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Emerson Koefoed posted an update 7 months, 3 weeks ago
HCK, coupled with ABAA, improves the F-score and bring alpha diversity metric value close to that of the BLASTn alpha diversity values when compared to QIIME, KRAKEN, and DADA2.
The developed HCK-ABAA approach allows better identification of the fungi community structures while avoiding use of a reference database for non-specific amplicons filtration. It results in a more robust and stable methodology over time. The software can be downloaded on the following link https//bitbucket.org/GottySG36/hck/src/master/.
The developed HCK-ABAA approach allows better identification of the fungi community structures while avoiding use of a reference database for non-specific amplicons filtration. It results in a more robust and stable methodology over time. The software can be downloaded on the following link https//bitbucket.org/GottySG36/hck/src/master/.In recent times, nanoparticles (NPs) have found increasing interest owing to their size, large surface areas, distinctive structures, and unique properties, making them suitable for various industrial and biomedical applications. Biogenic synthesis of NPs using microbes is a recent trend and a greener approach than physical and chemical methods of synthesis, which demand higher costs, greater energy consumption, and complex reaction conditions and ensue hazardous environmental impact. Several microorganisms are known to trap metals in situ and convert them into elemental NPs forms. They are found to accumulate inside and outside of the cell as well as in the periplasmic space. Despite the toxicity of NPs, the driving factor for the production of NPs inside microorganisms remains unelucidated. Several reports suggest that nanotization is a way of stress response and biodefense mechanism for the microbe, which involves metal excretion/accumulation across membranes, enzymatic action, efflux pump systems, binding at peptides, and precipitation. Moreover, genes also play an important role for microbial nanoparticle biosynthesis. The resistance of microbial cells to metal ions during inward and outward transportation leads to precipitation. Accordingly, it becomes pertinent to understand the interaction of the metal ions with proteins, DNA, organelles, membranes, and their subsequent cellular uptake. The elucidation of the mechanism also allows us to control the shape, size, and monodispersity of the NPs to develop large-scale production according to the required application. This article reviews different means in microbial synthesis of NPs focusing on understanding the cellular, biochemical, and molecular mechanisms of nanotization of metals.The spatial distribution of bacterioplankton communities in rivers is driven by multiple environmental factors, including local and regional factors. Local environmental condition is associated with effect of river water chemistry (through species sorting); ecological process in region is associated with effects of land use and geography. Here, we investigated variation in bacterioplankton communities (free-living, between 0.22 and 5 μm) in an anthropogenically disturbed river using high-throughput DNA sequencing of community 16S rRNA genes in order to investigate the importance of water chemistry, land use patterns, and geographic distance. Among environmental factors, sulfate (SO4 2-), manganese (Mn), and iron (Fe) concentrations were the water chemistry parameters that best explained bacterioplankton community variation. In addition, forest and freshwater areas were the land use patterns that best explained bacterioplankton community variation. Furthermore, cumulative dendritic distance was the geographic distance parameter that best explained bacterial community variation. Variation partitioning analysis revealed that water chemistry, land use patterns, and geographic distances strongly shaped bacterioplankton communities. In particular, the direct influence of land use was prominent, which alone contributed to the highest proportion of variation (26.2% in wet season communities and 36.5% in dry season communities). These results suggest that the mechanisms of species sorting and mass effects together control bacterioplankton communities, although mass effects exhibited higher contributions to community variation than species sorting. Given the importance of allochthonous bacteria input from various land use activities (i.e., mass effects), these results provide new insights into the environmental factors and determinant mechanisms that shape riverine ecosystem communities.Fertilizer practices can significantly impact the fruit quality and microbial diversity of the orchards. The fungi on the surface of fruits are essential for fruit storability and safety. However, it is not clear whether fertilization affects the fungal diversity and community structure on the surface of grape berries. Verubecestat cost Here, grape quality and the fungal diversity on the surface of grapes harvested from three fertilizer treatments were analyzed shortly after grape picking (T0) and following 8 days of storage (T1). The study involved three treatments (1) common chemical fertilizer for 2 years (CH); (2) increased organic fertilizer and reduced chemical fertilizer for 1 year (A.O); and (3) increased organic fertilizer and reduced chemical fertilizer for 2 years (B.O). The application of increased organic fertilizer and reduced chemical fertilizer increased the soluble solids content (SSC) of the grape berries and decreased the pH of the grape juice. A total of 827,947 high-quality fungal sequences were recovered l diversity, as well as the relative abundance (RA) of beneficial fungi on grape berry surfaces. The correlation analysis suggested that the pH of the grape juice was significantly negatively correlated with fungal diversity parameters.Carbon cycling in anoxic marine sediments is dependent on uncultured microbial communities. Niches of heterotrophic microorganisms are defined by organic matter (OM) type and the different phases in OM degradation. We investigated how OM type defines microbial communities originating from organic-rich, anoxic sediments from the Baltic Sea. We compared changes in the sediment microbial community, after incubation with different stable isotope labeled OM types , by using DNA stable isotope probing (DNA-SIP). Incorporation of 13C and/or 15N label was predominantly detected in members of the phyla Planctomycetes and Chloroflexi, which also formed the majority (>50%) of the original sediment community. While these phylum-level lineages incorporated label from all OM types, phylogenetic analyses revealed a niche separation at the order level. Members of the MSBL9 (Planctomycetes), the Anaerolineales (Chloroflexi), and the class Bathyarchaeota, were identified as initial degraders of carbohydrate-rich OM, while other uncultured orders, like the CCM11a and Phycisphaerales (Planctomycetes), Dehalococcoidia, and JG30-KF-CM66 (Chloroflexi), incorporated label also from protein and acetate.
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