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

Microplastics in freshwaters and drinking water: Critical review and assessment of data quality.

The accumulation of plastic litter in natural environments is a global issue. Concerns over potential negative impacts on the economy, wildlife, and human health provide strong incentives for improving the sustainable use of plastics. Despite the many voices raised on the issue, we lack a consensus on how to define and categorize plastic debris. This is evident for microplastics, where inconsistent size classes are used and where the materials to be included are under debate. While this is inherent in an emerging research field, an ambiguous terminology results in confusion and miscommunication that may compromise progress in research and mitigation measures. Therefore, we need to be explicit on what exactly we consider plastic debris. Thus, we critically discuss the advantages and disadvantages of a unified terminology, propose a definition and categorization framework, and highlight areas of uncertainty. Going beyond size classes, our framework includes physicochemical properties (polymer composition, solid state, solubility) as defining criteria and size, shape, color, and origin as classifiers for categorization. Acknowledging the rapid evolution of our knowledge on plastic pollution, our framework will promote consensus building within the scientific and regulatory community based on a solid scientific foundation.

/pdf/are-we-speaking-the-same-language-recommendations-for-a-5fcuvmoibz.pdf

Are We Speaking the Same Language? Recommendations for a Definition and Categorization Framework for Plastic Debris.

Microplastics (plastics < 5 mm, including nanoplastics which are < 0.1 μm) originate from the fragmentation of large plastic litter or from direct environmental emission. Their potential impacts in terrestrial ecosystems remain largely unexplored despite numerous reported effects on marine organisms. Most plastics arriving in the oceans were produced, used, and often disposed on land. Hence, it is within terrestrial systems that microplastics might first interact with biota eliciting ecologically relevant impacts. This article introduces the pervasive microplastic contamination as a potential agent of global change in terrestrial systems, highlights the physical and chemical nature of the respective observed effects, and discusses the broad toxicity of nanoplastics derived from plastic breakdown. Making relevant links to the fate of microplastics in aquatic continental systems, we here present new insights into the mechanisms of impacts on terrestrial geochemistry, the biophysical environment, and ecotoxicology. Broad changes in continental environments are possible even in particle-rich habitats such as soils. Furthermore, there is a growing body of evidence indicating that microplastics interact with terrestrial organisms that mediate essential ecosystem services and functions, such as soil dwelling invertebrates, terrestrial fungi, and plant-pollinators.

Therefore, research is needed to clarify the terrestrial fate and effects of microplastics. We suggest that due to the widespread presence, environmental persistence, and various interactions with continental biota, microplastic pollution might represent an emerging global change threat to terrestrial ecosystems.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.14020

Microplastics as an emerging threat to terrestrial ecosystems

Occurrence, identification and removal of microplastic particles and fibers in conventional activated sludge process and advanced MBR technology.

Microplastic pollution in inland waters is receiving growing attentions. Reservoirs are suspected to be particularly vulnerable to microplastic pollution. However, very limited information is currently available on pollution characteristics of microplastics in reservoir ecosystems. This work studied the distribution and characteristics of microplastics in the backwater area of Xiangxi River, a typical tributary of the Three Gorges Reservoir. Microplastics were detected in both surface water and sediment with concentrations ranging from 0.55 × 105 to 342 × 105 items km–2 and 80 to 864 items m–2, respectively. Polyethylene, polypropylene, and polystyrene were identified in surface water, whereas polyethylene, polypropylene, and polyethylene terephthalate, and pigments were observed in sediment. In addition, microplastics were also detected in the digestion tracts of 25.7% of fish samples, and polyethylene and nylon were identified. Redundancy analysis indicates a weak correlation between microplastics and w...

Occurrence and Characteristics of Microplastic Pollution in Xiangxi Bay of Three Gorges Reservoir, China

The Three Gorges Dam has significantly altered ecological and environmental conditions within the reservoir region, but how these changes affect bacterioplankton structure and function is unknown. Here, three widely accepted metagenomic tools were employed to study the impact of damming on the bacterioplankton community in the Xiangxi River. Our results indicated that bacterioplankton communities were both taxonomically and functionally different between backwater and riverine sites, which represent communities with and without direct dam effects, respectively. There were many more nitrogen cycling Betaproteobacteria (e.g., Limnohabitans), and a higher abundance of functional genes and KEGG orthology (KO) groups involved in nitrogen cycling in the riverine sites, suggesting a higher level of bacterial activity involved in generating more nitrogenous nutrients for the growth of phytoplankton. Additionally, the KO categories involved in carbon and sulfur metabolism, as well as most of the detected functional genes also showed clear backwater and riverine patterns. As expected, these diversity patterns all significantly correlated with environmental characteristics, confirming that the bacterioplankton communities in the Xiangxi River were really affected by environmental changes from the Three Gorges Dam. This study provides a first comparative metagenomic insight for evaluating the impacts of the large dam on microbial function.

/pdf/impacts-of-the-three-gorges-dam-on-microbial-structure-and-ynca2y3qpv.pdf

Impacts of the Three Gorges Dam on microbial structure and potential function

[Wang, Jingxian; Bi, Yonghong; Henkelmann, Bernhard; Zhu, Kongxian] Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China; [Wang, Jingxian; Pfister, Gerd; Schramm, Karl-Werner] German Res Ctr Environm Hlth GmbH, Helmholtz Ctr Munich, Mol EXpos MEX, D-85764 Neuherberg, Germany; [Wang, Jingxian; Schramm, Karl-Werner] TUM, Dept Biowissensch Grundlagen, Wissensch Zentrum Weihenstephan Fuer Ernaehrung &, D-85350 Freising Weihenstephan, Germany

Determination of PAH, PCB, and OCP in water from the Three Gorges Reservoir accumulated by semipermeable membrane devices (SPMD) (vol 75, pg 1119, 2009)（Correction）

http://eportfolio.lib.ksu.edu.tw/user/T/0/T093000204/repository/Determination%20of%20PAH,%20PCB,%20and%20OCP%20in%20water%20from%20the%20Three%20Gorges%20Reservoir%20accumulated%20by%20semipermeable%20membrane%20devices%20(SPMD).pdf

Yonghong Bi

Papers

Occurrence and Characteristics of Microplastic Pollution in Xiangxi Bay of Three Gorges Reservoir, China

Impacts of the Three Gorges Dam on microbial structure and potential function

Determination of PAH, PCB, and OCP in water from the Three Gorges Reservoir accumulated by semipermeable membrane devices (SPMD) (vol 75, pg 1119, 2009)（Correction）

Determination of PAH, PCB, and OCP in water from the Three Gorges Reservoir accumulated by semipermeable membrane devices (SPMD).

Responses of phytoplankton functional groups to the hydrologic regime in the Daning River, a tributary of Three Gorges Reservoir, China.