Identification of Viral Pathogen Diversity in Sewage Sludge by Metagenome Analysis

The large diversity of viruses that exist in human populations are potentially excreted into sewage collection systems and concentrated in sewage sludge. In the U.S., the primary fate of processed sewage sludge (class B biosolids) is application to agricultural land as a soil amendment. To characterize and understand infectious risks associated with land application, and to describe the diversity of viruses in human populations, shotgun viral metagenomics was applied to 10 sewage sludge samples from 5 wastewater treatment plants throughout the continental U.S, each serving between 100 000 and 1 000 000 people. Nearly 330 million DNA sequences were produced and assembled, and annotation resulted in identifying 43 (26 DNA, 17 RNA) different types of human viruses in sewage sludge. Novel insights include the high abundance of newly emerging viruses (e.g., <i>Coronavirus</i> HKU1, <i>Klassevirus</i>, and <i>Cosavirus</i>) the strong representation of respiratory viruses, and the relatively minor abundance and occurrence of <i>Enteroviruses</i>. Viral metagenome sequence annotations were reproducible and independent PCR-based identification of selected viruses suggests that viral metagenomes were a conservative estimate of the true viral occurrence and diversity. These results represent the most complete description of human virus diversity in any wastewater sample to date, provide engineers and environmental scientists with critical information on important viral agents and routes of infection from exposure to wastewater and sewage sludge, and represent a significant leap forward in understanding the pathogen content of class B biosolids

Indoor Emissions as a Primary Source of Airborne Allergenic Fungal Particles in Classrooms

This study quantifies the influence of ventilation and indoor emissions on concentrations and particle sizes of airborne indoor allergenic fungal taxa and further examines geographical variability, each of which may affect personal exposures to allergenic fungi. Quantitative PCR and multiplexed DNA sequencing were employed to count and identify allergenic fungal aerosol particles indoors and outdoors in seven school classrooms in four different countries. Quantitative diversity analysis was combined with building characterization and mass balance modeling to apportion source contributions of indoor allergenic airborne fungal particles. Mass balance calculations indicate that 70% of indoor fungal aerosol particles and 80% of airborne allergenic fungal taxa were associated with indoor emissions; on average, 81% of allergenic fungi from indoor sources originated from occupant-generated emissions. Principal coordinate analysis revealed geographical variations in fungal communities among sites in China, Europe, and North America (<i>p</i> < 0.05, analysis of similarity), demonstrating that geography may also affect personal exposures to allergenic fungi. Indoor emissions including those released with occupancy contribute more substantially to allergenic fungal exposures in classrooms sampled than do outdoor contributions from ventilation. The results suggest that design and maintenance of buildings to control indoor emissions may enable reduced indoor inhalation exposures to fungal allergens

Predicting Contaminant Adsorption in Black Carbon (Biochar)-Amended Soil for the Veterinary Antimicrobial Sulfamethazine

Commercial hardwood biochars ranging in N₂ specific surface area of 0.1–427 m²·g^–1 were added to an agricultural soil at 0, 1, or 2% levels to determine whether they would predictably reduce the pore water concentration of sulfamethazine (SMT). The soil and biochar-soil mixtures were preweathered under mild (2 d, 20 °C) or more severe (28 d, 40 °C) conditions before spiking. The carbon-normalized biochar-water distribution coefficient (<i>K</i>_BC) of the biochars varied by a factor of up to 10⁴, depending on biochar properties and SMT concentration. Except for the fast-pyrolysis biochar, <i>K</i>_BC greatly exceeded the soil organic carbon–water distribution coefficient <i>K</i>_OC. Sorption in the mixtures increased as expected with biochar and dose. However, sorption was dramatically overpredicted (by up to 10^2.5) by the sum of sorption to the individual components, indicating a strong weathering effect even under the mild conditions. The soil-subtracted weathered biochar-water isotherms were more linear, and the <i>K</i>_BC values approached or lay within the range of <i>K</i>_OC values reported for SMT in 19 soils. Biochars both in intimate contact with soil and placed in a membrane bag suspended in the solution showed reduced N₂–B.E.T. surface area after weathering, implicating fouling of the biochar surface by humic substances transferred through water. The results indicate that only highly surfaceous, carbonaceous biochars would be useful for stabilizing soil contaminated with compounds such as SMT. They also suggest that weathering may attenuate the contribution of native (environmental) black carbon to sorption of such compounds in soils and sediments

Relative abundances of bacteria in the indoor air, ventilation duct air, floor dust, and HVAC filter dust samples.

<p>Relative abundances of the 20 most common bacterial taxa in indoor air, ventilation duct air, HVAC filter dust, and floor dust. Indoor and ventilation duct air include PM₁₀ samples from indoor air when the room was occupied. Floor dust samples were sieved PM₃₇ floor dust and resuspended PM₁₀ floor dust taken after occupancy. HVAC filter dust represents samples from the filter of the building HVAC system that handled a variable mixture of outdoor air and indoor return air. Taxa are classified to the highest taxonomic level to which they could be confidently assigned. Error bars represent one standard error of the mean for nine indoor air PM₁₀ samples, four floor dust samples, and three HVAC duct samples. Groups shown represent 55% of floor dust, 83% of HVAC filter dust, 51% of indoor air taxa, and 46% of ventilation duct air taxa.</p

Airborne particulate matter, filter dust, and floor dust samples acquired and analyzed in this study.

<p>Airborne particulate matter, filter dust, and floor dust samples acquired and analyzed in this study.</p

The influence of floor dust resuspension and particle shedding on particle number concentrations of varying optical diameter.

<p>Plotted are the ratio of occupied indoor to simultaneous outdoor particle number concentrations for five size ranges from 0.3 µm to 10 µm under the following three conditions. Black bars represent the case of 30 people sitting on a carpeted floor that is covered with plastic sheeting (to prevent resuspension of floor dust). White bars represent one person walking on a carpeted floor covered with plastic sheeting. Gray bars represent one person walking on a carpeted floor (without plastic sheeting). Error bars indicate one standard error of the mean for replicate experiments. The experiment in which 30 people were sitting on a carpeted floor covered with plastic sheeting was conducted only once.</p

Enrichment of bacteria in airborne particulate matter and floor dust.

<p>Bacterial mass percentage (100×bacterial mass divided by total particle mass) in indoor air, outdoor air, and duct supply air samples and in the PM_2.5 and PM₁₀ size fraction of resuspended floor dust samples. Mass fractions were estimated assuming an average mass of 655 fg per bacterium <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034867#pone.0034867-Ilic1" target="_blank">[25]</a>. Box and whisker plots have the same interpretation as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034867#pone-0034867-g001" target="_blank">Figure 1</a>.</p

Additional file 2 of Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques

Additional file 2. Review history

Additional file 1 of Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques

Additional file 1. Includes all supplementary information, supplementary figures and supplementary tables