PyNAST: a flexible tool for aligning sequences to a template alignment
ABSTRACT The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API).
The availability of PyNAST will make the popular NAST algorithm more portable and thereby applicable to datasets orders of magnitude larger by allowing users to install PyNAST on their own hardware. Additionally because users can align to arbitrary template alignments, a feature not available via the original NAST web interface, the NAST algorithm will be readily applicable to novel tasks outside of microbial community analysis.
PyNAST is available at http://pynast.sourceforge.net.
Full-textDOI: · Available from: Todd Z DeSantis, Jun 28, 2015
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ABSTRACT: The increased application of graphene raises concerns about its environmental impact, but little information is available on the effect of graphene on the soil microbial community. This study evaluated the impact of graphene on the structure, abundance and function of the soil bacterial community based on quantitative real-time polymerase chain reaction (qPCR), pyrosequencing and soil enzyme activities. The results show that the enzyme activities of dehydrogenase and fluorescein diacetate (FDA) esterase and the biomass of the bacterial populations were transiently promoted by the presence of graphene after 4 days of exposure, but these parameters recovered completely after 21 days. Pyrosequencing analysis suggested a significant shift in some bacterial populations after 4 days, and the shift became weaker or disappeared as the exposure time increased to 60 days. During the entire exposure process, the majority of bacterial phylotypes remained unaffected. Some bacterial populations involved in nitrogen biogeochemical cycles and the degradation of organic compounds can be affected by the presence of graphene. Copyright © 2015 Elsevier B.V. All rights reserved.Journal of hazardous materials 10/2015; 297. DOI:10.1016/j.jhazmat.2015.05.017 · 4.33 Impact Factor
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ABSTRACT: Agricultural practices affect the bacterial community structure in soil. It was hypothesized that agricultural practices would also affect the bacteria involved in the degradation of crop residue. Soil was sampled from four different agricultural practices, i.e. conventional agriculture on the flat or on beds, or conservation agriculture on the flat or on beds. Cultivating crops on the flat is done traditionally, but cultivating crops on beds was introduced so as to avoid water logging during the rainy season and its potential negative effect on yields. Soil from these four treatments was amended in the laboratory with maize residue (Zea mays L.) or its neutral detergent fibre (NDF) fraction, mostly consisting of (hemi) cellulose, and incubated aerobically for 14 days. Maize residue was applied to soil as it is left in the field in conservation agriculture and NDF was added to study which bacteria were favoured by application of (hemi) cellulose. Soil was incubated aerobically while the carbon mineralization and the bacterial population were monitored. On the one hand, the relative abundance of phylotypes belonging to bacterial groups that preferred low nutrient environments was higher in soil with conservation agriculture (e.g. Acidobacteria 17.6%, Planctomycetes 1.7% and Verrucomicrobia 1.5%) compared to conventional practices (Acidobacteria 11.8%, Planctomycetes 0.9% and Verrucomicrobia 0.4%). On the other hand, the relative abundance of phylotypes belonging to bacterial groups that preferred nutrient rich environments, such as Actinobacteria, showed an opposite trend. It was 11.9% in conservation agriculture and 16.2% in conventional practices. The relative abundance of Arthrobacter (Actinobacteria) and Bacillales more than doubled when maize residue was applied to soil compared to the unamended soil and that of Actinomycetales when maize or NDF was applied. Application of organic material reduced the relative abundance of a wide range of bacterial groups, e.g. Acidobacteria, Bacteroidetes, Planctomycetes and Verrucomicrobia. It was found that application of organic material favoured the same bacterial groups that were more abundant in the soil cultivated conventionally while it reduced those that were favoured in conservation agricultureApplied Soil Ecology 06/2015; 90. DOI:10.1016/j.apsoil.2015.01.010 · 2.21 Impact Factor
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ABSTRACT: The long-term operation of efficient bioanodes supplied with waste‑derived organics is a key challenge for using bioelectrochemical systems as a waste valorization technology. Here, we describe a simple procedure that allowed maintaining highly efficient bioanodes supplied with biowaste. Current densities up to 14.8 A/m2 were obtained with more than 40% of the electrons introduced as biowaste being recovered in the electrical circuit. Three fed-batch reactors were started at different biowaste loading rates. A decline of coulombic efficiencies between 22 and 31% were recorded depending on the reactor over the first 3 weeks of operation. A renewal procedure of the anode was thereafter implemented, which led to a recovery of initial performances. The second and the third renewal, allowed maintaining stable high level performances with coulombic efficiency of approximately 40% over at least 3 weeks. Electroactive biofilm dynamics were monitored using 16S rRNA-gene amplicon sequencing. Retrieved sequences were dominated by Geobacter sulfurreducens-related reads (37% of total sequences), which proportion however varied along the experiment. Interestingly, sequences affiliated to various Bacteroidetes‑groups were also abundant, suggesting an adaptation of the anodic biofilm to the degradation of biowaste through metabolic interactions between microbial community members.Bioelectrochemistry 05/2015; DOI:10.1016/j.bioelechem.2015.05.007 · 3.87 Impact Factor