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

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

Positive ions that are available in soils absorb on grain surfaces. The total sum of cations that can be absorbed bij a soil/sediment at a certain PH is defined by the cation-exchange capacity (CEC, in meq g-1: mol equivalents per gram). The uptake of cations is an important parameter in agriculture and the larger the CEC, the more cations can be absorbed to the soil. The CEC depends highly on the pH of soil and sediments, where the CEC decreases with decreasing PH (increasing acidity). The exchange of ions on sediments occurs commonly fast on geological time scales, but the kinetics of adsorption in natural environments is still poorly understood. The strength of the bonding between the cations and the sediments varies from weak Van der Waals bondings (physical adsorption) to strong chemical bonds. The CEC is widely used for agricultural assessment because it is a measure of general soil fertility as well as an indicator of structural stability because CED is capabel of enhancing development of shrinkage cracks. The list below shows the CEC for different types of minerals. The data indicate that the CEC can vary over 2 orders of magnitude for various types of , minerals and can vary one order of magnitude within one soil type. Cation exchange capacity for different types of sediment (Eisma, 1992; Locher and de Bakker, 1990):

Cation exchange capacity.

A novel calcium-based magnetic biochar is effective in stabilization of arsenic and cadmium co-contamination in aerobic soils

Cadmium stress in paddy fields: Effects of soil conditions and remediation strategies

Effects of Pseudomonas chenduensis and biochar on cadmium availability and microbial community in the paddy soil.

The mechanisms underlying microbial community dynamics and co-occurrence patterns along ecological succession are crucial for understanding ecosystem recovery but remain largely unexplored. Here, we investigated community dynamics and taxa co-occurrence patterns in bacterial and fungal communities across a well-established chronosequence of post-mining lands spanning 54 years of recovery. Bacterial community structures became increasingly phylogenetically clustered with soil age at early successional stages and varied less at later successional stages. The dynamics of bacterial community phylogenetic structures were determined by the changes in the soil vegetation cover along succession. The dynamics of fungal community phylogenetic structures did not significantly correlate with soil age, soil properties or vegetation cover, and were mainly attributed to stochastic processes. Along succession, the common decrease in the bacterial co-occurrence complexity and in the average pairwise phylogenetic distances between co-occurring bacteria implied a decrease in potential bacterial cooperation. The increased complexity of fungal co-occurrence along succession was independent of phylogenetic relatedness between co-occurring fungi. This study provides new sights into ecological mechanisms underlying bacterial and fungal community succession.

Microbial phylogenetic relatedness links to distinct successional patterns of bacterial and fungal communities.

Longer Dry and Wet Spells Alter the Stochasticity of Microbial Community Assembly in Grassland Soils

The invention relates to the technical field of biochemistry and aims at providing a cadmium-contaminated paddy field soil microbial passivating agent. According to the technical scheme, for the cadmium-contaminated paddy field soil microbial passivating agent and application, the cadmium-contaminated paddy field soil microbial passivating agent is prepared from the following components including pseudomonas alcaligenes, bacillus subtilis, sulfate reducing bacteria, nutrients and a carrier. In microorganisms, the pseudomonas alcaligenes and the bacillus subtilis are mainly solidified by directly or indirectly adsorbing cadmium ions onto the surfaces of the microorganisms or into cells, so that the migration and the bioavailability of cadmium are lowered; and in addition, the pseudomonas alcaligenes has the effect of regulating a pH value of the soil. In the microorganisms, the sulfate reducing bacteria enables cadmium to be solidified in the soil by mainly reducing sulfate into sulfur ions to form cadmium sulfide with the cadmium. By applying the cadmium-contaminated paddy field soil microbial passivating agent, the cadmium in the soil can be passivated, and absorption of the cadmium ions by rice is greatly eliminated. The technical application is low in cost and convenient to operate and has very good popularization and application values.

Cadmium-contaminated paddy field soil microbial passivating agent

Cadmium (Cd) contamination has resulted in serious environmental pollution and threatens human health and ecosystems. Our recent studies have demonstrated that Pseudomonas chenduensis strain MBR can decrease Cd bio-availability and reduce Cd accumulation in rice; however, the transcriptional mechanisms underlying the bacterial response during and particularly after Cd bioremediation are still unclear. In this study, we used RNA-Seq to investigate the transcriptional profiles of strain MBR during and after Cd bioremediation. During Cd bioremediation, MBR removed all Cd2+ ions in solution within 24 h, accompanied by 564 upregulated and 363 downregulated expressed genes compared with that of the control (without Cd supplementation). Specifically, under Cd stress, the upregulation of czc (czcA, czcB, and czcC) and mer (merA, merT, merC, and merP) genes enabled Cd efflux from the cytoplasm and conferred resistance of MBR to Cd toxicity. The upregulation of genes (algK, algX, and alg44) related to biofilm formation enabled Cd absorption and contributed to Cd bioremediation. After Cd bioremediation, MBR was transferred to non-Cd medium, and the genes related to histidine metabolism and flagellar assembly still showed similar expression patterns as those during bioremediation (defined as Cd legacy effects). However, the genes involved in Cd resistance and bioremediation were not influenced by Cd legacy effects. This study provides new and thorough insights into the molecular mechanisms underlying Cd bioremediation by a functional microbe. • The upregulation of czc and mer genes is responsible for MBR resistance to Cd. • The upregulation of genes related to biofilm formation contributes to Cd bioremediation. • Cd effects on genes involved in histidine metabolism and flagellar assembly are long-lasting.

Transcriptional response of Pseudomonas chenduensis strain MBR to cadmium toxicity

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