No abstract

No abstract

No abstract

Arbuscular mycorrhizal fungi (AMF) are mutualistic with most species of plants and are known to influence plant community diversity and composition. To better understand natural plant communities and the ecological processes they control it is important to understand what determines the distribution and diversity of AMF. We tested three putative niche axes: plant species composition, disturbance history, and soil chemistry against AMF species composition to determine which axis correlated most strongly with a changing AMF community. Due to a scale dependency we were not able to absolutely rank their importance, but we did find that each correlated significantly with AMF community change at our site. Among soil properties, pH and NO(3) were found to be especially good predictors of AMF community change. In a similar analysis of the plant community we found that time since disturbance had by far the largest impact on community composition.

The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome amplification technique of multiple displacement amplification (MDA). However, MDA from a single chromosome copy suffers from amplification bias and a large loss of specificity from even very small amounts of DNA contamination, which makes assembling a genome difficult and completely finishing a genome impossible except in extraordinary circumstances. Gel microdrop cultivation allows culturing of a diverse microbial community and provides hundreds to thousands of genetically identical cells as input for an MDA reaction. We demonstrate the utility of this approach by comparing sequencing results of gel microdroplets and single cells following MDA. Bias is reduced in the MDA reaction and genome sequencing, and assembly is greatly improved when using gel microdroplets. We acquired multiple near-complete genomes for two bacterial species from human oral and stool microbiome samples. A significant amount of genome diversity, including single nucleotide polymorphisms and genome recombination, is discovered. Gel microdroplets offer a powerful and high-throughput technology for assembling whole genomes from complex samples and for probing the pan-genome of naturally occurring populations.

Widespread microbially mediated negative feedback indicates that plant community diversity and composition in tallgrass prairie are dependent on soil microorganisms. Native soil microorganisms should be considered in restoration efforts of tallgrass prairie and, potentially, other native plant communities.

BackgroundSingle cell genomics (SCG) is a combination of methods whose goal is to decipher the complete genomic sequence from a single cell and has been applied mostly to organisms with smaller genomes, such as bacteria and archaea. Prior single cell studies showed that a significant portion of a genome could be obtained. However, breakages of genomic DNA and amplification bias have made it very challenging to acquire a complete genome with single cells. We investigated an artificial method to induce polyploidy in Bacillus subtilis ATCC 6633 by blocking cell division and have shown that we can significantly improve the performance of genomic sequencing from a single cell.Methodology/Principal FindingsWe inhibited the bacterial cytoskeleton protein FtsZ in B. subtilis with an FtsZ-inhibiting compound, PC190723, resulting in larger undivided single cells with multiple copies of its genome. qPCR assays of these larger, sorted cells showed higher DNA content, have less amplification bias, and greater genomic recovery than untreated cells.SignificanceThe method presented here shows the potential to obtain a nearly complete genome sequence from a single bacterial cell. With millions of uncultured bacterial species in nature, this method holds tremendous promise to provide insight into the genomic novelty of yet-to-be discovered species, and given the temporary effects of artificial polyploidy coupled with the ability to sort and distinguish differences in cell size and genomic DNA content, may allow recovery of specific organisms in addition to their genomes.

The NCI Genomic Data Commons (GDC) was launched in 2016 and makes available over 2 petabytes (PB) of cancer genomic and associated clinical data to the research community. This dataset continues to grow and currently includes over 14,500 patients. The GDC is an example of a biomedical data commons, which collocates biomedical data with storage and computing infrastructure and commonly used web services, software applications, and tools to create a secure, interoperable, and extensible resource for researchers. The GDC is: i) a data repository for downloading data that has been submitted to it, and also a system that: ii) applies a common set of bioinformatics pipelines to submitted data; iii) re-analyzes existing data when new pipelines are developed; and, iv) allows users to build their own applications and systems that interoperate with the GDC using the GDC Application Programming Interface (API). We describe the GDC API and how it has been used both by the GDC itself and by third parties.