Winogradsky Column Research Articles

Pathway prediction of LDPE degradation using Winogradsky column and bacterial strains from municipal solid wastes

Pathway prediction of LDPE degradation using Winogradsky column and bacterial strains from municipal solid wastes

Mini Winnies: scaled down and transparent Winogradsky columns for microscopy in microbiology education.

Winogradsky columns were invented by Sergei Winogradsky in the 1880s and have commonly been used as a microbiology classroom learning tool in K-12 and collegiate education. However, they can be challenging to examine with microscopy. We scaled down Winogradsky columns into nuclear magnetic resonance (NMR) tubes and replaced the natural sediment with a transparent soil substitute toward the goal of observing the microbial growth under a bright-field microscope without column disassembly. Using this "Mini Winnie" approach, students can practice their microscopy skills while observing microbial growth inside the column after only days of incubation on the laboratory windowsill. Overall, we believe that the Mini Winnies provide a simple method for maximizing student engagement while giving them a greater understanding of how microorganisms interact in the environment.

Searching for bacterial plastitrophs in modified Winogradsky columns

IntroductionPlastic pollution has surged due to increased human consumption and disposal of plastic products. Microbial communities capable of utilizing plastic as a carbon source may play a crucial role in degrading and consuming environmental plastic. In this study, we investigated the potential of a modified Winogradsky column (WC) to enrich Connecticut landfill soil for plastic-degrading bacteria and genes.MethodsBy filling WCs with landfill soil and inorganic Bushnell Haas medium, and incorporating polyethylene (PE) strips at different soil layers, we aimed to identify bacterial taxa capable of degrading PE. We employed high-throughput 16S rRNA sequencing to identify the microbes cultivated on the plastic strips and the intervening landfill soil. We used PICRUSt2 to estimate the functional attributes of each community from 16S rRNA sequences.Results and discussionAfter 12 months of incubation, distinct colors were observed along the WC layers, indicating successful cultivation. Sequencing revealed significant differences in bacterial communities between the plastic strips and the intervening landfill-soil habitats, including increased abundance of the phyla Verrucomicrobiota and Pseudomonadota (néé Proteobacteria) on the strips. Based on inferred genomic content, the most highly abundant proteins in PE strip communities tended to be associated with plastic degradation pathways. Phylogenetic analysis of 16S rRNA sequences showed novel unclassified phyla and genera enriched on the plastic strips. Our findings suggest PE-supplemented Winogradsky columns can enrich for plastic-degrading microbes, offering insights into bioremediation strategies.

Literature Review: Winogradsky Column sebagai Metode Biologis untuk Degradasi Masker Medis (Disposable Mask)

The Covid-19 pandemic has had many negative impacts on human life. One of them is the large amount of medical mask waste. The purpose of this article is to collect and analyze articles regarding the use of the Winogradsky column in the degradation of plastic waste and medical masks. The method used in making this article is a review article. The articles used are relevant research articles from the last 10 years. After conducting research on the article, it was concluded that the decomposition of plastic waste using the Winogradsky column method proved successful in reducing the quality of polyethylene

Effect of alkaline leaching of phosphogypsum on sulfate reduction activity and bacterial community composition using different sources of anaerobic microbial inoculum

Phosphogypsum (PG), a by-product of the phosphate industry, is high in sulfate, (SO42−), which makes it an excellent substrate for sulfate-reducing bacteria (SRB) to produce hydrogen sulfide. This work aimed to optimize SO42− leaching from PG to achieve a high biological reduction of SO42− and generate high sulfide concentrations for subsequent use in the biological recovery of elemental sulfur. Five SRB consortia were isolated and enriched from: IS (Industrial sludges), MS (Marine sediments), WC (Winogradsky column), SNV (petroleum industry sediments) and PG (stored Phosphogypsum). The five consortia showed reduction activity when using PG leachate (with water) as source of SO42− and lactate, acetate, or glucose as the electron donor. The highest reduction rate (81.5 %) was registered using lactate and the IS consortium (81.5 %) followed by MS (79 %) and PG (71 %). To enhance the concentration of leached SO42− from PG for future utilization with the isolated consortia, PG was treated with NaOH solutions (2 % and 5 %). SO42− release of 97 % was achieved with a 5 % concentration and the resulting leachate was further diluted to target a SO42− concentration of 12.4 g·L−1 for utilization with the isolated consortia. Compared to water leachate, a significantly higher reduction rate was registered (2 g·L−1 of SO42) using the IS consortium, demonstrating limited inhibition effect of sulfide− concentration on SRB functionalities. Moreover, metagenomic analysis of the consortia revealed that using PG as a source of SO42− increased the abundance of Deltaproteobacteria, including known SRB like Desulfovibrio, Desulfomicrobium, and Desulfosporosinus, as well as novel SRB genera (Cupidesulfovibrio, Desulfocurvus, Desulfococcus) that showed, for the first time, significant potential as novel sulfate-reducers using PG as a SO42− source.

Degradation of LDPE Using the Winogradsky Column Containing Otteri Dumpsite Soil: Prediction of Mechanism and Metabolites Determination

Background of the Research: Plastic pollution has taken over the world. Toxicity of the plastics and other pollutants is enhanced due to the formation of microplastics and nano-plastics that attract Persistent Organic Pollutants (POPs). The need for the treatment of plastic waste in the current scenario led to the rise of various treatment processes. Biodegradation, an eco-friendly approach to eliminate plastics urged to discover plastic-utilizing bacteria and plastic-eating worms. Bacterial degradation of plastics has been extensively studied utilizing the entire microbial community. Hence, the current research focuses on the biodegradation of Low-Density polyethylene (LDPE) using Winogradsky Column constructed using dump yard soil. LDPE degradation was determined using FTIR and GC-MS analysis, which is used to analyze the degradation mechanism of LDPE. Methods: Sample Collection and Column Construction: The soil samples collected from the Chennai dump yard were used to construct Winogradsky columns. The column with LDPE and enrichment sources is used to study LDPE degradation. Analysis of LDPE Degradation: The LDPE sheet after incubation was washed with surfactant and ethanol. The dried sheet was analyzed for weight loss and the metabolites were identified using GC-MS analysis. The GC-MS chromatogram was used to determine the pattern of degradation by the microbial community in the dump yard soil. Results: The mass spectral analysis of GC peaks has been carried out using the electron ionization method, and ions were detected using positive ions scanning mode. The GC peaks appeared at 22.532 and 23.117 min in the control LDPE sheet, which was found to be nonadecane and octacosane, whereas, in the treated LDPE sheet, the GC peaks appeared at 22.467 and 23.062 min. The fragmentation pattern indicates the loss of m/z 14, which confirms the loss of methylene (-CH2-) fragments in alkyl chains. The difference in retention time could be correlated with the increase of CH2 in the alkyl chain length and molecular weight. Higher molecular weight alkanes, such as C16, C18, and C20 above appeared at higher retention times. The presence of longer alkyl chains indicates the LDPE polymer chains. The treated LDPE sample has been analyzed, and the fragmentation pattern indicates the presence of aliphatic chains of C16 or C18. Conclusion: The current study provides an efficient method to utilize the microbial community as a whole to degrade LDPE. The degradation mechanism of LDPE was determined using GC-MS analysis. The high molecular weight polymeric chain was degraded to small chains, and the formation of alcohol indicates the occurrence of terminal oxidation. Hence, this confirms the degradation of LDPE by the microbiome present in the dump yard soil.

The Effects of Roundup™ on Benthic Microbial Assemblages

Given the wide usage of Roundup, a common herbicide, the impacts of its presence in ecological communities are of great interest. Many studies have investigated the effects of glyphosate, the active ingredient in Roundup, on different factions of an ecosystem including on animals, plants, microorganisms, and nutrients. The current study expanded upon these works using Roundup instead of glyphosate to provide a realistic application in which to observe the development of microbial assemblages and nutrient composition in two different habitats. Winogradsky columns were prepared using benthic material from a ditch and a pond. Varying concentrations of Roundup were introduced to the columns at the beginning of the study and microbial growth and nutrient compositions from each column were measured weekly. The results indicate that the presence of Roundup has varying effects on microorganisms and nutrients. While photosynthetic microbes were negatively impacted, a shift in the microbial composition to heterotrophic microbes indicates that these microorganisms were able to utilize some ingredients in Roundup as a nutrient source. Additionally, the temporal analysis of nutrient compositions indicated that microbes metabolize glyphosate starting with the phosphate moiety even when the other compounds in Roundup are present. While these trends were observed in both benthic habitats, the composition of the ecological community can affect its ability to utilize the ingredients in Roundup as a nutrient source.

Winogradsky Bioelectrochemical System as a Novel Strategy to Enrich Electrochemically Active Microorganisms from Arsenic-Rich Sediments

Bioelectrochemical systems (BESs) have been extensively studied for treatment and remediation. However, BESs have the potential to be used for the enrichment of microorganisms that could replace their natural electron donor or acceptor for an electrode. In this study, Winogradsky BES columns with As-rich sediments extracted from an Andean watershed were used as a strategy to enrich lithotrophic electrochemically active microorganisms (EAMs) on electrodes (i.e., cathodes). After 15 months, Winogradsky BESs registered power densities up to 650 μWcm-2. Scanning electron microscopy and linear sweep voltammetry confirmed microbial growth and electrochemical activity on cathodes. Pyrosequencing evidenced differences in bacterial composition between sediments from the field and cathodic biofilms. Six EAMs from genera Herbaspirillum, Ancylobacter, Rhodococcus, Methylobacterium, Sphingomonas, and Pseudomonas were isolated from cathodes using a lithoautotrophic As oxidizers culture medium. These results suggest that the tested Winogradsky BES columns result in an enrichment of electrochemically active As-oxidizing microorganisms. A bioelectrochemical boost of centenarian enrichment approaches, such as the Winogradsky column, represents a promising strategy for prospecting new EAMs linked with the biogeochemical cycles of different metals and metalloids.

Development of a Remote, Course-Based Undergraduate Experience to Facilitate In Silico Study of Microbial Metabolic Pathways.

ABSTRACTCourse-based undergraduate research experiences (CUREs) often occur in a physical lab space, but they can also be offered remotely while maintaining course expectations and providing opportunity for authentic student engagement in research. Using a novel framework, remote Microbial Ecology CURE students used microbes isolated via antimicrobial-challenged Winogradsky columns to investigate phylogeny and metabolism through a hypothesis-driven meta-analysis (MA). Students used 16S rRNA and key metabolic enzymes to compare phylogeny; enzymes were modeled and evaluated for putative conserved domains, culminating in primer design and analysis. Using in silico tools facilitated student development of bioinformatics skills. The MA was subdivided into discrete sections in order to (i) provide a timeline for students to remain on schedule throughout a remote-learning lab experience, (ii) encourage feedback throughout the project, and (iii) facilitate student understanding of the experimental design. MA deliverables were designed to be specific figures with individual titles, legends, and analyses to enable their feedback for subsequent presentations. The six key formative deliverables included a word cloud (used to develop the works cited list and hypothesis), a 16S rRNA phylogenetic tree, an annotated metabolic pathway and three-dimensional model of the key metabolic enzyme, a phylogenetic tree based on the key metabolic enzyme, design and analysis of a primer set for the key metabolic enzyme, and a summative poster and graphical abstract. The MA project yielded poster presentations at virtual conferences, lab presentations, and written reports. Using the hypothesis-based MA model encouraged an authentic research experience, enabling students to develop, discuss, and progress in meaningful experiments.

Unruly objects: NFTs, blockchain technologies and bio-conservation

This article explores and challenges notions and methodologies of conservation, including the use of blockchain technologies as a means of establishing provenance of a physical BioArtwork, of the artist’s documentation encapsulating their intentions and of the conservator’s records required for the artwork’s ongoing care. The exploration is done through a case study of an art project called ‘Unruly Objects and Biological Conservation’ created by Anna Dumitriu with support from Alex May. The artwork consists of three items containing RFID tags sealed in resin – which point to the location of the artist’s documentation. Therefore, the works physically include instructions for maintaining their inherent concepts and materiality for the benefit of the conservators. Such instructions can often be difficult to track down, or become disassociated from the artwork while the digital preservation of this storage method also poses its own set of questions. The works also include biological material including mud from a bacterial ecosystem known as a Winogradsky Column, living plant material and SARS-CoV-2 (coronavirus) RNA from a plasmid construct.

Structure-Based Long-Term Biodegradation of the Azo Dye: Insights from the Bacterial Community Succession and Efficiency Comparison

In this study, microbial community dynamics were explored during biological degradation of azo dyes with different chemical structures. The effect of the different molecular structures of the azo dyes was also assessed against the simultaneous removal of color and the bacterial community. Winogradsky columns were inoculated with dewatered sludge and separately fed with six different azo dyes to conduct the sludge acclimatization process, and nine bacterial decolorizing strains were isolated and identified. The decolorization and biodegradation performances of the acclimated system and isolated strains were also determined. Results showed that the bacterial isolates involved in decolorization and the degradation of the azo dyes were mainly associated with the azo dye structure. After 24 h acclimatization at room temperature without specific illumination, immediate decolorization of methyl red (89%) and methyl orange (78%) was observed, due to their simple structure compared to tartrazine (73%). However, after 8 days of acclimatization, methyl red was easily decolorized up to 99%, and about 87% decolorization was observed for orange G (87%), due to its complex chemical structure. Higher degrees of degradation and decolorization were achieved with Pseudomonas geniculate strain Ka38 (Proteobacteria), Bacillus cereus strain 1FFF (Firmicutes) and Klebsiella variicola strain RVEV3 (Proteobacteria) with continuous shaking at 30 °C. The azo dyes with benzene rings were found to be easier to decolorize and degrade with similar microbial communities. Moreover, it seems that the chemical structures of the azo dyes, in a sense, drove the divergent succession of the bacterial community while reducing the diversity. This study gives a deep insight into the feasible structure-based artificial manipulation of bacterial communities and offers theoretical guidance for decolorizing azo dyes with mixed bacteria cultures.

Influencia de la proporción de celulosa y sulfato en la generación de voltaje en columnas de Winogradsky

It is possible to measure the voltage generation in Winogradsky columns by adding an electrical circuit with an anode (buried in sediment) and a cathode (submerged in water). The effect of cellulose/sulfate ratio on voltage generation in sediment columns has not been systematically investigated. Therefore, the aim of this work is the optimization by factorial design the cellulose/sulfate ratio to improve voltage generation in Winogradsky columns. Voltage was generated under different cellulose/sulfate ratios, from 0.08 to 2.57. The voltage in each Winogradsky columns was recorded for 45 days. The response surface model identified an optimal cellulose/sulfate ratio of 0.75 that produced voltage between 300 to 400 mV for several days. These devices represents an alternative for renewable energy generation and cellulose waste could be used as a carbon source.

Acetaminophen degradation using bacterial strains isolated from winogradsky column and phytotoxicity analysis of dump site soil

The increase in pollution increased the threat level of living organisms in the environment. Municipal Solid Waste is one of the most important wastes which contribute to polluted sites affecting livelihood. They pollute the water stream, marine environment ecology, soil fertility, and agriculture production. This, in turn, reduces the microflora of the marine environment, agricultural soil, and fertility. This could be analyzed by setting up a Winogradsky column using dumpsite soil samples. The current work was designed to study the municipal solid wastes from different dumpsite soil. Soil characterization revealed that the pH of Kodungaiyur and Otteri was 7.3 and 6.4. The bulk density was 0.067 g/cm3 and 0.069 g/cm3. The Porosity resulted to be 0.511 particle/volume and 0.513 particle/volume for Kodungaiyur and Otteri. The Kodungaiyur soil containing contaminants supplied with natural sources showed a 100% germination index, and Otteri soil containing contaminants supplied with natural sources showed a maximum vigour index. The presence of medicinal strips in the collected soil samples led to the study on Acetaminophen degradation. HB1 showed to be 79 ± 0.005% at optimum pH 5 containing 100 mg/L of Acetaminophen at day four among the isolated bacterial strains. Further, the intermediate formation was determined using FTIR and GC-MS. The isolated HB1 bacterial strain was identified as Staphylococcus hominis, which is heterotroph.

Analysis and microbial degradation of Low-Density Polyethylene (LDPE) in Winogradsky column

Plastic pollution is threatening the world and the life in it. Cost-effective and eco-friendly treatment is the need of the hour. Treating plastics using chemical methods adds up chemicals into the environment with toxic byproducts. The physical method, a slow and expensive process, is not the better alternative. The process should rely on the environmental sources producing eco-friendly byproducts. The byproducts such as biofuel could be utilized for a sustainable environment, but the conversion of plastics into biofuel is expensive. Hence, biodegradation is the better, sustainable, and cost-effective process for plastic/any other pollutant removal. The study focuses on the construction of Winogradsky column using dumpsite soil. The column amended with Low-Density Polyethylene (LDPE) serves as a carbon source for native microbes. The utilization of microbes in every niche for the degradation enhances the degradation of LDPE. The Otteri soil resulted in 35.4 ± 0.3%, while Kodungaiyur and agriculture soil show 29.7 ± 0.6% and 19.8 ± 0.8%. The AFM analysis shows the disruption of smooth LDPE surface by forming ridges and grooves, which further confirms the occurrence of degradation. The FTIR analysis shows the incorporation of OH, CO, and other CO–O–CO in the CH backbone of LDPE. The oxidation of LDPE will aid in cleavage and result in the process of weathering. The tensile strength decreased after LDPE treatment (23.88 MPa - control, 22.50 MPa – Kodungaiyur, and 14.92 MPa – Otteri). Thus, utilizing the native microbes present in every niche enhances the degradation of pollutants.

Winogradsky columns as a strategy to study typically rare microbial eukaryotes

Winogradsky columns have been widely used to study soil microbial communities, but the vast majority of those investigations have focused on the ecology and diversity of bacteria. In contrast, microbial eukaryotes (ME) have been regularly overlooked in studies based on experimental soil columns. Despite the recognized ecological relevance of ME in soil communities, investigations focused on ME diversity and the abundance of certain groups of interest are still scarce. In the present study, we used DNA metabarcoding (high-throughput sequencing of the V4 region of the 18S rRNA locus) to survey the ME diversity and abundance in an experimental Winogradsky soil column. Consistent with previous surveys in natural soils, our survey identified members of Cercozoa (Rhizaria; 31.2%), Apicomplexa and Ciliophora (Alveolata; 12.5%) as the predominant ME groups, but at particular depths we also detected the abundant presence of ME lineages that are typically rare in natural environments, such as members of the Vampyrellida (Rhizaria) and Breviatea (Amorphea). Our survey demonstrates that experimental soil columns are an efficient enrichment-culture approach that can enhance investigations about the diversity and ecology of ME in soils.

Large and interacting effects of temperature and nutrient addition on stratified microbial ecosystems in a small, replicated, and liquid-dominated Winogradsky column approach.

Aquatic ecosystems are often stratified, with cyanobacteria in oxic layers and phototrophic sulfur bacteria in anoxic zones. Changes in stratification caused by the global environmental change are an ongoing concern. Increasing understanding of how such aerobic and anaerobic microbial communities, and associated abiotic conditions, respond to multifarious environmental changes is an important endeavor in microbial ecology. Insights can come from observational and experimental studies of naturally occurring stratified aquatic ecosystems, theoretical models of ecological processes, and experimental studies of replicated microbial communities in the laboratory. Here, we demonstrate a laboratory‐based approach with small, replicated, and liquid‐dominated Winogradsky columns, with distinct oxic/anoxic strata in a highly replicable manner. Our objective was to apply simultaneous global change scenarios (temperature, nutrient addition) on this micro‐ecosystem to report how the microbial communities (full‐length 16S rRNA gene seq.) and the abiotic conditions (O2, H2S, TOC) of the oxic/anoxic layer responded to these environmental changes. The composition of the strongly stratified microbial communities was greatly affected by temperature and by the interaction of temperature and nutrient addition, demonstrating the need of investigating global change treatments simultaneously. Especially phototrophic sulfur bacteria dominated the water column at higher temperatures and may indicate the presence of alternative stable states. We show that the establishment of such a micro‐ecosystem has the potential to test global change scenarios in stratified eutrophic limnic systems.

Non-domestic wastewater treatment with fungal/bacterial consortium followed by Chlorella sp., and thermal conversion of the generated sludge.

The online version contains supplementary material available at 10.1007/s13205-021-02780-1.

Integrated approach in LDPE degradation – An application using Winogradsky column, computational modeling, and pathway prediction

Plastic pollution in the current scenario requires a sustainable and eco-friendly treatment process. Single-use plastics accumulate more than recyclable plastic wastes. Low-Density Polyethylene (LDPE) is one among the plastic family with inert characteristics. The traditional method, such as landfilling, develops pollution resistant micro-organisms. It is involved in the exploitation of the native microbes to the fullest. The soil of the Kodungaiyur, agriculture site, and Otteri dumpyard were used, which resulted in nearly 22.97 ± 2.7115%, 15.91667 ± 2.73775%, and 10.74 ± 0.502925% of LDPE degradation in 30 days without nutrient supplements. The enrichment of the column by organic nutrients increased the degradation of LDPE. The column enrichment was confirmed by the sulfur oxidizing bacteria (SOB) Escherichia coli and Pseudomonas stutzeri, which produced 195 mg/mL of sulfate ions. The FTIR of the LDPE degradation showed the polymer's oxygenation, while the electron microscopic images revealed cracks. In addition, an attempt was made to fit the experimental time-series data into suitable mathematical models to look at prediction and elementary forecasting. Three mathematical models, namely the customized moving averages model (CMAM), simple liinear regression model (SLRM), and a modified linear regression model (MLRM) with a lag, were able to represent the real experimental data complementarily.

Semi-continuous desulfurization of natural gas in photobioreactor by green sulfur-oxidizing bacterial consortia isolated from hot spring

Anoxygenic phototrophic bacteria are able to oxidize and remove hydrogen sulfide from natural sources by using inorganic substrates and light. In the present study, anoxygenic phototrophic bacteria were isolated from Vartoon hot spring (east of Isfahan Province, Iran) and used for removal of sulfide compounds from natural gas in a semi-continuous photobioreactor. Mat samples that obtained from the depth of spring were introduced into Winogradsky columns and kept in the presence of sunlight for 3–4 months until green and purple layers were composed. The layers were then transferred into mineral medium and incubated under anaerobic condition. The sequence of amplified 16S rDNA in green bacteria and an amplified sequence among the gene encoding photosynthetic reaction center in purple bacteria were used for molecular identification of bacteria. The bacterial growth based on the contents of bacteriochlorophylls and the extent of elemental sulfur production by the cells were measured after ethanol extraction. Molecular identification validated the presence of Chlorobium phaeobacteroides and Prosthecochloris vibrioformis from green sulfur bacteria in the consortium. The results indicated the most increase in bacteriochlorophylls c, d, and e content of mineral medium after bacterial growth. In addition, by releasing 62.4 mmol elemental sulfur, 79.30% increase was detected in sulfur content of the medium during 3 weeks. The consortium of sulfur-oxidizing phototrophic bacteria was potentially used for natural gas desulfurization in the semi-closed photobioreactor. This system is suggested as a replacement for chemoautotrophic systems in areas where there is sufficient access to sunlight.

It Takes a Village: Discovering and Isolating the Nitrifiers.

It has been almost 150 years since Jean-Jacques Schloesing and Achille Müntz discovered that the process of nitrification, the oxidation of ammonium to nitrate, is a biological process carried out by microorganisms. In the following 15 years, numerous researchers independently contributed paradigm shifting discoveries that formed the foundation of nitrification and nitrification-related research. One of them was Sergei Winogradsky, whose major accomplishments include the discovery of both lithotrophy (in sulfur-oxidizing bacteria) and chemoautotrophy (in nitrifying bacteria). However, Winogradsky often receives most of the credit for many other foundational nitrification discoveries made by his contemporaries. This accumulation of credit over time is at least in part due to the increased attention, Winogradsky receives in the scientific literature and textbooks as a “founder of microbiology” and “the founder of microbial ecology.” Here, some light is shed on several other researchers who are often overlooked, but whose work was instrumental to the emerging field of nitrification and to the work of Winogradsky himself. Specifically, the discovery of the biological process of nitrification by Schloesing and Müntz, the isolation of the first nitrifier by Grace and Percy Frankland, and the observation that nitrification is carried out by two distinct groups of microorganisms by Robert Warington are highlighted. Finally, the more recent discoveries of the chemolithoautotrophic ammonia-oxidizing archaea and complete ammonia oxidizers are put into this historical context.