The Archaeal Diversity and Population in a Drained Alkaline Saline Soil of the Former Lake Texcoco (Mexico)

Draining soil of the former Lake Texcoco, Mexico with pH > 10.0 and electrolytic conductivity (EC) > 100 dS m^?1 for 17 years has reduced pH to 7.8 and EC to 0.68 dS m^?1. Metagenomic DNA from the archaeal community was extracted directly from this soil and used as template to amplify the 16S ribosomal genes by PCR to construct gene libraries. Most of the cloned Archaea were related to mesophilic crenarchaeota and were not-yet-cultured. Sequence and phylogenetic analyses of these clones identified a group of Archaea with close affiliation to the ammonia-oxidizing Archaea. The cloned sequences from the drained soil diverged clearly from Haloarchaea found in the undrained soil from the lake.     

Characterization of five agricultural by-products as potential biofilter carriers

Biofiltration is the most commonly used biological gas treatment technology and is extensively used for the treatment of polluted air with gas flow rates of up to 2 x 10(5) m(3)/h. It involves a filter bed of organic matter serving both as carrier for microorganisms and as nutrient supplier. Polluted gas passes through the filter bed and is cleaned by biological activity. Biofiltration is not being developed in Latin America as in the USA, Canada or Europe; the main reason probably being the absence of specific technology and of potential organic carriers locally available. Five different agriculture by-products available in Latin America: peanut shells, rice husk, coconut shells, cane bagasse and maize stubble, were chemically, physically and structurally characterized for their potential use as biofilter carrier. It was found that peanut shells could be used as biofilter carrier and therefore would have potential biological application.     

The bacterial community in 'taberna' a traditional beverage of Southern Mexico

Aims: To characterize the bacterial community of taberna, an alcoholic traditional beverage from the Southern part of Mexico produced by the fermentation of the coyol palm sap (Acrocomia aculeate). Methods and Results: Bacterial 16S rDNA libraries were constructed from metagenomic DNA extracted during the fermentation process at 0, 60 and 108 h. A total of 154 clones were sequenced, and 13, 10 and nine unique sequences were found at each sampling time. At the onset of the fermentation, Zymomonas mobilis, Fructobacillus spp., Pantoea agglomerans and other Gammaproteobacteria were detected. After 60 h, lactic acid bacteria were found and 30% of clones in the library were related to Lactobacillus nagelii, L. sucicola and L. sp. By the end of the experiment, i.e. after 108 h, the bacterial community included Z. mobilis, Lact. nagelii and Acetobacter pasteurianus. Conclusions: Our results suggest that Z. mobilis population represented an important proportion of the bacterial community (60–80%), as well as the lactobacilli during the fermentation process. The bacterial diversity was low and decreased as the fermentation progressed. Significance and Impact of the Study: This culture‐independent study suggests that Z. mobilis and lactobacilli play an important role in the alcoholic fermentation of the taberna beverage.     

Influence of catclaw Mimosa monancistra on the dissipation of soil PAHs

Phytoremediation is a cost-effective biotechnology for decontamination of polycyclic aromatic hydrocarbons (PAHs)-polluted soils. A greenhouse experiment was conducted to determine the growth of Mimosa monancistra, a N2-fixing leguminous plants, and its capacity to remove phenanthrene, anthracene, and benzo(a)pyrene (BaP)from soil. The PAHs decreased shoot and root dry biomass of M. monancistra 2.7- and 3.9-fold, respectively, compared to uncontaminated soil and inhibited nodule formation. The removal of phenanthrene and anthracene was similar in vegetated and unvegetated soil, but the dissipation of BaP was significantly faster in vegetated soil as compared to unvegetated soil after 14, 56, 70, and 90 d. After 90 d, dissipation of BaP was 96% in vegetated soil and 87% in unvegetated soil. Nitrification and ammonification were not affected by the addition of PAHs as concentrations of NH4+, NO2-, and NO3- were similar in contaminated and uncontaminated vegetated soil. Growth of M. monancistra was inhibited by contamination with hydrocarbons, but removal of BaP was accelerated in the rhizosphere.     

A flexible framework for multi-particle refinement in cryo-electron tomography

Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) are increasingly used for macromolecular structure determination in situ. Here, we introduce a set of computational tools and resources designed to enable flexible approaches to STA through increased automation and simplified metadata handling. We create a bidirectional interface between the Dynamo software package and the Warp-Relion-M pipeline, providing a framework for ab initio and geometrical approaches to multiparticle refinement in M. We illustrate the power of working within this framework by applying it to EMPIAR-10164, a publicly available dataset containing immature HIV-1 virus-like particles (VLPs), and a challenging in situ dataset containing chemosensory arrays in bacterial minicells. Additionally, we provide a comprehensive, step-by-step guide to obtaining a 3.4-Å reconstruction from EMPIAR-10164. The guide is hosted on https://teamtomo.org/, a collaborative online platform we establish for sharing knowledge about cryo-ET.

Employing optimal computational methodology in cryo-electron tomography is not always easy; this article provides a set of tools and a complete guide to obtaining high-resolution structures from cryo-ET data.     

Sheep manure vermicompost supplemented with a native diazotrophic bacteria and mycorrhizas for maize cultivation

An orthogonal experimental design L9 (3(4)) with 10 repetitions was used to investigate the effect of Glomus claroideum (0, 1 or 2g(-1) plant), G. fasciculatum (0, 1 or 2g plant(-1)), native diazotrophic bacteria (0, 10(3) and 10(5) UFC ml(-1)) and sheep manure vermicompost (0%, 5% and 10% v/v) on maize plant growth, N and P in leaves and mycorrhization percent. Vermicompost explained most of the variation found for leaf number, wet weight, stem height, and diameter. Both mycorrhizas increased the plant wet weight but G. fasciculatum the most. Mycorrhization increased the P content, but not the N content. Mycorrhizal colonization increased when diazotrophic bacteria and vermicompost were added. It was found that weight of maize plants cultivated in peat moss amended with vermicompost increased when supplemented with G. fasciculatum and diazotrophic bacteria.     

Formulation of a liquid fertilizer for sorghum (Sorghum bicolor (L.) Moench) using vermicompost leachate

Leachate from vermicomposting contains large amounts of plant nutrients and can be used as liquid fertilizer, but normally diluted to avoid plant damage. The amount of nutrients applied is thus reduced so that an additional fertilizer is required. We investigated how dilution of vermicompost leachate combined with different concentrations of NPK triple 17 fertilizer, and polyoxyethylene tridecyl alcohol as dispersant and polyethylene nonylphenol as adherent to increase efficiency of fertilizer uptake, affected sorghum plant development. The vermicomposting leachate with pH 7.8 and electrolytic conductivity 2.6 dS m(-1), contained 834 mg K(+) l(-1), 247 mg NO(3)(-)l(-1) and 168 mg PO(4)(3-) l(-1), was free of pathogens and resulted in a 65 % germination index. Vermicompost leachate can be used as liquid fertilizer for the cultivation of sorghum without dilution and mixed with 140-170 g l(-1) of NPK triple 17 fertilizer and 2-3 ml(-1) of dispersant and 0-1 ml l(-1) adherent. It was found that vermicompost leachate stimulated plant development, but fertilization with NPK was required for maximum growth.     

Decomposition of leaves of huisache (Acacia tortuoso) and mesquite (Prosopis spp) in soil of the central highlands of Mexico

In the central highlands of Mexico, mesquite (Prosopis spp) and huisache (Acacia tortuoso), N₂ fixing trees or shrubs, dominate the vegetation and are used in an alley cropping system to prevent erosion and restore soil fertility. We investigated how much the leaves of both trees contribute to dynamics of carbon (C) and nitrogen (N) in soil by adding leaves of both species to soil sampled under the canopy of mesquite and huisache, outside their canopy and from fields cultivated with maize at three different sites and monitoring microbial biomass C, production of carbon dioxide (CO₂), and dynamics of inorganic N (ammonium and nitrate) in an aerobic incubation. The soluble fraction and N content of the mesquite leaves were larger than in the huisache leaves, but lignin and polyphenol content were lower. Evolution of CO₂ increased 2.7-times when mesquite and 2.4-times when huisache leaves were added to soil. During all stages of decomposition and in all treatments, C mineralization of leaves from mesquite was greater than from huisache leaves. Mesquite leaves induced an increase in mineral N of 25.6 mg N kg^–1 soil after 56 days and those of huisache 9.8 mg N kg^–1. Twenty-six percent of N from mesquite leaves and 11% of huisache was mineralized, if no priming effect was considered. Nitrogen release from the leaves was greater when the soil organic matter content was lower. It was found that soil under the canopy of mesquite and huisache effectively accumulated organic material, micro-organisms and valuable nutrients. In an alley cropping system huisache might be a better choice than mesquite as huisache grows faster than mesquite and sheds its leaves twice a year while mesquite only once, although the amount of N mineralized was larger from mesquite leaves than from those of huisache.     

Endoplasmic reticulum stress causes insulin resistance by inhibiting delivery of newly synthesized insulin receptors to the cell surface

Accumulation of unfolded proteins in the endoplasmic reticulum (ER) causes ER stress and activates a signaling network known as the unfolded protein response (UPR). Here we characterize how ER stress and the UPR inhibit insulin signaling. We find that ER stress inhibits insulin signaling by depleting the cell surface population of the insulin receptor. ER stress inhibits proteolytic maturation of insulin proreceptors by interfering with transport of newly synthesized insulin proreceptors from the ER to the plasma membrane. Activation of AKT, a major target of the insulin signaling pathway, by a cytosolic, membrane-bound chimera between the AP20187-inducible F_V2E dimerization domain and the cytosolic protein tyrosine kinase domain of the insulin receptor was not affected by ER stress. Hence, signaling events in the UPR, such as activation of the JNK mitogen-activated protein (MAP) kinases or the pseudokinase TRB3 by the ER stress sensors IRE1α and PERK, do not contribute to inhibition of signal transduction in the insulin signaling pathway. Indeed, pharmacologic inhibition and genetic ablation of JNKs, as well as silencing of expression of TRB3, did not restore insulin sensitivity or rescue processing of newly synthesized insulin receptors in ER-stressed cells.     

Bacterial community structure within an activated sludge reactor added with phenolic compounds

Biodegradation of phenolic compounds in bioreactors is well documented, but the changes in the bacterial populations dynamics during degradation were not that often. A glass bubble column used as reactor was inoculated with activated sludge, spiked with 2-chlorophenol, phenol and m-cresol after 28 days and maintained for an additional 56 days, while the 16S rRNA gene from metagenomic DNA was monitored. Proteobacteria (68.1%) dominated the inoculum, but the bacterial composition changed rapidly. The relative abundance of Bacteroidetes and Firmicutes decreased from 4.8 and 9.4 to <0.1 and 0.2% respectively, while that of Actinobacteria and TM7 increased from 4.8 and 2.0 to 19.2 and 16.1% respectively. Phenol application increased the relative abundance of Proteobacteria to 94.2% (mostly Brevundimonas 17.6%), while that of Bacteroidetes remained low (1.2%) until day 42. It then increased to 47.3% (mostly Leadbetterella 46.9%) at day 84. It was found that addition of phenolic compounds did not affect the relative abundance of the Alphaproteobacteria initially, but it decreased slowly while that of the Bacteroidetes increased towards the end.