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

Reports that promote persulfate-based advanced oxidation process (AOP) as a viable alternative to hydrogen peroxide-based processes have been rapidly accumulating in recent water treatment literature. Various strategies to activate peroxide bonds in persulfate precursors have been proposed and the capacity to degrade a wide range of organic pollutants has been demonstrated. Compared to traditional AOPs in which hydroxyl radical serves as the main oxidant, persulfate-based AOPs have been claimed to involve different in situ generated oxidants such as sulfate radical and singlet oxygen as well as nonradical oxidation pathways. However, there exist controversial observations and interpretations around some of these claims, challenging robust scientific progress of this technology toward practical use. This Critical Review comparatively examines the activation mechanisms of peroxymonosulfate and peroxydisulfate and the formation pathways of oxidizing species. Properties of the main oxidizing species are scrutinized and the role of singlet oxygen is debated. In addition, the impacts of water parameters and constituents such as pH, background organic matter, halide, phosphate, and carbonate on persulfate-driven chemistry are discussed. The opportunity for niche applications is also presented, emphasizing the need for parallel efforts to remove currently prevalent knowledge roadblocks.

/pdf/persulfate-based-advanced-oxidation-critical-assessment-of-ru3om4hbrg.pdf

Persulfate-Based Advanced Oxidation: Critical Assessment of Opportunities and Roadblocks.

Reactive species in advanced oxidation processes: Formation, identification and reaction mechanism

Carotenoids from microalgae: A review of recent developments.

Qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. The taxonomic identity, body of knowledge, safety concerns and antimicrobial resistance are assessed. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by 'qualifications'. No new information was found that would change the previously recommended QPS TUs and their qualifications. The list of microorganisms notified to EFSA was updated with 54 biological agents, received between April and September 2019; 23 already had QPS status, 14 were excluded from the QPS exercise (7 filamentous fungi, 6 Escherichia coli, Sphingomonas paucimobilis which was already evaluated). Seventeen, corresponding to 16 TUs, were evaluated for possible QPS status, fourteen of these for the first time, and Protaminobacter rubrum, evaluated previously, was excluded because it is not a valid species. Eight TUs are recommended for QPS status. Lactobacillus parafarraginis and Zygosaccharomyces rouxii are recommended to be included in the QPS list. Parageobacillus thermoglucosidasius and Paenibacillus illinoisensis can be recommended for the QPS list with the qualification 'for production purposes only' and absence of toxigenic potential. Bacillus velezensis can be recommended for the QPS list with the qualification 'absence of toxigenic potential and the absence of aminoglycoside production ability'. Cupriavidus necator, Aurantiochytrium limacinum and Tetraselmis chuii can be recommended for the QPS list with the qualification 'production purposes only'. Pantoea ananatis is not recommended for the QPS list due to lack of body of knowledge in relation to its pathogenicity potential for plants. Corynebacterium stationis, Hamamotoa singularis, Rhodococcus aetherivorans and Rhodococcus ruber cannot be recommended for the QPS list due to lack of body of knowledge. Kodamaea ohmeri cannot be recommended for the QPS list due to safety concerns.

https://efsa.onlinelibrary.wiley.com/doi/pdf/10.2903/j.efsa.2020.5965

Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 13: suitability of taxonomic units notified to EFSA until September 2020.

Photochemical reactions contribute to the transformation of contaminants and biogeochemically important substrates in environmental aquatic systems. Recent research has demonstrated that halogen radicals (e.g., Cl•, Br•, Cl2•–, BrCl•–, Br2•–) impact photochemical processes in sunlit estuarine and coastal waters rich in halides (e.g., chloride, Cl–, and bromide, Br–). In addition, halogen radicals participate in contaminant degradation in some engineered processes, including chlorine photolysis for drinking water treatment and several radical-based processes for brine and wastewater treatment. Halogen radicals react selectively with substrates (with bimolecular rate constants spanning several orders of magnitude) and via several potential chemical mechanisms. Consequently, their role in photochemical processes remains challenging to assess. This review presents an integrative analysis of the chemistry of halogen radicals and their contribution to aquatic photochemistry in sunlit surface waters and engineer...

Halogen Radical Oxidants in Natural and Engineered Aquatic Systems.

Several reports have highlighted that many plant growth-promoting endophytic bacteria (PGPE) can assist their host plants in coping with various biotic and abiotic stresses. However, information about the PGPE colonizing in the halophytes is still scarce. This study was designed to isolate and characterize PGPE from salt-accumulating halophyte Salicornia europaea grown under extreme salinity and to evaluate in vitro the bacterial mechanisms related to plant growth promotion. A total of 105 isolates were obtained from the surface-sterilized roots, stems, and assimilation twigs of S. europaea. Thirty-two isolates were initially selected for their ability to produce 1-aminocyclopropane-1-carboxylate deaminase as well as other properties such as production of indole-3-acetic acid and phosphate-solubilizing activities. The 16S rRNA gene-sequencing analysis revealed that these isolates belong to 13 different genera and 19 bacterial species. For these 32 strains, seed germination and seedling growth in axenically grown S. europaea seedlings at different NaCl concentrations (50-500 mM) were quantified. Five isolates possessing significant stimulation of the host plant growth were obtained. The five isolates were identified as Bacillus endophyticus, Bacillus tequilensis, Planococcus rifietoensis, Variovorax paradoxus, and Arthrobacter agilis. All the five strains could colonize and can be reisolated from the host plant interior tissues. These results demonstrate that habitat-adapted PGPE isolated from halophyte could enhance plant growth under saline stress conditions.

Isolation of Endophytic Plant Growth-Promoting Bacteria Associated with the Halophyte Salicornia europaea and Evaluation of their Promoting Activity Under Salt Stress.

While saline soils account for 6.5% of the total land area globally, it comprises about 70% of the area in northwestern China. Microbiota in these saline soils are particularly important because they are critical to maintaining ecosystem services. However, little is known about the microbial diversity and community composition in saline soils. To investigate the distribution patterns and edaphic determinants of bacterial communities in saline soils, we collected soil samples across the hypersaline Ebinur Lake shoreline in northwestern China and assessed soil bacterial communities using bar-coded pyrosequencing. Bacterial communities were diverse, and the dominant phyla (>5% of all sequences) across all soil samples were Gammaproteobacteria, Actinobacteria, Firmicutes, Alphaproteobacteria, Bacteroidetes and Betaproteobacteria. These dominant phyla made a significant (P < 0.05) contribution to community structure variations between soils. Halomonas, Smithella, Pseudomonas and Comamonas were the indicator taxa across the salinity gradient. Bacterial community composition showed significant (P < 0.05) correlations with salt content and soil pH. Indeed, bacterial phylotype richness and phylogenetic diversity were also higher in soils with middle-level salt rates, and were significantly (P < 0.05) correlated with salt content and soil pH. Overall, our results show that both salinity and pH are the determinants of bacterial communities in saline soils in northwest China.

Soil pH is equally important as salinity in shaping bacterial communities in saline soils under halophytic vegetation

Recently, nonspherical nanoparticles took attention due to advanced properties of these structures. We report the study of the nonlinear optical properties of copper oxide nanoellipsoids using 800 nm and 400 nm, 60 fs pulses. The optical limiting effect of copper oxide nanoellipsoids is analyzed. The influence of band gap of copper nanoparticles and copper oxide nanoellipsoids on their nonlinear optical response was studied. For the first time, the low- and high-order nonlinear optical responses of copper nanoellipsoids were studied. The magnitudes of nonlinear optical parameters of the suspension of copper oxide nanoellipsoids were measured to be γ = 1.23 × 10−15 cm2 W−1, and β = 1.0 × 10−11 cm W−1 respectively. We observed the four-fold enhancement of the nonlinear optical refraction of copper oxide nanoellipsoids at the wavelength of 400 nm, 60 fs probe pulses compared to 800 nm radiation. We also analyzed the high-order nonlinear response of CuO nanoellipsoids through generation of high-order harmonics of 800 nm, 60 fs pulses in the plasmas produced during laser ablation of the nanoellipsoid-contained targets. We demonstrated the harmonics up to the 35th order (E = 50 eV) in case of single-color pump and 24th (30 eV) in case of two-color pump.

/pdf/nonlinear-optical-characterization-of-copper-oxide-lytwv3iwsf.pdf

Ke Zhang

Papers

Halogen Radical Oxidants in Natural and Engineered Aquatic Systems.

Isolation of Endophytic Plant Growth-Promoting Bacteria Associated with the Halophyte Salicornia europaea and Evaluation of their Promoting Activity Under Salt Stress.

Soil pH is equally important as salinity in shaping bacterial communities in saline soils under halophytic vegetation

Nonlinear optical characterization of copper oxide nanoellipsoids

Biogeographical distribution of bacterial communities in saline agricultural soil