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

Autecology of Vibrio vulnificus and Vibrio parahaemolyticus in tropical waters

Water and shellfish samples collected from estuaries, mangroves, and beaches along the coast of Puerto Rico were examined for Vibrio vulnificus and Vibrio parahaemolyticus. An array of water quality parameters were also measured simultaneous with bacteria sampling. Both species of vibrio were associated with estuary and mangrove locations, and neither was isolated from sandy beaches. Densities of V. vulnificus were negatively correlated with salinity, 10--15 ppt being optimal. V. parahaemolyticus was isolated from sites with salinities between 20 and 35 ppt, the highest densities occurring at 20 ppt. Densities of Vibrio spp. and V. parahaemolyticus for a tropical estuary surpassed those reported for temperate estuaries by several orders of magnitude. Both densities of total Vibrio spp. and V. parahaemolyticus in the water were directly related to densities of fecal coliforms, unlike V. vulnificus. The incidence of ONPG(+) strains among sucrose({minus}) Vibrio spp. served as an indicator of the frequency of V. vulnificus in this group. More than 63% of the V. vulnificus isolated were pathogenic. V. vulnificus and V. parahaemolyticus occupy clearly separate niches within the tropical estuarine-marine ecosystem

Final technology report for D-Area oil seepage basin bioventing optimization test, environmental restoration support

One method proposed for the cleanup of the D-Area Oil Seepage Basin was in situ bioremediation (bioventing), involving the introduction of air and gaseous nutrients to stimulate contaminant degradation by naturally occurring microorganisms. To test the feasibility of this approach, a bioventing system was installed at the site for use in optimization testing by the Environmental Biotechnology Section of the Savannah River Technology Center. During the interim action, two horizontal wells for a bioventing remediation system were installed eight feet below average basin grade. Nine piezometers were also installed. In September of 1996, a generator, regenerative blower, gas cylinder station, and associated piping and nutrient injection equipment were installed at the site and testing was begun. After baseline characterization of microbial activity and contaminant degradation at the site was completed, four injection campaigns were carried out. These consisted of (1) air alone, (2) air plus triethylphosphate (TEP), (3) air plus nitrous oxide, and (4) air plus methane. This report describes results of these tests, together with conclusions and recommendations for further remediation of the site. Natural biodegradation rates are high. Oxygen, carbon dioxide, and methane levels in soil gas indicate substantial levels of baseline microbial activity. Oxygen is used by indigenous microbes for biodegradation of organics via respiration and hence is depleted in the soil gas and water from areas with high contamination. Carbon dioxide is elevated in contaminated areas. High concentrations of methane, which is produced by microbes via fermentation once the oxygen has been depleted, are found at the most contaminated areas of this site. Groundwater measurements also indicated that substantial levels of natural contaminant biodegradation occurred prior to air injection

Comparison of Thaumarchaeotal populations from four deep sea basins.

The nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. We demonstrated that there were significant differences in the abundance and diversity of Thaumarchaeotes between these four basins. The diversity of Thaumarchaeotal oligotypes differed between basins with many oligotypes only present in one of the four basins, which suggests that their distribution showed biogeographic patterning. There were also significant differences in Thaumarchaeotal community structure between these basins. This would suggest that geographically distant, yet geochemically similar basins may house distinct Thaumarchaeaotal populations. These findings suggest that Thaumarchaeota are very diverse and that biogeography in part contributes in determining the diversity and distribution of Thaumarchaeotes

High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris.

Cell membranes represent the "front line" of cellular defense and the interface between a cell and its environment. To determine the range of proteins and protein complexes that are present in the cell membranes of a target organism, we have utilized a "tagless" process for the system-wide isolation and identification of native membrane protein complexes. As an initial subject for study, we have chosen the Gram-negative sulfate-reducing bacterium Desulfovibrio vulgaris. With this tagless methodology, we have identified about two-thirds of the outer membrane- associated proteins anticipated. Approximately three-fourths of these appear to form homomeric complexes. Statistical and machine-learning methods used to analyze data compiled over multiple experiments revealed networks of additional protein-protein interactions providing insight into heteromeric contacts made between proteins across this region of the cell. Taken together, these results establish a D. vulgaris outer membrane protein data set that will be essential for the detection and characterization of environment-driven changes in the outer membrane proteome and in the modeling of stress response pathways. The workflow utilized here should be effective for the global characterization of membrane protein complexes in a wide range of organisms

Ground water and soil remediation: In situ air stripping using horizontal wells

An innovative environmental restoration technology, in situ air stripping, has been demonstrated at the US Department of Energy (DOE) Savannah River Site (SRS) in South Carolina. This process, using horizontal wells, is designed to concurrently remediate unsaturated-zone soils and ground water containing Volatile Organic Compounds (VOC). In situ technologies have the potential to substantially reduce costs and time required for remediation as well as improve effectiveness of remediation. Horizontal wells were selected to deliver and extract fluids from the subsurface because their geometry can maximize the efficiency of a remediation system and they have great potential for remediating contaminant sources under existing facilities. The first demonstration of this new technology was conducted for a period of twenty weeks. A vacuum was first drawn on the vadose zone well until a steady-state removal of VOCs was obtained. Air was then injected at three different rates and at two different temperatures. An extensive characterization program was conducted at the site and an extensive monitoring network was installed prior to initiation of the test. Significant quantities of VOCs have been removed from the subsurface (equivalent to an eleven-well, 500-gpm, pump-and-treat system at the same site). Concentrations of VOCs in the ground water have been significantly reduced in a number of the monitoring wells

Detection of Siderite (FeCO3) in Glen Torridon Samples by the Mars Science Laboratory Rover

Siderite (FeCO3) has been detected in Gale Crater for the first time by the Mars Science Laboratory (MSL) Curiosity and is seen in multiple samples in the Glen Torridon (GT) region. The identification of siderite is based on evolved gas analysis (EGA) data from the Sample Analysis at Mars (SAM) instrument and X-ray diffraction (XRD) data from the Chemistry and Mineralogy (CheMin) instrument. Curiosity descended off of the Vera Rubin ridge (VRR) into the Glen Torridon region on Sol 2300. Glen Torridon is of particular interest because a strong clay mineral signature had been detected by orbital instruments [1]. To date, four drilled samples have been collected at two different drill locations: Kilmarie and Aberlady from adjacent blocks at the base of the south side of VRR in the Jura member and Glen Etive 1 and 2 on the same block in the Knockfarril member

Mineralogy of Vera Rubin Ridge in Gale Crater from the Mars Science Laboratory CheMin instrument

Gale crater was selected as the landing site for the Mars Science Laboratory Curiosity rover because of orbital evidence for a variety of secondary minerals in the lower slopes of Aeolis Mons (aka Mount Sharp) that indicate changes in aqueous conditions over time. Distinct units demonstrate orbital spectral signatures of hematite, phyllosilicate (smectite), and sulfate minerals, which suggest that ancient aqueous environments in Gale crater varied in oxidation potential, pH, and water activity. Vera Rubin ridge (VRR) is the first of these units identified from orbit to have been studied by Curiosity. Orbital near-infrared data from VRR show a strong band at 860 nm indicative of hematite. Before Curiosity arrived at VRR, the hypotheses to explain the formation of hematite included (1) precipitation at a redox interface where aqueous Fe2+ was oxidized to Fe3+, and (2) acidic alteration of olivine in oxic fluids. Studying the composition and sedimentology of the rocks on VRR allow us to test and refine these hypotheses and flesh out the depositional and diagenetic history of the ridge. Here, we focus on the mineralogical results of four rock powders drilled from and immediately below VRR as determined by CheMin

Legionella in Puerto Rico cooling towers

Water samples from air conditioning cooling towers receiving different treatment protocols on five large municipal buildings in San Juan, Puerto Rico were assayed for various species and serogroups of Legionella spp. using direct immunofluorescence. Several water quality parameters were also measured with each sample. Guinea pigs were inoculated with water samples to confirm pathogenicity and recover viable organisms. Legionella pneumophila (1-6), L. bozemanii, L. micdadei, L. dumoffii, and L. gormanii were observed in at least one of the cooling towers. L. pneumophila was the most abundant species, reaching 10{sup 5} cells/ml, within the range that is considered potentially pathogenic to humans. A significantly higher density of L. pneumophila was observed in the cooling tower water that was not being treated with biocides. Percent respiration (INT) and total cell activity (AODC), were inversely correlated with bacterial density. This study demonstrates that Legionella spp. are present in tropical air-conditioning cooling systems, and without continuous biocide treatment may reach densities that present a health risk