Source Apportionment of Polycyclic Aromatic Hydrocarbons in Illinois River Sediment

The accumulation of over six million metric tons of sediment annually in the Illinois River Valley degrades its recreational, commercial, and ecological value. This necessitates dredging a large volume of sediment to restore water depth and makes beneficial reuse of the sediment a priority. Unfortunately, many reuse applications are limited by contamination from polycyclic aromatic hydrocarbons (PAHs), particularly benzo(a)pyrene in the sediments. Existing contaminant standards do not consider whether the sources of PAHs are from current petroleum combustion-based inputs or whether they represent "legacy pollution" such as coal dust released from barges, trucks, and storage. The latter is typically found in black carbon form that might be less bioavailable, and thus may not represent as high a risk for beneficial reuse. A source apportionment (SA) analysis was undertaken to identify the sources of PAHs to the Illinois River and to determine if they come from these potentially low bioavailable forms. Priority PAHs were analyzed in 80 sediment cores sampled from Illinois River pools and backwater lakes between Hennepin, Illinois and the Peoria Lock and Dam. PAH diagnostic ratio analysis and a Positive Matrix Factorization (PMF) multivariate receptor model were used to characterize the PAH dataset, identify specific sources of pollutants, and quantify source contributions to the river sediment. Predicted sources from the SA analysis were identified using a database of compiled reference PAH profiles for coal dust, coal tar sealcoat, motor oils, biosolids, as well as fossil fuel combustion residues from gasoline and diesel engines, power plants, and coke production. Three sources (S1, S2, and S3) were required to reconstruct most of the variation in the Illinois River contaminant dataset by PMF source apportionment. PMF results suggested that a mixed upland source and coal-derived sources including coal tar sealcoat (S1 and S2, 75%) were major contributors to sediment PAHs in the Illinois River, as well as a diffuse traffic-based source (S3, 25%). Liquid petroleum was not identified as a signficant source of PAHs to Illinois River sediment. Coal dust was not uniquely resolved from the coal-derived sources and thus could not be assessed for reduced PAH bioavailability. Finally, comparison of PMF results with those from the widely-used PAH diagnostic ratio method indicated that the latter does a relatively poor job of uniquely resolving PAH sources in the sediments.This research was funded by the Illinois Sustainable Technology Center (ISTC), a division of the Prairie Research Institute at the University of Illinois at Urbana-Champaign (Grant no. HWR10219).Ope

MultiCellDS: a community-developed standard for curating microenvironment-dependent multicellular data

Exchanging and understanding scientific data and their context represents a significant barrier to advancing research, especially with respect to information siloing. Maintaining information provenance and providing data curation and quality control help overcome common concerns and barriers to the effective sharing of scientific data. To address these problems in and the unique challenges of multicellular systems, we assembled a panel composed of investigators from several disciplines to create the MultiCellular Data Standard (MultiCellDS) with a use-case driven development process. The standard includes (1) digital cell lines, which are analogous to traditional biological cell lines, to record metadata, cellular microenvironment, and cellular phenotype variables of a biological cell line, (2) digital snapshots to consistently record simulation, experimental, and clinical data for multicellular systems, and (3) collections that can logically group digital cell lines and snapshots. We have created a MultiCellular DataBase (MultiCellDB) to store digital snapshots and the 200+ digital cell lines we have generated. MultiCellDS, by having a fixed standard, enables discoverability, extensibility, maintainability, searchability, and sustainability of data, creating biological applicability and clinical utility that permits us to identify upcoming challenges to uplift biology and strategies and therapies for improving human health

MultiCellDS: a standard and a community for sharing multicellular data

Cell biology is increasingly focused on cellular heterogeneity and multicellular systems. To make the fullest use of experimental, clinical, and computational efforts, we need standardized data formats, community-curated "public data libraries", and tools to combine and analyze shared data. To address these needs, our multidisciplinary community created MultiCellDS (MultiCellular Data Standard): an extensible standard, a library of digital cell lines and tissue snapshots, and support software. With the help of experimentalists, clinicians, modelers, and data and library scientists, we can grow this seed into a community-owned ecosystem of shared data and tools, to the benefit of basic science, engineering, and human health

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

Field Measurements and Modeling of Ebullition-Facilitated Flux of Heavy Metals and Polycyclic Aromatic Hydrocarbons from Sediments to the Water Column

Gas ebullition-facilitated transport of metals and polycyclic aromatic hydrocarbons (PAHs) from sediment was investigated in 14 urban waterway locations. Gas ebullition varied widely over four seasons (range 2–450 mmol m^–2 d^–1, mean 140 ± 90 mmol m^–2 d^–1) and was highly temperature dependent. Ebullition-facilitated metal fluxes were large: 50 ± 13 mg m^–2 d^–1 (Fe), 2.6 ± 0.71 mg m^–2 d^–1 (Zn), 1.5 ± 0.28 mg m^–2 d^–1 (Pb), and 0.19 ± 0.06 mg m^–2 d^–1 (Cr). Ebullition-facilitated PAH fluxes were also large: 0.61 ± 0.27 mg m^–2 d^–1 for anthracene, 0.65 ± 0.28 mg m^–2 d^–1 for benzo­[a]­pyrene, 0.72 ± 0.28 mg m^–2 d^–1 for chrysene, 3.51 ± 1.23 mg m^–2 d^–1 for fluoranthene, 0.23 ± 0.08 mg m^–2 d^–1 for naphthalene, 3.84 ± 1.47 mg m^–2 d^–1 for phenanthrene, and 2.46 ± 0.86 mg m^–2 d^–1 for pyrene. The magnitude of these fluxes indicates that gas ebullition is an important pathway for release of both PAHs and heavy metals from buried sediments. Multivariate regression analysis of the in situ gas ebullition flux and ebullition-facilitated contaminant flux suggests that metal transport likely is due to sediment particle resuspension, whereas PAH transport is due to both contaminant partitioning to gas bubbles and to sediment resuspension. These results indicate that assumptions regarding the natural recovery potential of ebullition-active sediments should be made with caution