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

Fungal spores can account for large proportions of air particulate matter, and they may potentially influence the hydrological cycle and climate as nuclei for water droplets and ice crystals in clouds, fog, and precipitation. Moreover, some fungi are major pathogens and allergens. The diversity of airborne fungi is, however, not well-known. By DNA analysis we found pronounced differences in the relative abundance and seasonal cycles of various groups of fungi in coarse and fine particulate matter, with more plant pathogens in the coarse fraction and more human pathogens and allergens in the respirable fine particle fraction (<3 μm). Moreover, the ratio of Basidiomycota to Ascomycota was found to be much higher than previously assumed, which might also apply to the biosphere.

High Diversity of Fungi in Air Particulate Matter

Chemical stabilization remediation for heavy metals in contaminated soils on the latest decade: Available stabilizing materials and associated evaluation methods－A critical review

Airborne bacterial communities of outdoor environments and their associated influencing factors.

Recent pandemic outbreak of the corona-virus disease 2019 (COVID-19) has raised widespread concerns about the importance of the bioaerosols. They are atmospheric aerosol particles of biological origins, mainly including bacteria, fungi, viruses, pollen, and cell debris. Bioaerosols can exert a substantial impact on ecosystems, climate change, air quality, and public health. Here, we review several relevant topics on bioaerosols, including sampling and detection techniques, characterization, effects on health and air quality, and control methods. However, very few studies have focused on the source apportionment and transport of bioaerosols. The knowledge of the sources and transport pathways of bioaerosols is essential for a comprehensive understanding of the role microorganisms play in the atmosphere and control the spread of epidemic diseases associated with them. Therefore, this review comprehensively summarizes the up to date progress on the source characteristics, source identification, and diffusion and transport process of bioaerosols. We intercompare three types of diffusion and transport models, with a special emphasis on a widely used mathematical model. This review also highlights the main factors affecting the source emission and transport process, such as biogeographic regions, land-use types, and environmental factors. Finally, this review outlines future perspectives on bioaerosols.

/pdf/the-source-and-transport-of-bioaerosols-in-the-air-a-review-4ct78tur1u.pdf

The source and transport of bioaerosols in the air: A review

Comparative study of the airborne microbial communities and their functional composition in fine particulate matter (PM2.5) under non-extreme and extreme PM2.5 conditions

Soil stabilization is a remedial technique that reduces the exposure of the soil environment to soil contaminants. Its efficacy can be assessed by determining whether the environmental availability of a contaminant decreases following treatment. We evaluated several chemical leaching treatments by assessing both contaminant leachability and bioaccumulation in the earthworm Eisenia fetida, and determined the most effective treatment for achieving soil stabilization. Soil samples contaminated with As, Cd, Cu, Pb, and/or Zn were collected from abandoned mine areas and stabilized by adding limestone and steel slag (5% and 2% w/w, respectively). All leaching and earthworm tests were conducted using both contaminated and stabilized soils. In addition to bioaccumulation in earthworms, several toxicity parameters (number of cocoons, growth changes, and survival rates) were also assessed to determine the effects of the treatments on the earthworms. The study showed that treatment of soil with EDTA-NH4OAc resulted in a significant decrease in contaminant leachability following soil stabilization. There was an increase in survival and growth of earthworms exposed to the stabilized soil compared with those exposed to the non-stabilized soil. Bioaccumulation in earthworms was found to be statistically correlated with the leachability of As by EDTA-NH4OAc. We conclude that limestone and steel slag effectively decreased the availability of heavy metals in the soil and reduced the toxicity to earthworms. Leaching with EDTA-NH4OAc has the potential to be predictive in estimating the bioavailability of As in soils, but further studies are needed if it is to be proposed as a standard method.

Assessment of the stabilization of heavy metal contaminants in soils using chemical leaching and an earthworm bioassay

Reverse osmosis (RO) membrane biofouling is a critical issue in seawater desalination. However, biofouling characteristics are not fully understood owing to the complex structure of the fouling layer. Therefore, the objective of this study is to investigate how the biofouling characteristics of RO membranes are associated with bacterial and archaeal communities and their physiological (surface structure, elemental composition, and thickness) and metabolic characteristics in different locations of the RO membrane element. Raw seawater, feedwater, first- and last-located RO membrane elements, and brine were collected from a full-scale (50 m3 per day) intermittently operated seawater reverse osmosis (SWRO) desalination plant. Bacteria were found to be the most dominant biofouling microorganism on the RO membrane surface rather than archaea or diatoms. This study highlights that the very first element of the RO membrane receiving inflow had fouled biofilm with more heterogeneous morphologies and chemical composition compared with the very last element of the RO membrane where the outflow is discharged. In contrast, the microbial communities in both biofilms were similar to each other during the period of desalination operation. The most dominant bacterial species in the biofilm of RO membranes were Pelagibius, Parvibaculum, Legionella, Hyphomicrobium, and Sphingomonas. Moreover, their physiological and metabolic characteristics, such as salt tolerance, high pressure tolerance, and/or oligotrophic properties may provide advantages for their adaptation and dominance in RO membrane biofilms. A substantial difference in microbial diversity was observed between the feedwater and RO membranes, suggesting that more attention should be given to the biofilm, rather than the feedwater, when investigating how biofouling is developed and eventually controlled.

Structural heterogeneity yet high similarity of the microbial community on reverse osmosis membrane-driven biofilms during seawater desalination

Impedance–based haptenation of skin sensitizers with self–assembled monolayer of gold nanoparticles and cysteine modified screen printed carbon electrode

Azilah Abd Aziz

Papers

Comparative study of the airborne microbial communities and their functional composition in fine particulate matter (PM2.5) under non-extreme and extreme PM2.5 conditions

Assessment of the stabilization of heavy metal contaminants in soils using chemical leaching and an earthworm bioassay

Structural heterogeneity yet high similarity of the microbial community on reverse osmosis membrane-driven biofilms during seawater desalination

Impedance–based haptenation of skin sensitizers with self–assembled monolayer of gold nanoparticles and cysteine modified screen printed carbon electrode