planet.

Genome expression of Thermococcus barophilus and Thermococcus kodakarensis in response to different hydrostatic pressure conditions

Coupling of Fenton reaction and white rot fungi for the degradation of organic pollutants

The usage of a large number of industrial resources and the discharge of harmful pollutants have caused serious damage to the environment and ultimately affect the ecosystem and human health. Bioremediation is a green, sustainable and low-cost technology for the treatment of environmental pollutants, which includes the process of environmental remediation using plants, animals, microorganisms and so on. Among them, algae have the characteristics of rapid growth, wide distribution, strong stress resistance, large enrichment, and can convert pollutants into chemical products, so they play an important role in bioremediation. In this review, we introduce the types of pollutants existing in the environment, analyze the mechanism of algae for environmental remediation, and then describe the research progress of algae in the process of degradation and remediation of different pollutants. Finally, the shortages and limitations of bioremediation using algae are discussed, and its future development is prospected.

Degradation of toxic agrochemicals and pharmaceutical pollutants: Effective and alternative approaches toward photocatalysis

Introduction: The purification of genomic DNA (gDNA) and total RNA (RNA) from various specimen types using a single sample is currently in high demand in genomic settings due to the limitation of available biological material. There is an increased need for simultaneous isolation of nucleic acids in cancer genetics for use in downstream applications such as genotyping, microarrays or next generation sequencing. The Qiagen AllPrep® technique provides a comprehensive solution for extraction of gDNA and RNA from a single specimen. In this study, we tested the AllPrep® kits for concurrent isolation of gDNA and RNA from five different sample types. Materials and Methods: Genomic DNA and RNA were extracted simultaneously according to Qiagen AllPrep® manufacturer's instructions from five specimen types: bone marrow mononuclear cells (BMMC), cryopreserved cultured cell lines, whole blood, fresh frozen and FFPE samples. Quantity and quality of both nucleic acids were assessed by the NanoDrop 2000 and Qubit fluorometer 2.0. Purified gDNA from BMMC, fresh frozen, whole blood and FFPE samples was further evaluated by library preparation, targeted hybridization capture and sequencing on an Illumina NextSeq500. FastQ files were submitted to a Clinical Genome Analytics (CGA) pipeline for quality metrics analysis. Results: The AllPrep® technique resulted in effective isolation of high quality gDNA and RNA (Table1). All set wet lab and sequencing QC metrics were met for each sample type. Conclusion: We have successfully verified the AllPrep® method can be used for simultaneous extraction of both gDNA and RNA using the same input material without compromising the yield or purity of both final products. This simple procedure based on spin column technology not only gave the advantage of generating high quality results using limited specimen resources, but also decreased the hands on time by 3.5 hours and cost when compared to extraction done with two separate kits. Table 1.Represents average QC results and SD for each specimen type. **n = 8 for sequencing metricsgenomic DNAgenomic DNAtotal RNAtotal RNASample TypeOD260/280Total Yield (ng)OD260/280Total Yield (ng)Mean Target Coverage% DuplicationBMMC (n = 3)1.853033.31.9413855206.34%Whole Blood (n = 2)1.818936.51.881335566.96.47%Fresh Frozen (n = 2)1.69312752.0432375345.44.02%FFPE Specimen (n = 16)1.665133.41.9410524.1**748.2**6.10%Cultured Cell Lines (n = 5)1.8442981.9810489N/AN/ATotal Average (n = 28)1.736898.141.9510443624.75.92%Standard Deviation (SD).249180.90.110616.2228.30.013% Citation Format: Aleksandra Ras, Samantha Helm, Kevin Kelly, Vanessa Spotlow, Guruprasad Ananda, Gregory Tsongalis. Simultaneous isolation of genomic DNA and total RNA using the Qiagen AllPrep® method. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3634.

During the rainy season deterioration in the quality of water, supplied through dug wells and tube wells, near an abandoned limestone quarry was reported. The abandoned quarry is now being used as an urban waste disposal site. The problem was further complicated by hospitalization of several inhabitants who were using this water for domestic purposes. Looking into the consequences, chemical analysis of water from the quarry, dug wells and tube wells was carried out. The water was found to be contaminated. The transportation of pollutants from the quarry to the groundwater system was facilitated by karst features. Furthermore, four major sources—domestic waste disposal, water conservation structures, landfills, and water wells—contributing to pollution were identified. This case study is an attempt to provide an understanding of how the karst features facilitate groundwater contamination. It will help us answer a few questions such as why karst hydrogeology deserves special attention in urban expansion and what protective measures should be planned in view of rapid urbanization.

Development of innovative nano-sized materials for multi-functional photo-catalysis application is gaining extraordinary importance worldwide. In this sense, several metal chalcogenides nano-particles (NPs), such as TiO2,ZnO,CuO, Fe3O4, FeS, ZnS, CdSNPs etc. and their composite have been synthesized and established as effective heterogenous recyclable catalyst for conducting several photo-chemical applications to the society. When the nano-particleshave capability to absorb solar light energy, the performance for photo-catalysis has been increased much more. In this chapter it has elaborated that how the light energy even solar energy can be used to drive interesting technologies to be utilised in daily life and everyday consumer products. It has been also been presented detailed information on a photo-catalysis based number of commercial products such as hydrogen-fuel generation devices as alternative energy source from water splitting, environmental pollution remediation and technology through degradation of pollutants, air purification devices, UV-protection and self-cleaning techniques on textile-clothing solar panel, self-cleaning glasses, tiles, paint materials etc.

The abundance and distribution of microorganisms and their potential for mineralizing polycyclic aromatic hydrocarbons (PAHs) were measured in subsurface sediment samples at two geographically separate buried coal-tar sites. At a relatively undisturbed forested site in the northeastern United States, metabolic adaptation to the PAHs was evident: Radiolabeled naphthalene and phenanthrene were converted to (14)CO2 in core material from inside but not outside a plume of groundwater contamination. However, at the urban site in the midwestern United States these PAHs were mineralized in sediments from both contaminated and uncontaminated boreholes. Thus, clear qualitative evidence showing an adaptational response by the subsurface microbial community was not obtained at the urban site. Instead, subtler clues suggesting metabolic adaptation by subsurface microorganisms from the urban site were discerned by comparing lag periods and extents of (14)CO2 production from radiolabeled PAHs added to samples from contaminated and uncontaminated boreholes. Despite slightly higher PAH mineralization activity in contaminated borehole samples, p-hydroxybenzoate was mineralized equally in all samples from the urban site regardless of location. No striking trends in the abundances of actinomycetes, fungi, and either viable or total bacteria were encountered. However, colonies of the soil bacterium, Bacillus mycoides, were detected on enumeration plates of several samples from unsaturated and saturated zones in both urban boreholes. Furthermore, other common soil bacteria, Myxococcus xanthus and Chromobacterium violaceum, were identified in samples from the uncontaminated urban borehole. The occurrence of bacteria usually restricted to surface soil, combined with the observation of fragments of building materials in many of the core samples, suggested that past excavation and backfilling operations may have caused mixing of surface soil with subsurface materials at the urban site. We speculate that this mixing, as well as non-coal-tar-derived sources of PAHs, contributed to the PAH-mineralizing activity present in the sediment samples from the uncontaminated urban borehole.

In this study, Illumina sequencing platform was applied in sequencing rat pancreas, counting expression of target points, analyzing expression differences among blank group, model group and Huangqi Liuyi decoction group and exploring the therapeutic effect and mechanism of Huangqi Liuyi decoction on type 2 diabetes mellitus. According to the result, 24.25% of these genes belonged to the unknown functional class, which was the largest classification unit according to the classification analysis of genes by eggNOG. The rest were classified as energy conversion, amino acid transport and metabolism, nucleotide transport and metabolism, carbohydrate transport and metabolism, coenzyme transport and metabolism, and lipid transport and metabolism, etc.Huangqi Liuyi decoction may play a therapeutic role in the treatment of type 2 diabetes mellitus through four metabolic pathways, namely environmental information processing, cellular process, organismal system and human diseases according to KEGG enrichment analysis. This study shows that, Huangqi Liuyi decoction can significantly improve the fasting blood glucose and glycosylated hemoglobin in type 2 diabetic rats.

Acanthamoeba healyi: Expressed gene profiles with enhanced virulence after mouse-brain passage