Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fast-tree-computing-large-minimum-evolution-trees-with-4grq0gwfpy.pdf

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

The science of the total environment

Governing the Commons

Emerging organic contaminants in groundwater: A review of sources, fate and occurrence

In the last few decades, pharmaceuticals, credited with saving millions of lives, have emerged as a new class of environmental contaminant. These compounds can have both chronic and acute harmful effects on natural flora and fauna. The presence of pharmaceutical contaminants in ground waters, surface waters (lakes, rivers, and streams), sea water, wastewater treatment plants (influents and effluents), soils, and sludges has been well doccumented. A range of methods including oxidation, photolysis, UV-degradation, nanofiltration, reverse osmosis, and adsorption has been used for their remediation from aqueous systems. Many methods have been commercially limited by toxic sludge generation, incomplete removal, high capital and operating costs, and the need for skilled operating and maintenance personnel. Adsorption technologies are a low-cost alternative, easily used in developing countries where there is a dearth of advanced technologies, skilled personnel, and available capital, and adsorption appears to be the most broadly feasible pharmaceutical removal method. Adsorption remediation methods are easily integrated with wastewater treatment plants (WWTPs). Herein, we have reviewed the literature (1990-2018) illustrating the rising environmental pharmaceutical contamination concerns as well as remediation efforts emphasizing adsorption.

Pharmaceuticals of Emerging Concern in Aquatic Systems: Chemistry, Occurrence, Effects, and Removal Methods.

Abstract Land-applied municipal biosolids, produced from municipal wastewater treatment sludge, contributes to microplastics contamination in agroecosystems. The impacts of biosolids on microplastic concentrations in agricultural soil have been previously investigated, however, the potential for microplastics transport from biosolid-amended croplands has not been previously quantified. In this study, manure and biosolids were applied to field plots, runoff was collected following natural precipitation events and the potential of bacterial biofilm to grow on different microplastic morphologies was investigated. Higher concentrations of microplastics were detected in runoff from plots with land-applied biosolid in comparison with manure-amended and control plots. Fibers and fragments were the most frequently detected plastic morphologies in runoff, correlated with their decreased surface roughness. The potential of biosolids to contribute to microplastic contamination to U.S. surface waters was quantified which is among the first to quantify the potential for nonpoint source microplastic contamination of surface waters adjacent to agricultural production areas. 

/pdf/higher-concentrations-of-microplastics-in-runoff-from-r4w6b574.pdf

Higher concentrations of microplastics in runoff from biosolid-amended croplands than manure-amended croplands

COVID-19 related antiviral drugs are less adsorbable on sediment under alkaline and high cation conditions

This study was conducted to examine, at the county level, the relationship between pediatric cancers incidence rate and atrazine and nitrate mean concentrations in surface and groundwater. A negati...

Geospatial Distribution of Age-adjusted Incidence of the Three Major Types of Pediatric Cancers and Waterborne Agrichemicals in Nebraska

Monitoring Nonprescription Drugs in Surface Water in Nebraska (USA)

Bridges are located in very close proximity to receiving waters, and regulatory agencies often require specific stormwater control measures for bridge deck runoff. While there is some information available on roadway runoff, few studies have focused on bridge deck runoff. Currently, there is no information available regarding the impacts of bridge deck runoff on receiving waters in Nebraska. Due to the cost, maintenance, and design issues associated with implementing structural controls for bridge deck runoff, it is important to develop a better understanding of the relationship between bridge deck runoff and potential impacts to receiving streams. The objectives of this research were to evaluate the quality of bridge deck runoff; to determine the effects of bridge deck runoff on surface water bodies in Nebraska by evaluating water and sediment chemistry; and to evaluate the effects of bridge deck runoff on aquatic life. The goal was to identify the potential environmental impacts of bridge deck runoff on receiving streams, and to determine design criteria that could be used by NDOR or regulatory agencies to identify when structural controls for bridge deck runoff may be necessary to protect instream water quality and aquatic life. Throughout the course of the project, the authors conducted in-stream dry weather sampling, sediment sampling, wet weather bridge runoff sampling, and preliminary toxicity testing. Statistical analysis of upstream and downstream in-stream samples showed that bridges did not impact the quality of the water body. Sediment sampling did not show an increase in streambed sediment concentrations from downstream to upstream. The concentrations of bridge runoff samples were higher than literature event mean concentration (EMC) values. This was mainly due to the fact that the summer of 2012 had only two rain events of significant size and there was a large antecedent dry period (ADP) between storms, making the samples much more concentrated. Two runoff events were also used in a 48-hour 5 dilution series toxicity test with fat head minnows, and no negative effects were found. These preliminary results show that there were no apparent effects of bridges on water quality and aquatic life.

Shannon L. Bartelt-Hunt

Papers

Higher concentrations of microplastics in runoff from biosolid-amended croplands than manure-amended croplands

COVID-19 related antiviral drugs are less adsorbable on sediment under alkaline and high cation conditions

Geospatial Distribution of Age-adjusted Incidence of the Three Major Types of Pediatric Cancers and Waterborne Agrichemicals in Nebraska

Monitoring Nonprescription Drugs in Surface Water in Nebraska (USA)

Evaluation of the Environmental Impacts of Bridge Deck Runoff — Preliminary Draft