Diverse Environmental Samples Research Articles

Molecular Insights into Bile Salt Hydrolase-Positive Lactobacilli: A PCR-Based Identification Approach

Bile salt hydrolase (BSH)-positive Lactobacilli play a crucial role in gut health and have been associated with various physiological benefits. This study presents a comprehensive molecular investigation into the identification of BSH-positive Lactobacilli using a polymerase chain reaction (PCR)-based approach. The methodology involves the targeted amplification of specific genetic markers associated with BSH activity, enabling the precise discrimination of these beneficial bacteria within complex microbial communities. The study encompasses the design and validation of PCR primers specific to BSH-encoding genes, ensuring the accurate detection of BSH-positive Lactobacilli strains. Utilizing this molecular tool, we conducted extensive screenings across diverse environmental samples, revealing the prevalence and diversity of BSH positive strains in various ecosystems.

Effects of different assembly strategies on gene annotation in activated sludge

Activated sludge comprises diverse bacteria, fungi, and other microorganisms, featuring a rich repertoire of genes involved in antibiotic resistance, pollutant degradation, and elemental cycling. In this regard, hybrid assembly technology can revolutionize metagenomics by detecting greater gene diversity in environmental samples. Nonetheless, the optimal utilization and comparability of genomic information between hybrid assembly and short- or long-read technology remain unclear. To address this gap, we compared the performance of the hybrid assembly, short- and long-read technologies, abundance and diversity of annotated genes, and taxonomic diversity by analysing 46, 161, and 45 activated sludge metagenomic datasets, respectively. The results revealed that hybrid assembly technology exhibited the best performance, generating the most contiguous and longest contigs but with a lower proportion of high-quality metagenome-assembled genomes than short-read technology. Compared with short- or long-read technologies, hybrid assembly technology can detect a greater diversity of microbiota and antibiotic resistance genes, as well as a wider range of potential hosts. However, this approach may yield lower gene abundance and pathogen detection. Our study revealed the specific advantages and disadvantages of hybrid assembly and short- and long-read applications in wastewater treatment plants, and our approach could serve as a blueprint to be extended to terrestrial environments.

A hierarchical cerium metal organic framework-graphene oxide heterostructure composite for rapid and efficient scavenging of fluoride

The rational design of functional heretrostructures with integrated advantages for the efficient adsorption and removal of fluoride is important for water pollution control. In this study, a cerium metal organic framework-graphene oxide heterostructure composite (CeMOF@GO) is successfully prepared through ultrasonic irradiation and vapor diffusion-assisted interfacial growth. CeMOF@GO with hierarchical structure boosts the mass transport of fluoride with adsorption time reduced to 25 min. By virtue of the specific ligand exchange between adsorbed H2O/OH− at metal defect sites and fluoride ions, such unique CeMOF@GO can be utilized for fluoride removal, showing satisfactory adsorption capacity (151.5 mg g−1), excellent specific affinity (with a distribution coefficient of up to 21.865 L g−1), glorious salt tolerance (8.0 mol L−1 of nitrate), wide pH applicability and eminent recycling ability. The practical application of CeMOF@GO is well demonstrated by the selective scavenging of fluoride from diverse environmental water samples. This work is expected to provide a reliable defluorination approach, and bridge the gap between academic MOF-based adsorbent research and practical environmental application.

Examining Antimicrobial Resistance in Escherichia coli: A Case Study in Central Virginia's Environment.

While environmental factors may contribute to antimicrobial resistance (AMR) in bacteria, many aspects of environmental antibiotic pollution and resistance remain unknown. Furthermore, the level of AMR in Escherichia coli is considered a reliable indicator of the selection pressure exerted by antimicrobial use in the environment. This study aimed to assess AMR variance in E. coli isolated from diverse environmental samples, such as animal feces and water from wastewater treatment plants (WWTPs) and drainage areas of different land use systems in Central Virginia. In total, 450 E. coli isolates obtained between August 2020 and February 2021 were subjected to susceptibility testing against 12 antimicrobial agents approved for clinical use by the U.S. Food and Drug Administration. Approximately 87.8% of the tested isolates were resistant to at least one antimicrobial agent, with 3.1% showing multi-drug resistance. Streptomycin resistance was the most common (73.1%), while susceptibility to chloramphenicol was the highest (97.6%). One isolate obtained from WWTPs exhibited resistance to seven antimicrobials. AMR prevalence was the highest in WWTP isolates, followed by isolates from drainage areas, wild avians, and livestock. Among livestock, horses had the highest AMR prevalence, while cattle had the lowest. No significant AMR difference was found across land use systems. This study identifies potential AMR hotspots, emphasizing the environmental risk for antimicrobial resistant E. coli. The findings will aid policymakers and researchers, highlighting knowledge gaps in AMR-environment links. This nationally relevant research offers a scalable AMR model for understanding E. coli ecology. Further large-scale research is crucial to confirm the environmental impacts on AMR prevalence in bacteria.

Compound Similarity Network as a Novel Data Mining Strategy for High-Throughput Investigation of Degradation Pathways of Organic Pollutants in Industrial Wastewater Treatment.

Identification of degradation products and pathways is crucial for investigating emerging pollutants and evaluation of wastewater treatment methods. Nontargeted analysis is a powerful tool to comprehensively investigate the degradation pathways of organic pollutants in real-world wastewater samples but often generates large data sets, making it difficult to effectively locate the exact information on interests. Herein, to efficiently establish the linkages among compounds in the same degradation pathways, we introduce a compound similarity network (CSN) as a novel data mining strategy for LC-MS-based nontargeted analysis of complex wastewater samples. Different from molecular networks that cluster compounds based on MS/MS spectra similarity, our CSN strategy harnesses molecular fingerprints to establish linkages among compounds and thus is spectra-independent. The effectiveness of CSN was demonstrated by nontargeted identification of degradation pathways and products of organic pollutants in leather industrial wastewater that underwent laboratory-scale activated carbon adsorption (ACD) and ozonation treatments. Utilizing CSN in interpreting nontargeted data, we tentatively annotated 4324 compounds in the untreated leather industrial wastewater, 3246 after ACD, and 3777 after ACD/ozonation. We located 145 potential degradation pathways of organic pollutants in the ACD/ozonation process using CSN and validated 7 pathways with 15 chemical standards. CSN also revealed 5 clusters of emerging pollutants, from which 3 compounds were selected for in vitro cytotoxicity study to evaluate their potential biohazards as new pollutants. As CSN offers an efficient way to connect massive compounds and to find multiple degradation pathways in a high-throughput manner, we anticipate that it will find wide applications in nontargeted analysis of diverse environmental samples.

Culture-independent detection of low-abundant Clostridioides difficile in environmental DNA via PCR.

Clostridioides difficile represents a major burden to public health. As a well-known nosocomial pathogen whose occurrence is highly associated with antibiotic treatment, most examined C. difficile strains originated from clinical specimen and were isolated under selective conditions employing antibiotics. This suggests a significant bias among analyzed C. difficile strains, which impedes a holistic view on this pathogen. In order to support extensive isolation of C. difficile strains from environmental samples, we designed a detection PCR that targets the hpdBCA-operon and thereby identifies low abundances of C. difficile in environmental samples. This operon encodes the 4-hydroxyphenylacetate decarboxylase, which catalyzes the production of the antimicrobial compound para-cresol. Amplicon-based analyses of diverse environmental samples demonstrated that the designed PCR is highly specific for C. difficile and successfully detected C. difficile despite its absence in general 16S rRNA gene-based detection strategies. Further analyses revealed the potential of the hpdBCA detection PCR sequence for initial phylogenetic classification, which allows assessment of C. difficile diversity in environmental samples via amplicon sequencing. Our findings furthermore showed that C. difficile strains isolated under antibiotic treatment from environmental samples were originally dominated by other strains according to PCR amplicon results. This provided evidence for selective cultivation of under-represented but antibiotic-resistant isolates. Thereby, we revealed a substantial bias in C. difficile isolation and research.IMPORTANCEClostridioides difficile is a main cause of diarrheic infections after antibiotic treatment with serious morbidity and mortality worldwide. Research on this pathogen and its virulence has focused on bacterial isolation from clinical specimens under antibiotic treatment, which implies a substantial bias in isolated strains. Comprehensive studies, however, require an unbiased strain collection, which is accomplished by isolation of C. difficile from diverse environmental samples and avoidance of antibiotic-based enrichment strategies. Thus, isolation can significantly benefit from our C. difficile-specific detection PCR, which rapidly verifies C. difficile presence in environmental samples and further allows estimation of the C. difficile diversity by using next-generation sequencing.

Glyphosate detection via a nanomaterial-enhanced electrochemical molecularly imprinted polymer sensor

Glyphosate (GLY) is a widely used herbicide with an important role in agriculture. It effectively controls weeds, enhancing agricultural yield and product quality. However, its use raises significant concerns such as potential risks to non-target ecosystems and human health. In response to these concerns, we develop an electrochemical sensor with a molecularly imprinted polymer (MIP) and gold nanoparticles for GLY detection. The sensor includes a screen-printed carbon electrode (SPCE) functionalized with gold nanoparticles and a self-assembled polyvinyl carboxylic acid chloride (PVC-COOH) layer. GLY compounds interact with carboxylic groups and are encapsulated by a polymer of methacrylic acid (MAA) cross-linked with ethylene glycol dimethacrylate (EGDMA). Electrochemical performance was assessed using differential pulse voltammetry (DPV), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS). Morphological characterization was performed using scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and atomic force microscopy (AFM). The sensor exhibits impressive selectivity, detecting GLY within a range of 273–1200 pg/mL with minimal interference from other pesticides. It boasts a low detection limit of 0.8 pg/mL (signal-to-noise ratio S/N = 3) by DPV and 0.001 pg/mL by EIS. The sensor’s versatility extends to various sample types, including surface water, agricultural wastewater, soil, and cucumber, demonstrating high recovery rates (> 96.05%) and low relative standard deviation (RSD) (< 5.7%). The developed MIP sensor is proven to be a valuable tool for rapid and highly sensitive detection of GLY in diverse environmental and agri-food samples.

Occurrence and distribution of microplastics in the adjacent environment of Yellow River Delta, China

In the precent study, the microplastics (MPs) pollution level was evaluated in diverse environmental samples from the Yellow River Delta. The results indicated that the abundance of MPs in water, sediment and soil samples ranged from 0.50 to 7.83 items·L−1, 200 to 4200 items·kg−1, and 100 to 1400 items·kg−1, respectively. Film form of MPs was dominant in water, while fiber MPs were dominant in both sediment and soil samples. In all samples, most MPs were < 1 mm in size. White was the main color in water, black was the main color in sediment and soil samples. The most common MPs type was polyethylene (33 %) in water, while rayon accounted for the majority of MPs in sediment (42 %) and soil (70 %) samples. The redundancy analysis results showed that MPs in water and sediment were more affected by water quality, while soil MPs were easily affected by landscape pattern.

Development of a Novel Internally Controlled HrpB1 Gene-Based Real-Time qPCR Assay for Detection of Burkholderia pseudomallei.

Melioidosis, caused by category B bioterrorism agent Burkholderia pseudomallei, is a seasonal disease of tropical and subtropical regions with a high mortality rate. An early and culture-independent detection ofB. pseudomalleiis required for the appropriate disease management and prevention. The present study is designed to identify novel and unique sequences ofB. pseudomalleiand development of quantitative polymerase chain reaction (qPCR) assay. A novel B. pseudomallei-specific target sequence was identified by in silico analysis for the qPCR assay development. The specificity of the developed assay was assessed using purified DNA of 65 different bacterial cultures, and the sensitivity was estimated using a cloned target gene. Further, a type III secretion protein HrpB1 (HrpB1) gene-based duplex qPCR assay incorporating suitable extraction and amplification control was developed, and its viability was assessed in different clinical and environmental matrices for the detection of B. pseudomallei. In this study, an 80-nucleotide-longB. pseudomallei-specific region within the geneHrpB1was identified by computational analysis. The developedHrpB1-based qPCR assay was highly specific forB. pseudomalleidetection when evaluated with 65 different bacterial cultures. The sensitivity of the qPCR assay with theHrpB1-recombinant plasmid was found to be five copies per qPCR reaction. The assay's detection limit was found to be 5 × 102 CFU/mL for human blood and urine, 5 × 101 CFU/mL in river water, and 2 × 103 CFU/gm in paddy field soil. The results of the study showed the applicability of a novelHrpB1-based qPCR assay for sensitive and specific detection ofB. pseudomalleiin diverse clinical and environmental samples.

Dancing the Nanopore limbo – Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction

BackgroundWhile genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies of short-reads often result in incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. Although Nanopore sequencing has increasingly been used in microbial metagenomics as long reads greatly improve the assembly quality of MAGs, the recommended DNA quantity usually exceeds the recoverable amount of DNA of environmental samples. Here, we evaluated lower-than-recommended DNA quantities for Nanopore library preparation by determining sequencing quality, community composition, assembly quality and recovery of MAGs.ResultsWe generated 27 Nanopore metagenomes using the commercially available ZYMO mock community and varied the amount of input DNA from 1000 ng (the recommended minimum) down to 1 ng in eight steps. The quality of the generated reads remained stable across all input levels. The read mapping accuracy, which reflects how well the reads match a known reference genome, was consistently high across all libraries. The relative abundance of the species in the metagenomes was stable down to input levels of 50 ng. High-quality MAGs (> 95% completeness, ≤ 5% contamination) could be recovered from metagenomes down to 35 ng of input material. When combined with publicly available Illumina reads for the mock community, Nanopore reads from input quantities as low as 1 ng improved the quality of hybrid assemblies.ConclusionOur results show that the recommended DNA amount for Nanopore library preparation can be substantially reduced without any adverse effects to genome recovery and still bolster hybrid assemblies when combined with short-read data. We posit that the results presented herein will enable studies to improve genome recovery from low-biomass environments, enhancing microbiome understanding.

A sensitive method to determine 210Po and 210Pb in environmental samples by alpha spectrometry using CuS micro-precipitation

A new sensitive method to determine polonium-210 (210Po) and lead-210 (210Pb) in a diversity of environmental samples was developed. For fresh and marine waters, Po was pre-concentrated using a titanium (III) hydroxide (Ti(OH)3) co-precipitation. Solid environmental samples were digested with nitric acid (HNO3) and hydrogen peroxide (H2O2). The alpha thin layer source was prepared using CuS micro-precipitation and 210Po was measured by alpha spectrometry. Lead-210 was left to decay for up to a year and indirectly measured via its progeny, 210Po. The chemical recoveries for 210Po and 210Pb were high, 90% and 97%, respectively, for a large variety of samples and a very low minimum detectable activity (MDA) was obtained. The method was validated using standardized solutions and certified reference materials.

Activated carbon synthesized from Arecanut catechu L. as a sustainable precursor intercalated TiO2 modified electrode for the detection of fungicide Dichlorophen

Pesticides, such as dichlorophen (DCP), pose serious threats to the ecosystem and human health. Hence, developing an efficient and sensitive detection method is crucial for environmental monitoring and remediation. In this study, we present a novel composite material comprised of TiO2 intercalated areca nut husk-derived activated carbon for the ultrasensitive detection of dichlorophen. The activated carbon is derived through a well-established activation process using areca nut husk waste, a sustainable biomass material. The material's irregular structure and large surface area provide abundant adsorption sites for the target analyte, DCP. The integration of TiO2 nanoparticles further enhances the detection capability due to their exceptional catalytic properties. Upon exposure to DCP, their interaction with the surface of composite material leads to measurable changes in its electrical and chemical properties. Cyclic voltammetry (CV) and square wave voltammetry (SWV) techniques are used to validate the performance of the fabricated electrode. The developed ultrasensitive detection method exhibits remarkable DL (detection limit, 1.01 × 10−8 M) and QL (quantification limit, 3.36 × 10−8 M) values, hence can be a promising alternative for environmental monitoring, industrial safety, and public health applications. The synergistic effect between activated carbon and TiO2 nanoparticles ensures a highly sensitive and selective response to DCP. Consequently, this advanced sensor system has great potential for detecting and quantifying dichlorophen concentrations in diverse environmental samples.

Eu-MOF based fluorescence probe for ratiometric and visualization detection of Cu2+

Water contamination caused by heavy metals represents an urgent global issue. Cu2+, a potential trace heavy metal pollutant, can accumulate in the human body through the food chain, leading to excessive levels that give rise to diverse health complications. Hence, in this investigation, a novel and efficacious fluorescent probe named Eu-BTB was developed for the detection of Cu2+, employing 1,3,5-triphenyl(4-carboxyphenyl) (H3BTB) as the ligand and Eu3+ as the metallic framework. The probe demonstrates exceptional fluorescence characteristics. The interaction between the probe ligand BTB and Eu3+ triggers an antenna effect, heightening the emission efficiency of Eu3+ while preserving its intrinsic emission. The introduction of Cu2+ competes with BTB for binding, thus quelling the antenna effect and inducing a fluorescence alteration. Within the concentration range of 0.05–10 μM, the fluorescence intensity-to-Cu2+ concentration ratio exhibits a robust linear correlation, with a remarkably low detection limit of 10 nM and a rapid response time of 3 min. The fluorescent probe has been effectively deployed for the detection of copper ions in water across diverse environmental conditions, with the obtained outcomes being validated via the conventional approach of inductively coupled plasma mass spectrometry (ICP-MS). The Eu-BTB probe showcases the advantages of simplicity, swiftness, and broad applicability, thus affirming its potential for the prompt and accurate detection of Cu2+ in diverse environmental water samples.

Cypermethrin toxicity in the environment: analytical Insight into detection methods and microbial degradation pathways.

The unrestricted utilization of xenobiotic compounds has sparked widespread concern by the world's growing population. A synthetic pyrethroid called cypermethrin (CP) is commonly utilized as an insecticide in horticulture, agriculture, and pest control. The high toxicity levels of accumulated CP have prompted environmental concerns; it damages soil fertility, and an ecosystem of essential bacteria, and causes allergic reactions and tremors in humans by affecting their nervous systems. The damage caused by CP to groundwater, food, and health makes it imperative that new effective and sustainable alternatives are investigated. Microbial degradation has been established as a reliable technique for mineralizing CP into less toxic chemicals. Among the many enzymes produced by bacteria, carboxylesterase enzymes are determined to be the most efficient in the CP breakdown process. High-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS) has been reported as the best methods for determining CP and its metabolized products, with detection limits as low as ppb from diverse environmental samples. The current study describes the ecotoxicological impact of CP and innovative analytical techniques for their detection. The newly isolated CP-degrading bacterial strains have been evaluated in order to develop an efficient bioremediation strategy. The proposed pathways and the associated critical enzymes in the bacterial mineralization of CP have also been highlighted. Additionally, the strategic action to control CP toxicity has been discussed.

Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis

At particular stages during their life cycles, fungi use multiple strategies to form specialized structures to survive unfavorable environmental conditions. These strategies encompass sporulation, as well as cell-wall melanization, multicellular tissue formation or even dimorphism. The resulting structures are not only used to disperse to other environments, but also to survive long periods of time awaiting favorable growth conditions. As a result, these specialized fungal structures are part of the microbial seed bank, which is known to influence the microbial community composition and contribute to the maintenance of diversity. Despite the importance of the microbial seed bank in the environment, methods to study the diversity of fungal structures with improved resistance only target spores dispersing in the air, omitting the high diversity of these structures in terms of morphology and environmental distribution. In this study, we applied a separation method based on cell lysis to enrich lysis-resistant fungal structures (for instance, spores, sclerotia, melanized yeast) to obtain a proxy of the composition of the fungal seed bank. This approach was first evaluated in-vitro in selected species. The results obtained showed that DNA from fungal spores and from yeast was only obtained after the application of the enrichment method, while mycelium was always lysed. After validation, we compared the diversity of the total and lysis-resistant fractions in the polyextreme environment of the Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano. Environmental samples were collected from the salt flat and from microbial mats in small surrounding ponds. Both the lake sediments and microbial mats were dominated by Ascomycota and Basidiomycota, however, the diversity and composition of each environment differed at lower taxonomic ranks. Members of the phylum Chytridiomycota were enriched in the lysis-resistant fraction, while members of the phylum Rozellomycota were never detected in this fraction. Moreover, we show that the community composition of the lysis-resistant fraction reflects the diversity of life cycles and survival strategies developed by fungi in the environment. To the best of our knowledge this is the first time that the fungal diversity is explored in the Salar de Huasco. In addition, the method presented here provides a simple and culture independent approach to assess the diversity of fungal lysis-resistant cells in the environment.

Molybdenum oxide grafted-polyaniline nanocomposite modified ITO electrode for electrochemical sensing of arsenic oxyanion

Potentiometric sensing of oxyanions such as arsenate over self-assembly engineered and chemically responsive molybdenum dioxide grafted polyaniline (PANI/MoO3) plated ITO glass electrode has been reported. FT-IR, XRD, SEM, EDX, STEM-mapping, Raman spectroscopy, and N2 adsorption-desorption measurements were used to determine the impact of molecular architecture on the structure, morphology, and physical characteristics of PANI/MoO3. The obtained result implies the synthesis of a porous hybrid nanostructured material with enhanced orientated crystallinity, enhanced adsorption capacity, and responsiveness because of an optimized molecular structure and crystallinity alignment. The limit of detection (LOD) for detecting As(V) ions by using PANI/MoO3 composite/ITO electrodes based on the differential pulse voltammetry technique (DPV) was found to be around 0.15 ppb. The interaction between arsenate and molybdate oxyanions led to the development of an induced potential, which helped to clarify the sensing mechanism, charge transfer, and shifting characteristics. For the on-site detection of residual arsenate in diverse environmental samples, the analytical performance of the produced electrode in a genuine sample was also investigated.

Metabolomic responses in livers of female and male zebrafish (Danio rerio) following prolonged exposure to environmental levels of zinc oxide nanoparticles

Zinc oxide nanoparticles (ZnONPs) are widespread pollutants that are present in diverse environmental samples. Here, we determined metabolomic and bioenergetic responses in the liver of female and male zebrafish exposed to a prolonged environmentally relevant concentration of ZnONPs. Metabolome analysis revealed that exposure to 500 μg/L ZnONPs reduced the abundance of metabolites in the tricarboxylic acid (TCA) cycle by modulating the activities of rate-limiting enzymes α-ketoglutarate dehydrogenase and isocitrate dehydrogenase. Moreover, oxidative phosphorylation (OXPHOS) was negatively impacted in the liver based upon decreased activities of mitochondrial Complex I and V in both female and male livers. Our results revealed that bioenergetic responses were not attributed to dissolved Zn2+ and were not sex-specific. However, the metabolic responses in liver following exposure to ZnONPs did show sex-specific responses. Females exposed to ZnONPs compensated for the energetic stress via increasing fatty acids and amino acids metabolism, while males compensated to ZnONPs exposure by adjusting amino acids metabolism, based upon transcript profiles. This study demonstrates that zebrafish adjust the transcription of metabolic enzymes in the liver to compensate for metabolic disruption following ZnONPs exposure. Taken together, this study contributes to a comprehensive understanding of risks related to ZnONPs exposure in relation to metabolic activity in the liver.Environmental implication Zinc oxide nanoparticles (ZnONPs) are widely used in industry and are subsequently released into environments. However, biological responses between female and male following ZnONPs exposure has never been compared. Our data revealed for the first time that female and male zebrafish showed comparable bioenergetic responses, but different metabolic responses to ZnONPs at an environmentally relevant dose. Females compensated for the energetic stress via increasing fatty acids and amino acids metabolism, while males compensated to ZnONPs exposure by adjusting amino acids metabolism in livers. This study reveals that sex may be an important variable to consider in risk assessments of nanoparticles released into environments.

Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater

Single-cell genomics is applied to environmental samples as a method to solve the problems of current metagenomics. However, in the fluorescence-activated cell sorting-based cell isolation and subsequent whole genome amplification, the sorting efficiency and the sequence quality are greatly affected by the type of target environment, limiting its adaptability. Here, we developed an improved single-cell genomics platform, named SAG-gel, which utilizes gel beads for single-cell isolation, lysis, and whole genome amplification. To validate the versatility of SAG-gel, single-cell genome sequencing was performed with model bacteria and microbial samples collected from eight environmental sites, including soil and seawater. Gel beads enabled multiple lysis treatments. The genome coverage with model bacteria was improved by 9.1–25%. A total of 734 single amplified genomes were collected from the diverse environmental samples, and almost full-length 16S rRNA genes were recovered from 57.8% of them. We also revealed two marine Rhodobacter strains harboring nearly identical 16S rRNA genes but having different genome contents. In addition, searching for viral sequences elucidated the virus-host linkage over the sampling sites, revealing the geographic distribution and diverse host range of viruses.

Cu-PyC MOF with oxidoreductase-like catalytic activity boosting colorimetric detection of Cr(VI) on paper

Hexavalent chromium ions (Cr(VI)) are highly toxic and prone to bioaccumulation in the natural environment. This study sought to develop a facile and cost-effective approach to on-site monitoring Cr(VI) content in diverse environmental samples. We synthesized copper-based MOF nanozymes (Cu-PyC MOF) and developed a simple colorimetric method by which to detect Cr(VI) on paper-based devices. The colorimetric product is obtained using the MOF nanozyme as a catalyst, Cr(VI) as an oxidant, 3,3′,5,5′-tetramethylbenzidine (TMB) as a chromogenic substrate to produce a bluish-green color observable by the naked eye or a UV–visible spectrophotometer. After Cu-PyC MOF was suspended in an acidic buffer, it remained stable and showed oxidoreductase-like catalytic activity, which in turn boosts Cr(VI) reduction. The proposed scheme enables the detection of Cr(VI) within 3 min over a linear range of 0.5–50 μM with a low detection limit of 0.051 μM. The proposed nanozyme-based colorimetric method exhibits excellent reusability and selectivity over other 27 interference ions and can be used in real sample analysis.

An optimized protocol for estimating cellulase activity in biological samples

Cellulase is a microbial enzyme responsible for degrading the β-1,4 glycoside bond in polysaccharide cellulose, which is abundant in various animal foodstuffs. Cellulase is an important industrial enzyme used for various purposes, including biopolishing textile fibers, softening garments, biostoning denim fabric, and removing excess color from textiles. In the food industry, cellulase is combined with pectinase and hemicellulase. Therefore, the need for a reliable, fast, and inexpensive cellulase activity protocol that could be used with diverse biological and environmental samples is great. This study developed a novel method to quantify cellulase activity using picric acid (PCA), which reacts with generated glucose molecules to produce mahogany red picramic acid. This PCA-cellulase method uses sodium hydroxide instead of sodium carbonate to provide alkalinity in the reaction solution, increasing the stability of picramic acid and the sensitivity and linearity of the reaction. It also overcomes the limitations of previous methods. It is notable for its dependence on few chemicals with low concentrations compared to previous methods that depend on many chemicals with high concentrations. The PCA-cellulase method was optimized using the Box–Behnken design, and its accuracy was determined using a response surface approach. A Bland–Altman cellulase activity graph was used to validate the PCA-cellulase method with a correlation coefficient of 0.9991. Therefore, the novel PCA-cellulase method provides accurate results that are comparable to existing methods.