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Pseudenhygromyxa WMMC2535, a representative of the myxobacteria (family Nannocystaceae ), was isolated from a ragged sea hare in the Florida Keys, and its genome was sequenced using PacBio technology. The WMMC2535 genome sequence is the first of this genus and validates the notion that myxobacteria represent outstanding sources of structurally diverse natural products.
ABSTRACT To enable an in-depth survey of the metabolic potential of complex soil microbiomes, we performed ultra-deep metagenome sequencing, collecting >1 Tb of sequence data from three grassland soils representing different precipitation regimes.
Here, we report the draft genome sequence of Arthrobacter sp. strain ATCC 49987, consisting of three contigs with a total length of 4.4 Mbp. Based on the genome sequence, we suggest reclassification of Arthrobacter sp. strain ATCC 49987 as Pseudarthrobacter sp. strain ATCC 49987.
Here, we report the draft, nearly complete genome sequence of the human oral actinobacterium Schaalia odontolytica strain ORNL0103, which was isolated in association with “Candidatus Saccharibacteria” HMT352 strain ORNL0105. The genome was sequenced using a combination of Pacific Biosciences and Illumina platforms and encodes 1,948 proteins and 60 RNAs.
Luteolibacter sp. strain Populi is a bacterium from the phylum Verrucomicrobiota, isolated from the rhizosphere of a black cottonwood tree, Populus trichocarpa, from the Cascade mountains in Washington. Its 6.6-Mb chromosome was completely sequenced using Oxford Nanopore long-read sequencing and is predicted to encode 5,301 proteins and 60 RNAs.
ABSTRACT We report whole-genome sequences of eight bacteria isolated from laboratory-kept Macrocystis pyrifera gametophytes. The bacterial culture collection is maintained in cryostorage and will be utilized in future applications as inoculants. The genomes were assembled using Oxford Nanopore Technology long-read sequencing.
We report on complete genome sequences of five Pseudomonas soil isolates that are capable of metabolizing pentose sugars and aromatic monomers. These complete genome sequence data provide insight into possible alternative hosts for the production of biofuels and bio-based chemicals from lignocellulosic feedstock.
Reported here is a coding-complete genome sequence of a SARS CoV-2 variant obtained from raw wastewater samples at the University of Tennessee—Knoxville campus. This sequence provides insight into SARS CoV-2 variants that circulate on large college campuses but remain mostly undetected.
A thermophilic methanogen was enriched in coculture from Washburn Hot Springs (Yellowstone National Park, USA), grown on carbon dioxide and hydrogen, and subsequently sequenced. The reconstructed 1.65-Mb genome sequence for Methanothermobacter thermautotrophicus WHS contributes to our understanding of hydrogenotrophic, CO 2 -reducing methanogenesis in geothermal ecosystems.
We report the genome sequence of Dysgonomonas hofstadii DSM 104969T, a type strain isolated from a human surgical wound. The genome has 5.03 Mbp and a guanine-cytosine content of 39.27%. The complete genome sequence will facilitate studies of D. hofstadii and its pathogenic potential, particularly in relation to multidrug resistance.
Here, we report the genome sequence of Tenacibaculum mesophilum strain ECR, which was isolated from the river/ocean interface at Trunk River, Falmouth, Massachusetts, USA. The isolation and sequencing were performed as part of the 2016 and 2018 Microbial Diversity courses at the Marine Biological Laboratory in Woods Hole, Massachusetts, USA.
Sulfurospirillum sp. strain ACS DCE couples growth with reductive dechlorination of tetrachloroethene to cis-1,2-dichloroethene at pH values as low as 5.5. The genome sequence of strain ACS DCE consists of a circular 2,737,849-bp chromosome and a 39,868-bp plasmid and carries 2,737 protein-coding sequences, including two reductive dehalogenase genes.
We sequenced six actinobacterial genomes isolated from a salt mine and from soil in a high-mountain Páramo ecosystem. The strains belonged to the genera Streptomyces , Nesterenkonia , and Isoptericola and were sequenced due to their antimicrobial and cytotoxic activities.
Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations of diversity. For instance, the completeness of reference databases cannot be generally estimated since it depends on the extant diversity sampled to date, which, with the exception of a few habitats such as the human gut, remains severely undersampled. Further, estimation of the degree of coverage of a microbial community by a metagenomic data set is prohibitively time-consuming for large data sets, and coverage values may not be directly comparable between data sets obtained with different sequencing technologies. Here, we extend Nonpareil, a database-independent tool for the estimation of coverage in metagenomic data sets, to a high-performance computing implementation that scales up to hundreds of cores and includes, in addition, a k -mer-based estimation as sensitive as the original alignment-based version but about three hundred times as fast. Further, we propose a metric of sequence diversity ( N d ) derived directly from Nonpareil curves that correlates well with alpha diversity assessed by traditional metrics. We use this metric in different experiments demonstrating the correlation with the Shannon index estimated on 16S rRNA gene profiles and show that N d additionally reveals seasonal patterns in marine samples that are not captured by the Shannon index and more precise rankings of the magnitude of diversity of microbial communities in different habitats. Therefore, the new version of Nonpareil, called Nonpareil 3, advances the toolbox for metagenomic analyses of microbiomes.
Bacterial mRNA sequencing is inefficient due to the abundance of ribosomal RNA that is challenging to deplete. While commercial kits target rRNA from common bacterial species, they are frequently inefficient when applied to divergent species, including those from environmental isolates. Similarly, other methods typically employ large probe sets that tile the entire length of rRNAs; however, such approaches are infeasible when applied to many species. Therefore, we present EMBR-seq+, which requires fewer than 10 oligonucleotides per rRNA by combining rRNA blocking primers with RNase H-mediated depletion to achieve rRNA removal efficiencies of up to 99% in diverse bacterial species. Furthermore, in more complex microbial co-cultures between Fibrobacter succinogenes strain UWB7 and anaerobic fungi, EMBR-seq+ depleted both bacterial and fungal rRNA, with a fourfold improvement in bacterial rRNA depletion compared with a commercial kit, thereby demonstrating that the method can be applied to non-model microbial mixtures. Notably, for microbes with unknown rRNA sequences, EMBR-seq+ enables rapid iterations in probe design without requiring to start experiments from total RNA. Finally, efficient depletion of rRNA enabled systematic quantification of the reprogramming of the bacterial transcriptome when cultured in the presence of the anaerobic fungi Anaeromyces robustus or Caecomyces churrovis. We observed that F. succinogenes strain UWB7 downregulated several lignocellulose-degrading carbohydrate-active enzymes in the presence of anaerobic gut fungi, suggesting close interactions between two cellulolytic species that specialize in different aspects of biomass breakdown. Thus, EMBR-seq+ enables efficient, cost-effective, and rapid quantification of the transcriptome to gain insights into non-model microbial systems.
We evaluate the Cretaceous stratigraphy and carbon sequestration potential of the northern Baltimore Canyon Trough (NBCT) using >10,000 km of multi-channel seismic profiles integrated with geophysical logs, biostratigraphy, and lithology from 29 offshore wells. We identify and map six sequences resolved primarily at the stage level. Accommodation was dominated by thermal and non-thermal subsidence, though sequence boundaries correlate with regional and global sea-level changes, and the record is modified by igneous intrusion, active faulting, and changes in sediment supply and sources. Our stratigraphic maps illustrate a primary southern (central Appalachian) Early Cretaceous source that migrated northward during the Aptian and Albian. During the Cenomanian, sedimentation rates in the NBCT increased and depocenters shifted northward and landward. We show that deposition occurred in three phases: (1) earlier Cretaceous paleoenvironments were primarily terrestrial indicated by variable amplitude, chaotic seismic facies, serrated gamma logs, and heterolithic sandstones and mudstones with terrestrial microfossils; (2) the Albian to Cenomanian was dominated by deltaic paleoenvironments indicated by blocky, funnel-shaped, gamma-ray logs and clinoforms characterized by continuous high-amplitude seismic reflections with well-defined terminations; and (3) the Cenomanian and younger was marine shelf, inferred from mudstoneprone lithologies, peak gamma-ray values in well logs, and foraminiferal evidence. Long-term transgression and maximum water depths at the Cenomanian/Turonian boundary correlative with Ocean Anoxic Event 2 were followed by a regression and relative sea-level fall. We show that porous and permeable sandstones of three Aptian to Cenomanian highstand systems tracts are high-volume reservoirs for supercritical CO 2 storage that are confined by overlying deep water mudstones.
The temperature changes in the PbHfO{sub 3} structure in the temperature range of 20 < t < 400 Degree-Sign C have been studied by X-ray powder diffraction. The sequence of phase changes with an increase in temperature was found to be as follows: orthorhombic phase Pbam (O1), orthorhombic phase C2mm (O2), tetragonal phase P4mm (T), and cubic phase Pm3m (C). The C2mm and P4mm phases are ferroelectric, which is confirmed by measuring the dependences {epsilon}(t). The similarity of the transition pattern obtained with the known transition sequences for ferroelectric (barium titanate, potassium niobate, and lead titanate) and antiferroelectric (lead zirconate) oxides is analyzed.
Massively Parallel and Portable Genomic Sequence Analysis (mappgene) is a sequencing analysis workflow for high performance computing. It incorporates novel technologies to simplify and accelerate genetics research.