Reconstructing terrestrial nutrient cycling using stable nitrogen isotopes in wood

Although recent anthropogenic effects on the global nitrogen (N) cycle have been significant, the consequences of increased anthropogenic N on terrestrial ecosystems are unclear. Studies of the impact of increased reactive N on forest ecosystems—impacts on hydrologic and gaseous loss pathways, retention capacity, and even net primary productivity— have been particularly limited by a lack of long-term baseline biogeochemical data. Stable nitrogen isotope analysis (ratio of ¹⁵N to ¹⁴N, termed δ¹⁵N) of wood chronologies offers the potential to address changes in ecosystem N cycling on millennial timescales and across broad geographic regions. Currently, nearly 50 studies have been published utilizing wood δ¹⁵N records; however, there are significant differences in study design and data interpretation. Here, we identify four categories of wood δ¹⁵N studies, summarize the common themes and primary findings of each category, identify gaps in the spatial and temporal scope of current wood δ¹⁵N chronologies, and synthesize methodological frameworks for future research by presenting eight suggestions for common methodological approaches and enhanced integration across studies. Wood δ¹⁵N records have the potential to provide valuable information for interpreting modern biogeochemical cycling. This review serves to advance the utility of this technique for long-term biogeochemical reconstructions

OTUreporter: a modular automated pipeline for the analysis and report of amplicon data

While 16S rRNA gene amplicon sequencing is not considered a state-of-the-art technique any more, it is now considered a well-matured technique for the routine screening of samples of microbiological interest. The maturity of the technique with the lower costs, have provided an increased demand even in areas foreign to typical research.<br> <br> OTUreporter was developed aiming to bridge the gap between a sequencing service provider without dedicated bioinformatics personnel, and a non-expert customer. OTUreporter was also designed keeping in mind customers with limited computing resources for the initial stages of the amplicon data analysis.<br> <br> Unlike many automated 16S rRNA gene amplicon tools such those made available by sequencing companies (e.g. Illumina's "16S Metagenomics" tool), OTUreporter is not a "black box" and uses software that it is actually used in research context for this matters.<br> <br> OTUreporter accesses BaseSpace directly to gather amplicon data and sequencing run details, avoiding any need for the manual download. The main program used in the background is mothur. OTUreporter uses a slightly modified version of the MiSeqSOP protocol for processing the amplicon data.<br> <br> The final output of OTUreporter is a report. The report summarises the details, not only of the analysis, but also of the sequencing jobs themselves. The report, based on a RMarkdown template, creates two different outputs of the same report: a slimmer printer-friendly pdf document, and an extended html output with interactive content.<br> <br><div> OTUreporter is currently in beta testing at the Ramaciotti Centre for Genomics.</div><div><br></div><div>If you use OTUreporter or reuse any of its contents, please cite the repository at Bitbucket (https://bitbucket.org/xvazquezc/otureporter) or this poster as: <br></div><div>Vázquez-Campos, X., Chilton, A., Koval, J., Tree, J. J., & Wilkins, M. R. OTUreporter: a modular automated pipeline for the analysis and report of amplicon data. Sydney Bioinformatics Research Symposium 2018. 15 Jun 2018. Sydney, NSW, Australia. DOI: <a rel="noreferrer noopener" target="_blank">10.6084/m9.figshare.6521171.</a><br><br></div

Qiita: rapid, web-enabled microbiome meta-analysis

Gonzalez A, Navas-Molina JA, Kosciolek T, et al. Qiita: rapid, web-enabled microbiome meta-analysis. Nature Methods. 2018;15(10):796-798

biocore/emp: Release for manuscript publication (doi:10.1038/nature24621)

Release of the EMP GitHub repository for archiving in Zenodo (DOI: 10.5281/zenodo.1009693) for publication of the manuscript on EMP 16S Release 1 in Nature. The title of that manuscript is "A communal catalogue reveals Earth's multiscale microbial diversity", and its DOI is 10.1038/nature24621