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

http://sealight.persiangig.com/document/1.pdf

Use of iron oxide nanomaterials in wastewater treatment: a review.

China faces great challenges in protecting its soil from contamination caused by rapid industrialization and urbanization over the last three decades. Recent nationwide surveys show that 16% of the soil samples, 19% for the agricultural soils, are contaminated based on China’s soil environmental quality limits, mainly with heavy metals and metalloids. Comparisons with other regions of the world show that the current status of soil contamination, based on the total contaminant concentrations, is not worse in China. However, the concentrations of some heavy metals in Chinese soils appear to be increasing at much greater rates. Exceedance of the contaminant limits in food crops is widespread in some areas, especially southern China, due to elevated inputs of contaminants, acidic nature of the soil and crop species or cultivars prone to heavy metal accumulation. Minimizing the transfer of contaminants from soil to the food chain is a top priority. A number of options are proposed, including identification of the sources of contaminants to agricultural systems, minimization of contaminant inputs, reduction of heavy metal phytoavailability in soil with liming or other immobilizing materials, selection and breeding of low accumulating crop cultivars, adoption of appropriate water and fertilizer management, bioremediation, and change of land use to grow nonfood crops. Implementation of these strategies requires not only technological advances, but also social-economic evaluation and effective enforcement of environmental protection law.

Soil Contamination in China: Current Status and Mitigation Strategies

Organic dyes are one of the largest groups of pollutants released into wastewaters from textile and other industrial processes. Because of potential toxicity of the dyes and their visibility in surface waters, removal and degradation of organic dyes have been a matter of considerable interest. A wide range of methods have been developed, amongst which the heterogeneous photocatalysis involving titanium dioxide (TiO2) appears to be the most promising technology. This paper presents a critical review of novel achievements in the modification of TiO2 photocatalytic systems aimed at: enhanced TiO2 photocatalytic efficiency; complete mineralization of organic dyes; efficient utilization of visible and/or solar light; stability and reproducibility of the modified TiO2; recycle and reuse in real wastewater treatment.

Tailored titanium dioxide photocatalysts for the degradation of organic dyes in wastewater treatment: A review

https://repository.hanyang.ac.kr/bitstream/20.500.11754/110830/1/Heavy%20metals%20in%20food%20crops%20Health%20risks%2c%20fate%2c%20mechanisms%2c%20and%20management.pdf

Heavy metals in food crops: Health risks, fate, mechanisms, and management

Simultaneous alleviation of cadmium and arsenic accumulation in rice by applying zero-valent iron and biochar to contaminated paddy soils

Silica nanoparticles alleviate cadmium toxicity in rice cells: Mechanisms and size effects.

Foliar application of two silica sols reduced cadmium accumulation in rice grains.

Red soil is an important soil resource, which bears substantial implication for sustainable development of agriculture and healthy growth of economy. However, the red soil in China has been deteriorating in recent years and facing many threats, such as soil erosion, acidification, and pollution. Among these, contamination of heavy metals, particularly arsenic and cadmium pollution in paddy soils of the red soil regions, has become a major environmental concern. In this paper, we reviewed recent publications on iron redox cycling and its coupling to the fate of heavy metals and metalloids. The most exciting findings on the iron biogeochemistry processes include dissimilatory iron reduction, Fe(II) oxidation, and Fe2+-catalyzed recrystallization of iron (hydro)oxides, all of which contribute to the immobilization of heavy metals. Although these findings are mainly based on laboratory experiments, they provide guidance for exploring innovative remediation strategies for controlling pollution of heavy metals in paddy soils of the red soil regions. We also summarized how the iron redox cycling may be affected by other biogeochemical processes or active constituents, such as the nitrogen cycling, the sulfur cycling and humic substances. It appears that the mechanisms underlying the interactions among these multiple components and processes are not sufficiently understood and may require further studies. Finally, future research needs pertaining to iron redox cycling coupled to the fate of heavy metals are suggested. The results summarized in this review may provide insights for solving the heavy metal pollution of paddy soils in the red soil regions.

Iron Redox Cycling Coupled to Transformation and Immobilization of Heavy Metals: Implications for Paddy Rice Safety in the Red Soil of South China

Kinetics of nitrate (NO3−) reduction and ferrous iron (Fe(II)) oxidation in paddy soil were investigated under anoxic conditions at circumneutral pH using three different treatments (i.e., Lactate + Fe(II), Lactate + NO3−, and Lactate + NO3− + Fe(II)). The results revealed that NO3− could be rapidly reduced to nitrite (NO2−) within two days in treatments of Lactate + NO3− and Lactate + NO3− + Fe(II), and the presence of Fe(II) facilitated the NO2− reduction. Whereas no obvious Fe(II) oxidation was observed in treatment of Lactate + Fe(II), Fe(II) oxidation took place only when NO3− was added. Illumina high-throughput sequencing used to profile the diversity and abundance of microbial communities showed that the phyla of Proteobacteria and Firmicutes had a dominant presence in all three treatments with lactate. Acidaminobacter, Proteiniclasticum, Alkaliphilus, and Natronincola_Anaerovirgula were found to be the dominant genera during NO3− reduction without Fe(II) after addition of lactate, and all were seldom reported to be associated with NO3− reduction. Azospira, Zoogloea, and Dechloromonas dominated during NO3− reduction in the presence of Fe(II), and all are betaproteobacterial NO3−-reducing bacteria that do not produce ammonium as end products of NO3− reduction. Whereas Azospira, Zoogloea, and Dechloromonas have been isolated or identified from NO3−-reducing Fe(II) oxidation culture previously, the NO2− produced by these NO3− reducing bacteria can also oxidize Fe(II) abiotically, resulting in facilitated NO2− disappearance in the treatment of Lactate + NO3− + Fe(II). These findings increase our understanding of the processes of NO3− reduction in the absence and presence of Fe(II) in anoxic paddy soil at circumneutral pH and extend our knowledge of the microbial communities involved in these processes.

Changes in the composition and diversity of microbial communities during anaerobic nitrate reduction and Fe(II) oxidation at circumneutral pH in paddy soil

Tongxu Liu

Papers

Simultaneous alleviation of cadmium and arsenic accumulation in rice by applying zero-valent iron and biochar to contaminated paddy soils

Silica nanoparticles alleviate cadmium toxicity in rice cells: Mechanisms and size effects.

Foliar application of two silica sols reduced cadmium accumulation in rice grains.

Iron Redox Cycling Coupled to Transformation and Immobilization of Heavy Metals: Implications for Paddy Rice Safety in the Red Soil of South China

Changes in the composition and diversity of microbial communities during anaerobic nitrate reduction and Fe(II) oxidation at circumneutral pH in paddy soil