Biology subjects

Majumder, E. L.- W.

Publications and source records attributed to Majumder, E. L.- W..

8 recordsLinked to original sources

bioRxiv2026

Aquifer microbial communities differentially display metabolisms capable of secondary effects on uranium speciation across a former metal processing site

Groundwater contamination presents challenges across world, yet remediation solutions in variably oxidized regions are limited and many co-interactions between contaminant metals and microbial reactions occur. Here we present a genomic and metabolic study into the biogeochemistry of a uranium-contaminated surficial aquifer site in Riverton, WY. We identified unique communities that varied based on geochemistry, geography, and compartment, matching microbial subsurface studies. Cross-site metabolism tests showed communities had functional capabilities of nitrogen respiration, manganese reduction, iron reduction, and sulfide oxidization. No sites showed evidence of microbial U-bioreduction nor ammonium oxidation. Only former tailings area groundwater and ditch surface water sites nearest a retention pond, and a downgradient oxbow lake exhibited sulfate reduction metabolisms. This was contrary to our hypothesis of near-river downgradient groundwater sites having U and S reduction capability. Most communities which showed S reduction capacity exhibited Fe oxidation capacity. Modeling demonstrated U as calcium uranyl carbonates. Based on our metabolism tests and known mineral and microbial metabolism reduction potentials, this suggests U reduction could only be achieved via abiotic reaction with biogenic sulfide. Of eleven sites tested, it is possible in four. This has impact on future site-specific remediation plans and understanding of microbial reactions in variably reduced zones. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/729369v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@1926923org.highwire.dtl.DTLVardef@13486f9org.highwire.dtl.DTLVardef@1895a91org.highwire.dtl.DTLVardef@990213_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical Abstract TextWe performed microbial membership and metabolism measurements across a uranium-contaminated sites surface and ground waters, then performed analyses relating these metrics to geochemistry at the site. Findings showed variations in the membership, yet mainly similar functional capabilities. Metabolic differences were explained in relationship to uranium cycling and remediation implications.

microbiology↗

bioRxiv2025

Patterns of Microbial Succession and Niche Differentiation Across Depth and Age in a Landfill Have Implications for Management Strategies

Despite microorganisms being primarily responsible for landfill material decomposition, limited characterization has been performed across both landfill depth and age. Here, we investigated the microbial communities and physicochemical parameters in two active and two closed landfill wells from surface to bottom, as well as fill dirt and leachate at a sanitary landfill near Madison, Wisconsin, USA. Amplicon community sequencing fungi, bacteria and archaea revealed distinct microbial community structures across landfill sites. The observed patterns of microbial community succession by depth and age mirror the known phases of the landfill life cycle. Younger surface samples were dominated by aerobic fungi, which transitioned to fermentative bacteria and methanogenic archaea in older, deeper, layers. Simultaneously, high species richness was preserved across landfill ages, while reduced evenness at specific depths support spatial niche differentiation. In conjunction with the lack of trends found for physicochemical parameters by depth, this supports niche differentiation driven by the highly heterogenous waste inputs. This study provides the first comprehensive vertical profile of bacterial, fungal, and archaeal communities across landfill depths and ages, highlighting the influence of these parameters on physicochemical factors and microbial distribution within landfills. These results have implications for improving landfill management, including renewable gas energy production, minimizing emissions, and increasing degradation rates.

microbiology↗

bioRxiv2025

Lifetime exposure to known and emerging groundwater contaminants significantly alters poultry microbiome and metabolome

The exposome encompasses all lifetime environmental exposures affecting health. Its complexity and high data dimensionality make it challenging to link specific exposure combinations to adverse health outcomes. Establishing relevant exposome criteria is key to addressing current knowledge gaps. This study evaluated contaminant levels in Wisconsin groundwater and their effects on host health. We focused on three co-occurring chemicals that were detected at concentrations exceeding groundwater standards, nitrate, atrazine and imidacloprid, and the emerging contaminant, microplastics. In this study, broilers were exposed to a low dose chemical mixture (35,000 ppb nitrate + 1.7 ppb atrazine + 0.58 ppb imidacloprid) and high dose chemical mixture (100,000 ppb nitrate + 3,000 ppb atrazine + 3,000 ppb imidacloprid) or polyethylene microplastics (PE MPs) for 49 days. We observed that both ternary mixtures and PE fiber MPs significantly altered the cecal microbiomes as determined by the enrichment of genera, Fournierella, Ruminococcus and an unclassified genus in the family Coriobacteriaceae. In addition, +PE fiber presence dysregulated metabolic pathways associated with bile acid biosynthesis and lipid metabolism. Similarly, perturbations to cecal microbial activity for both ternary chemical mixtures were confirmed via modulation of six metabolites including methylisopelletierine which had a higher total ion intensity than the control group. Interestingly, there were no detectable pathological effects to either the +PE fiber or ternary mixture treatment groups. Overall, the data presented here demonstrates that low doses of environmental contaminants are sufficient to dysregulate cecal taxonomic composition and microbial activity without inducing detectable pathological effects. ImportanceWe found that exposure to mixtures of environmental toxins caused gut dysbiosis observed by changes to the chicken cecal microbiome and metabolome. This highlights the importance of conducting such studies with environmentally relevant mixtures of contaminants at detected concentrations to understand the actual risks associated with exposures like drinking contaminated groundwater over a long period of time. Our findings demonstrate that gut microbial metabolites, now known to be key regulators and signaling molecules in a wide range of host health issues, are the source of the negative health outcomes; superseding cell death or pathological damage that are caused by acute exposures. These changes have implications for predicting negative long-term chronic health outcomes.

systems biology↗

bioRxiv2025

Acute exposure to groundwater contaminants mixture of nitrate, atrazine and imidacloprid impacts growth kinetics of poultry cecal microbiomes and significantly decreases Caco-2 cell viability

Atmospheric deposition, and agricultural runoff or erosion events have substantially contributed to groundwater pollution throughout the USA. This can become troublesome in states like Wisconsin where 68% of the population rely on groundwater for their drinking water source. As such, exposome research must account for the complexity and frequency of environmental exposures. This study aimed to elucidate chemical-biological interactions and adverse outcome pathways associated with an environmentally relevant mixture of agricultural chemicals detected in Wisconsin groundwater via in vitro and in silico methodologies. Using in vitro models, we determined that a ternary mixture of environmentally relevant concentrations of nitrate, atrazine and imidacloprid resulted in an overt decline in growth rate to the poultry cecal microbiome compared to each chemical singularly. Further, there was a decrease in Caco-2 cell viability in various two-chemical combinations. In silico methods analyzed contaminants detected in Wisconsin groundwater wells from across the state and prioritized two groundwater wells as potential for health concerns. Prioritized chemicals in these groundwater wells were linked to nine gene targets and several adverse outcome pathways. In all, the results demonstrated that there is chemical-biological interaction between these model organisms agricultural and chemical mixtures at real world exposure concentrations. HighlightsO_LIin silico methods were able to predict potential adverse effects for communities utilizing these groundwater wells C_LIO_LI8 out of 9 chemicals prioritized with in silico tools were herbicides C_LIO_LIA ternary mixture of nitrate, imidacloprid and atrazine resulted in a decline in growth rate for poultry cecal microbiome C_LIO_LICaco-2 cells significantly impacted by two-chemical combinations but not ternary mixtures C_LI

pharmacology and toxicology↗

bioRxiv2024

The usual and unusual functions of thioredoxins in the metabolism and stress-response of sulfate-reducing bacteria

Thioredoxins are small, universal, disulfide isomerase proteins with required functions in oxidative stress response and RNA synthesis, among others. However, little is known about how anaerobic organisms maintain their intracellular redox balance or how thioredoxins may function differently under anaerobic metabolism. In this study, we investigated the roles of thioredoxins in sulfate-reducing microorganisms (SRMs). SRMs use sulfate as their primary electron acceptor in respiration to produce sulfide and are found in various environments including marine, freshwater sediments, guts and biofilms on ferrous metals where corrosion occurs. We found SRMs lack common redox maintenance molecules and macromolecules but have many and varied thioredoxins belonging to three types. Then, we probed their functions in the model SRM, Desulfovibrio vulgaris Hildenborough (DvH), by an in vivo disulfide bond capture proteomics experiment in both non-stressed and oxidatively stressed conditions. Our results demonstrated that thioredoxin 1 (Trx1) was essential in DvH and selectively responded to oxidative stress. Our data supported its role in RNA synthesis and energy transduction since Trx1 interacted with DsrC and QmoB. Thioredoxin 3 (Trx3), an atypical thioredoxin, was observed to have roles in sulfur transfer and dissimilatory sulfur metabolism. Next, DvH thioredoxin system protein encoding genes were deleted and single deletion mutant strains were tested for growth phenotypes under a variety of different electron donors, acceptors and toxic metal stresses. It is found that dissimilatory sulfate reduction improves resistance of DvH to metal stress. It appeared the sulfide provided certain protection to DvH from silver and uranium stress. ImportanceWe put forth new functions for thioredoxins and a more robust understanding of sulfate reducing microorganisms physiology. Thioredoxin is of general interest because it has been widely studied for redox homeostasis or cancer therapies dealing with the excess of reactive oxygen species (ROS). Our results indicated that these proteins do have functions in stress response, even in microorganisms that generate large amounts of sulfide. We also identified interaction partners for an atypical thioredoxin, suggesting distinct roles from conserved thioredoxin. Mechanisms of metal stress response were found to be different than direct oxidative stress. Thioredoxin did not appear to be involved in uranium reduction electron transfer pathways, contradicting a hypothesis from the literature.

microbiology↗

bioRxiv2024

Co-occurrence of Direct and Indirect Extracellular Electron Transfer Mechanisms during Electroactive Respiration in a Dissimilatory Sulfate Reducing Bacterium

Extracellular electron transfer (EET) propels microbial fuel cell (MFC) technology and contributes to the mobility of redox active minerals and microbial syntrophy in nature. Sulfate-reducing bacteria (SRB), especially the genus Desulfovibrio corrode metal electrodes but are of interest for sulfate-containing MFCs providing wastewater treatment. Although extensive studies on SRB-mediated metal electrode corrosion have been done, there remain knowledge gaps on SRB EET to electrodes. We aimed to determine SRB EET mechanisms towards improving SRB performance in MFC wastewater treatment. Our MFCs with Desulfovibrio vulgaris Hildenborough (DvH), a model SRB, indicated that DvH can harvest and send electrons to the carbon cloth electrode. Electricity production with a maximum power density of [~]0.074 W/m2 was observed when the ratio of lactate (electron and carbon donor) to sulfate (electron acceptor) was 60:20 and 0:10 in the anodic and cathodic chamber, respectively. Patterns in current production compared to variations of electron donor/acceptor ratios in the anode and cathode suggested that attachment of DvH to the electrode and biofilm density were critical for effective electricity generation. Analysis of DvH biofilms at different conditions (planktonic dissimilatory sulfate reduction respiration vs. electroactive respiration) by electron microscopy indicated DvH utilized filaments that resemble nano-pili to attach on electrodes and facilitate EET from cell-to-cell and to the electrode. Proteomics profiling of electroactive respiration proteins indicated DvH adapted to electroactive respiration by presenting more pili-, flagellar-related proteins and histidine kinases on electrodes. To investigate the role of pili and biofilm, we grew two DvH mutants in MFCs under the same conditions. The mutant with a deletion of the major pilus-producing gene yielded less voltage and far less attachment to the electrode, suggesting the importance of pili in EET. The mutant with a deficiency in biofilm formation, however, did not eliminate current production indicating the existence of indirect EET. Untargeted metabolomics profiling showed flavin-based metabolites, potential electron shuttles, were dysregulated between respiration modes. This work revealed the metabolic flexibility of DvH to thrive in less than ideal conditions with solid surfaces as both an electron acceptor (growth on anode) and donor (growth on cathode) by using a combination of direct and indirect EET mechanisms. Understanding DvH EET mechanism could enhance the application of DvH in MFCs treating wastewater. ImportanceWe explored the application of Desulfovibrio vulgaris Hildenborough in microbial fuel cells (MFC) and investigated its potential extracellular electron transfer (EET) mechanism. We also conducted untargeted proteomics and metabolomics profiling, offering insights into how DvH adapts metabolically to different electron donors and acceptors. An understanding of the EET mechanism and metabolic flexibility of DvH holds promise for future uses including bioremediation or enhancing efficacy in MFCs for wastewater treatment applications.

microbiology↗

bioRxiv2024

Root exudation and rhizosphere microbial recruitment are influenced by novel plant trait diversity in carrot genotypes

Root exudate composition can influence rhizosphere microbial recruitment and is tightly controlled by plant genetics. However, little research has profiled root exudate in vegetable crops or determined their role in rhizosphere microbial community and metabolite composition. It is also not well understood how root exudates and resulting rhizosphere dynamics shift across plant trait diversity and with the development of novel crop genotypes. To address these knowledge gaps, this study paired metabolomics and microbiome analyses to evaluate associations between the composition of exudates, soil bacterial and fungal communities, and soil metabolites across four genotypes of organically produced carrot of differential breeding histories, including two experimental genotypes. Plant genotypes modified soil microbial diversity and composition, and differentially recruited bacterial taxa with demonstrated potential for plant-growth related functions including ammonia oxidation, nitrogen fixation, and phytohormone production. Bacterial rhizosphere recruitment from bulk soil was genotype and root exudate-mediated, while fungal recruitment was not. Moreover, root exudate composition was distinct in an heirloom genotype and a novel nematode resistant genotype, compared to other genotypes tested. Root exudate and rhizosphere metabolite composition was decoupled, and soil metabolites strongly associated with fungal, but not bacterial communities. Taken together, the results of this study suggest that novel crop trait diversity and breeding histories hold consequences for the functional potential of soils through the diversification of root exudate mediated plant-microbe interactions.

microbiology↗

bioRxiv2023

Co-exposure to Polyethylene Fiber and Salmonella enterica Typhimurium Alters Microbiome and Metabolome of in vitro Chicken Cecal Mesocosms

Humans and animals encounter a summation of exposures during their lifetime (the exposome). In recent years, the scope of the exposome has begun to include microplastics. Microplastics (MPs) have increasingly been found in locations where there could be an interaction with Salmonella enterica Typhimurium, one of the commonly isolated serovars from processed chicken. In this study, the microbiota response to a 24-hour co-exposure to Salmonella enterica Typhimurium and/or low-density polyethylene (PE) microplastics in an in vitro broiler cecal model was determined using 16S rRNA amplicon sequencing (Illumina) and untargeted metabolomics. Community sequencing results indicated that PE fiber with and without S. Typhimurium yielded a lower Firmicutes/Bacteroides ratio compared to other treatment groups, which is associated with poor gut health, and overall had greater changes to the cecal microbial community composition. However, changes in the total metabolome were primarily driven by the presence of S. Typhimurium. Additionally, the co-exposure to PE Fiber and S. Typhimurium caused greater cecal microbial community and metabolome changes than either exposure alone. Our results indicate that polymer shape is an important factor in effects resulting from exposure. It also demonstrates that microplastic-pathogen interactions cause metabolic alterations to the chicken cecal microbiome in an in vitro chicken cecal model. IMPORTANCEResearching the exposome, a summation of exposure of ones lifespan, will aid in determining the environmental factors that contribute to disease states. There is an emerging concern that microplastic-pathogen interactions in the gastrointestinal tract of broiler chickens may lead to an increase in Salmonella infection across flocks and eventually increased incidence of human salmonellosis cases. In this research article, we elucidated the effects of co-exposure to polyethylene microplastics and Salmonella enterica serovar Typhimurium on the ceca microbial community. Salmonella presence caused strong shifts in the cecal metabolome but not the microbiome. The inverse was true for polyethylene fiber. Polyethylene powder had almost no effect. The co-exposure had worse effects than either alone. This demonstrates that exposure effects to the gut microbial community are contaminant specific. When combined, the interactions between exposures exacerbate changes to the gut environment. The results herein support current Salmonella mitigation efforts and understanding microplastics-pathogen interactions.

systems biology↗