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Editors contains: "Newton, Irene L."

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  1. ; ; ; ; ; ; ( , Microbiology Resource Announcements)
    Newton, Irene L. (Ed.)
    ABSTRACT

    Paenibacillussp. strain RC67 was isolated from the Harvard Forest long-term soil warming experiment. The assembled genome is a single contig with 7,963,753 bp and 99.4% completion. Genome annotation suggests that the isolate is of a novel bacterial species.

     
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    Free, publicly-accessible full text available November 16, 2024
  2. ; ; ; ( , Microbiology Resource Announcements)
    Newton, Irene L. (Ed.)
    ABSTRACT Here, we report the impact of glyphosate on bacterial populations in sediment microcosms, determined using 16S amplicon sequencing and shotgun metagenomics with source material from a suburban creek. The 16S amplicon and metagenomic data reveal that members of the genus Pseudomonas are increased by the treatment. 
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  3. ; ; ( , Microbiology Resource Announcements)
    Newton, Irene L. (Ed.)
    Here, we report the draft genome and annotation of Candidatus Nardonella dryophthoridicola strain NARMHE1, obtained via Oxford Nanopore sequencing of the ovaries of its host, the weevil Metamasius hemipterus, from a population from southeast Brazil. 
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  4. ; ; ( , Microbiology Resource Announcements)
    Newton, Irene L. (Ed.)
    ABSTRACT A common method for quantifying microbial abundances in situ is through metagenomic read recruitment to genomes and normalizing read counts as reads per kilobase (of genome) per million (bases of recruited sequences) (RPKM). We created RRAP (RPKM Recruitment Analysis Pipeline), a wrapper that automates this process using Bowtie2 and SAMtools. 
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  5. ; ; ; ( , Microbiology Resource Announcements)
    Newton, Irene L. (Ed.)
    ABSTRACT Microbial communities using anammox bacteria to remove nitrogen are increasingly important in wastewater treatment. We report on 25 metagenome-assembled genomes of low-abundance microbes from a partial nitritation anammox bioreactor system that have not been described previously. These data add to the body of information about this important wastewater treatment system. 
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  6. ; ( , Microbiology Resource Announcements)
    Newton, Irene L. (Ed.)
    ABSTRACT Here, we present virMine 2.0, the next generation of the virMine software tool. virMine 2.0 uses an exclusion technique to remove nonviral data from sequencing reads and scores the remaining data based on relatedness to viral elements, eliminating the sole dependency on homology identification. 
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  7. ; ; ; ( , Microbiology Resource Announcements)
    Newton, Irene L. (Ed.)
    ABSTRACT Here, we report on eight sediment metagenomes obtained from an alkaline hot spring, with their corresponding metagenome-assembled genomes. Samples had been incubated for 48 h with various substrate amendments in conjunction with the amino acid analog l -homopropargylglycine in a study targeted at identifying anabolicly active uncultured thermophilic archaea and bacteria. 
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  8. ; ( , Microbiology Resource Announcements)
    Newton, Irene L. (Ed.)
    ABSTRACT Clear and effective figures are central to successfully communicating scientific data. Here, we present ggpubfigs, an R package with colorblind-friendly color palettes and extensions of the ggplot2 graphic system, which helps make publication-quality scientific figures from quantitative data; ggpubfigs is an open-source and user-friendly tool that is available from https://github.com/JLSteenwyk/ggpubfigs . 
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  9. ; ; ; ( , Microbiology Resource Announcements)
    Newton, Irene L. (Ed.)
    ABSTRACT We analyzed five metagenome-assembled genomes (MAGs) belonging to the rare, yet-uncultured phylum CSSED10-310 recovered from the anoxic sediments of Zodletone Spring (Oklahoma). Our analysis suggests their potential involvement in sulfite respiration. 
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  10. ; ; ( , Microbiology Resource Announcements)
    Newton, Irene L. (Ed.)
    ABSTRACT Here, we present 36 metagenomes, 59 metatranscriptomes, and 373 metagenome-assembled genomes (MAGs) from Chesapeake and Delaware Bay water samples. This data set will be useful for studying microbial biogeochemical cycling in estuaries. 
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