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

Plastic litter is widely acknowledged as a global environmental threat, and poor management and disposal lead to increasing levels in the environment. Of recent concern is the degradation of plastics from macro- to micro- and even to nanosized particles smaller than 100 nm in size. At the nanoscale, plastics are difficult to detect and can be transported in air, soil, and water compartments. While the impact of plastic debris on marine and fresh waters and organisms has been studied, the loads, transformations, transport, and fate of plastics in terrestrial and subsurface environments are largely overlooked. In this Critical Review, we first present estimated loads of plastics in different environmental compartments. We also provide a critical review of the current knowledge vis-a-vis nanoplastic (NP) and microplastic (MP) aggregation, deposition, and contaminant cotransport in the environment. Important factors that affect aggregation and deposition in natural subsurface environments are identified and c...

/pdf/microplastics-and-nanoplastics-in-aquatic-environments-151u4ngf12.pdf

Microplastics and Nanoplastics in Aquatic Environments: Aggregation, Deposition, and Enhanced Contaminant Transport

Plant roots serve a multitude of functions in the plant including anchorage, provision of nutrients and water, and production of exudates with growth regulatory properties. The root–soil interface, or rhizosphere, is the site of greatest activity within the soil matrix. Within this matrix, roots affect soil structure, aeration and biological activity as they are the major source of organic inputs into the rhizosphere, and are also responsible for depletion of large supplies of inorganic compounds. Roots are very complicated morphologically and physiologically, and their metabolites are often released in large quantities into the soil rhizosphere from living root hairs or fibrous root systems. Root exudates containing root-specific metabolites have critical ecological impacts on soil macro and microbiota as well as on the whole plant itself. Through the exudation of a wide variety of compounds, roots impact the soil microbial community in their immediate vicinity, influence resistance to pests, support beneficial symbioses, alter the chemical and physical properties of the soil, and inhibit the growth of competing plant species. In this review, we outline recent research on root exudation and the role of allelochemicals in the rhizosphere by studying the case of three plants that have been shown to produce allelopathic root exudates: black walnut, wheat and sorghum

The role of root exudates and allelochemicals in the rhizosphere

Halloysite clay minerals are ubiquitous in soils and weathered rocks where they occur in a variety of particle shapes and hydration states. Diversity also characterizes their chemical composition, cation exchange capacity and potassium selectivity. This review summarizes the extensive but scattered literature on halloysite, from its natural occurrence, through its crystal structure, chemical and morphological diversity, to its reactivity toward organic compounds, ions and salts, involving the various methods of differentiating halloysite from kaolinite. No unique test seems to be ideal to distinguish these 1:1 clay minerals, especially in soils. The occurrence of 2:1 phyllosilicate contaminants appears, so far, to provide the best explanation for the high charge and potassium selectivity of halloysite. Yet, hydration properties of the mineral probably play a major role in ion sorption. Clear trends seem to relate particle morphology and structural Fe. However, future work is required to understand the possible mechanisms linking chemical, morphological, hydration and charge properties of halloysite.

Halloysite clay minerals — a review

Polycyclic aromatic hydrocarbons: environmental pollution and bioremediation

Eighteen biochar samples were produced from the pyrolysis of Douglas fir wood (DFW), Douglas fir bark (DFB), and hybrid poplar wood (HP) at six temperatures (623, 673, 723, 773, 823 and 873 K) in a lab scale spoon reactor. Changes in the bulk composition of the biochar produced were examined by elemental and proximate analyses. The mass fraction of volatiles, oxygen and the ratios of oxygen to carbon (O/C) and hydrogen to carbon (H/C) decreased linearly with pyrolysis temperature. Surface properties of all the biochars produced (SEM morphology, CO 2 and N 2 adsorption, XPS analysis, Boehm titration, cation exchange capacity (CEC) and ζ-potential) were also studied. The removal of volatiles resulted in the gradual creation of microporosity detectable by CO 2 adsorption but which was difficult to detect with N 2 adsorption, suggesting that the chars contain micropores mostly less than 1 nm in entrance dimension. The XPS and Boehm titration confirmed that most oxygenated surface functional groups (presence of carbonyl, carboxyl and hydroxyl groups) are gradually removed as pyrolysis temperature increases. The changes in surface charge were studied by ζ-potential measurements and were found to vary directly with the content of oxygenated functional groups. Properties that depend on both surface area and the surface oxygenated functional groups, such as the cation exchange capacity, showed a more complex behavior. The composition of the ash and associated properties such as pH and electric conductivity (EC) were also measured. The total alkaline content increases with pyrolysis temperature leading to higher pHs and ECs.

Influence of feedstock source and pyrolysis temperature on biochar bulk and surface properties

Allophane and Imogolite

We compared five different methods, static sessile drop, dynamic sessile drop, Wilhelmy plate, thin-layer wicking, and column wicking, to determine the contact angle of colloids typical for soils and sediments. The colloids (smectite, kaolinite, illite, goethite, hematite) were chosen to represent 1:1 and 2:1 layered aluminosilicate clays and sesquioxides, and were either obtained in pure form or synthesized in our laboratory. Colloids were deposited as thin films on glass slides, and then used for contact angle measurements using three different test liquids (water, formamide, diiodomethane). The colloidal films could be categorized into three types: (1) films without pores and with polar-liquid interactions (smectite), (2) films with pores and with polar-liquid interactions (kaolinite, illite, goethite), and (3) films without pores and no polar-liquid interactions (hematite). The static and dynamic sessile drop methods yielded the most consistent contact angles. For porous films, the contact angles decreased with time, and we consider the initial contact angle to be the most accurate. The differences in contact angles among the different methods were large and varied considerably: the most consistent contact angles were obtained for kaolinite with water, and illite with diiodomethane (contact angles were within 3 degrees); but mostly the differences ranged from 10 degrees to 40 degrees among the different methods. The thin-layer and column wicking methods were the least consistent methods.

James B. Harsh

Papers

Influence of feedstock source and pyrolysis temperature on biochar bulk and surface properties

Allophane and Imogolite

Comparison of different methods to measure contact angles of soil colloids

The mechanism of Zn2+ adsorption on calcite

The role of biochar porosity and surface functionality in augmenting hydrologic properties of a sandy soil.