Clay flocculation effect on microbial community composition in water and sediment

Clay-based flocculation techniques have been developed to mitigate harmful algal blooms; however, the potential ecological impacts on the microbial community are poorly understood. In this study, chemical measurements were combined with 16S rRNA sequencing to characterize the microbial community response to different flocculation techniques, including controls, clay flocculation, clay flocculation with zeolite, and clay flocculation with O2 added zeolite capping. Sediment bacterial biomass measured by PLFA were not significantly altered by the various flocculation techniques used. However, 16S rRNA sequencing revealed differences in water microbial community structure between treatments with and without zeolite capping. The differences were related to significant reductions of total nitrogen (TN), total phosphorus (TP) and ammonia (NH4+) concentration and increase of nitrate (NO3-) concentration in zeolite and O2 loaded zeolite capping. The relative abundance of ammonia oxidizing bacteria increased four-fold in zeolite capping microcosms, suggesting zeolite promoted absorbed ammonia removal in the benthic zone. Zeolite-capping promoted bacteria nitrogen cycling activities at the water-sediment interface. Potential pathogens that are usually adapted to eutrophic water bodies were reduced after clay flocculation. This study demonstrated clay flocculation did not decrease bacterial populations overall and may reduce regulatory indicators and pathogenic contaminants in water. Zeolite capping may also help prevent nutrients from being released back into the water thus preventing additional algal blooms

Oil biodegradation and bioremediation: A tale of the two worst spills in U.S. history

The devastating environmental impacts of the Exxon Valdez spill in 1989 and its media notoriety made it a frequent comparison to the BP Deepwater Horizon spill in the popular press in 2010, even though the nature of the two spills and the environments impacted were vastly different. Fortunately, unlike higher organisms that are adversely impacted by oil spills, microorganisms are able to consume petroleum hydrocarbons. These oil degrading indigenous microorganisms played a significant role in reducing the overall environmental impact of both the Exxon Valdez and BP Deepwater Horizon oil spills

Evaluating various composite sampling modes for detecting pathogenic SARS-CoV-2 virus in raw sewage

Inadequate sampling approaches to wastewater analyses can introduce biases, leading to inaccurate results such as false negatives and significant over- or underestimation of average daily viral concentrations, due to the sporadic nature of viral input. To address this challenge, we conducted a field trial within the University of Tennessee residence halls, employing different composite sampling modes that encompassed different time intervals (1 h, 2 h, 4 h, 6 h, and 24 h) across various time windows (morning, afternoon, evening, and late-night). Our primary objective was to identify the optimal approach for generating representative composite samples of SARS-CoV-2 from raw wastewater. Utilizing reverse transcription-quantitative polymerase chain reaction, we quantified the levels of SARS-CoV-2 RNA and pepper mild mottle virus (PMMoV) RNA in raw sewage. Our findings consistently demonstrated that PMMoV RNA, an indicator virus of human fecal contamination in water environment, exhibited higher abundance and lower variability compared to pathogenic SARS-CoV-2 RNA. Significantly, both SARS-CoV-2 and PMMoV RNA exhibited greater variability in 1 h individual composite samples throughout the entire sampling period, contrasting with the stability observed in other time-based composite samples. Through a comprehensive analysis of various composite sampling modes using the Quade Nonparametric ANCOVA test with date, PMMoV concentration and site as covariates, we concluded that employing a composite sampler during a focused 6 h morning window for pathogenic SARS-CoV-2 RNA is a pragmatic and cost-effective strategy for achieving representative composite samples within a single day in wastewater-based epidemiology applications. This method has the potential to significantly enhance the accuracy and reliability of data collected at the community level, thereby contributing to more informed public health decision-making during a pandemic

Microbial Interactions With Dissolved Organic Matter Drive Carbon Dynamics and Community Succession

Knowledge of dynamic interactions between natural organic matter (NOM) and microbial communities is critical not only to delineate the routes of NOM degradation/transformation and carbon (C) fluxes, but also to understand microbial community evolution and succession in ecosystems. Yet, these processes in subsurface environments are usually studied independently, and a comprehensive view has been elusive thus far. In this study, we fed sediment-derived dissolved organic matter (DOM) to groundwater microbes and continually analyzed microbial transformation of DOM over a 50-day incubation. To document fine-scale changes in DOM chemistry, we applied high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and soft X-ray absorption spectroscopy (sXAS). We also monitored the trajectory of microbial biomass, community structure and activity over this time period. Together, these analyses provided an unprecedented comprehensive view of interactions between sediment-derived DOM and indigenous subsurface groundwater microbes. Microbial decomposition of labile C in DOM was immediately evident from biomass increase and total organic carbon (TOC) decrease. The change of microbial composition was closely related to DOM turnover: microbial community in early stages of incubation was influenced by relatively labile tannin- and protein-like compounds; while in later stages the community composition evolved to be most correlated with less labile lipid- and lignin-like compounds. These changes in microbial community structure and function, coupled with the contribution of microbial products to DOM pool affected the further transformation of DOM, culminating in stark changes to DOM composition over time. Our study demonstrates a distinct response of microbial communities to biotransformation of DOM, which improves our understanding of coupled interactions between sediment-derived DOM, microbial processes, and community structure in subsurface groundwater

Fuzzy Systems Modeling of In Situ Bioremediation of Chlorinated Solvents

Abstract. The full-scale in situ bioremediation demonstration conducted at DOE's Savannah River Site revealed a wide range of spatial and temporal variations of concentrations of VOCs, enzymes, and biomass in groundwater and vadose zone monitoring boreholes over the field site. One of the powerful modern approaches to analyze uncertain and imprecise data is based on the use of methods of fuzzy systems modeling. Using fuzzy modeling we analyzed the spatio-temporal TCE and PCE concentrations and methanotroph densities in groundwater to assess the effectiveness of different campaigns of air stripping and bioremediation, and to determine the fuzzy relationship between these compounds. Our analysis revealed some details about the processes involved in remediation, which were not identified in the previous studies of the SRS demonstration. We also identified some future directions for using fuzzy systems modeling, such as the evaluation of the mass balance of the vadose zone -groundwater system, and the development of fuzzy-ruled methods for optimization of managing remediation activities, predictions, and risk assessment. Savannah River Bioremediation Experiment. In 1992-93, a large-scale vadose zone-groundwater bioremediation demonstration was conducted at the Savannah River Site by injecting several types of gases (ambient air, methane, and nitrous oxide and triethyl phosphate mixtures) through a horizontal well in the groundwater at a 175 ft depth. Simultaneously, soil gas was extracted through a parallel horizontal well in the vadose zone at a 80 ft depth (Hazen et al., 1997). Essential Features of Fuzzy Systems Modeling. Fuzzy systems modeling is an effective method to simulate the performance of a system that is uncertain because of vagueness or "fuzziness," which are inherent in th

Fuzzy systems modeling of in situ bioremediation of chlorinatedsolve n ts

A large-scale vadose zone-groundwater bioremediationdemonstration was conducted at the Savannah River Site (SRS) by injectingseveral types of gases (ambient air, methane, and nitrous oxide andtriethyl phosphate mixtures) through a horizontal well in the groundwaterat a 175 ft depth. Simultaneously, soil gas was extracted through aparallel horizontal well in the vadose zone at a 80 ft depth Monitoringrevealed a wide range of spatial and temporal variations ofconcentrations of VOCs, enzymes, and biomass in groundwater and vadosezone monitoring boreholes over the field site. One of the powerful modernapproaches to analyze uncertain and imprecise data chemical data is basedon the use of methods of fuzzy systems modeling. Using fuzzy modeling weanalyzed the spatio-temporal TCE and PCE concentrations and methanotrophdensities in groundwater to assess the effectiveness of differentcampaigns of air stripping and bioremediation, and to determine the fuzzyrelationship between these compounds. Our analysis revealed some detailsabout the processes involved in remediation, which were not identified inthe previous studies of the SRS demonstration. We also identified somefuture directions for using fuzzy systems modeling, such as theevaluation of the mass balance of the vadose zone - groundwater system,and the development of fuzzy-ruled methods for optimization of managingremediation activities, predictions, and risk assessment

Ultramicrobacteria Genome Database Project

Ultramicrobacteria (UMB) are a largely uncultured, globally abundant, and metabolically active group of bacteria. UMB have cell diameters ≤0.3μm, cell volumes ≤0.1 μm3, and small streamlined genomes. Recent findings indicate that UMB aid in bioremediation and nutrient cycling, but future investigations and comprehension of current findings are skewed by highly variable nomenclature and a lack of databases for functional, genomic, geochemical, or spatial data specific to candidate UMB. We aim to develop a user-friendly open-access database of various UMB candidates linked to an open-access online map where researchers can gather genomic, spatial, and geochemical data. Our comprehensive review of literature and genomic databases revealed several mis-identified UMB candidates, unique highly-conserved fermentation pathways, and novel membrane proteins. We are actively updating this resource and working to link this database to the K-base bioinformatics platform on the Oak Ridge National Laboratory Supercomputer. This database is one of the first steps towards further investigations of the function, structure, and potential biotechnical applications of UMB

The unique chemistry of Eastern Mediterranean water masses selects for distinct microbial communities by depth

Peer reviewedPublisher PD

Process Control Minitoring by Stress Response

Environmental contamination with a variety of pollutants hasprompted the development of effective bioremediation strategies. But howcan these processes be best monitored and controlled? One avenue underinvestigation is the development of stress response systems as tools foreffective and general process control. Although the microbial stressresponse has been the subject of intensive laboratory investigation, theenvironmental reflection of the laboratory response to specific stresseshas been little explored. However, it is only within an environmentalcontext, in which microorganisms are constantly exposed to multiplechanging environmental stresses, that there will be full understanding ofmicrobial adaptive resiliency. Knowledge of the stress response in theenvironment will facilitate the control of bioremediation and otherprocesses mediated by complex microbial communities

Draft Genome Sequence for Desulfovibrio africanus Strain PCS.

Desulfovibrio africanus strain PCS is an anaerobic sulfate-reducing bacterium (SRB) isolated from sediment from Paleta Creek, San Diego, CA. Strain PCS is capable of reducing metals such as Fe(III) and Cr(VI), has a cell cycle, and is predicted to produce methylmercury. We present the D. africanus PCS genome sequence