Microorganisms are ubiquitous in the biosphere, playing a crucial role in both biogeochemistry of the planet and human health. However, identifying these microorganisms and defining their function are challenging. Widely used approaches in comparative metagenomics, 16S amplicon sequencing and whole genome shotgun sequencing (WGS), have provided access to DNA sequencing analysis to identify microorganisms and evaluate diversity and abundance in various environments. However, advances in parallel high-throughput DNA sequencing in the past decade have introduced major hurdles, namely standardization of methods, data storage, reproducible interoperability of results, and data sharing. The National Ecological Observatory Network (NEON), established by the National Science Foundation, enables all researchers to address queries on a regional to continental scale around a variety of environmental challenges and provide high-quality, integrated, and standardized data from field sites across the U.S. As the amount of metagenomic data continues to grow, standardized procedures that allow results across projects to be assessed and compared is becoming increasingly important in the field of metagenomics. We demonstrate the feasibility of using publicly available NEON soil metagenomic sequencing datasets in combination with open access Metagenomics Rapid Annotation using the Subsystem Technology (MG-RAST) server to illustrate advantages of WGS compared to 16S amplicon sequencing. Four WGS and four 16S amplicon sequence datasets, from surface soil samples prepared by NEON investigators, were selected for comparison, using standardized protocols collected at the same locations in Colorado between April-July 2014. The dominant bacterial phyla detected across samples agreed between sequencing methodologies. However, WGS yielded greater microbial resolution, increased accuracy, and allowed identification of more genera of bacteria, archaea, viruses, and eukaryota, and putative functional genes that would have gone undetected using 16S amplicon sequencing. NEON open data will be useful for future studies characterizing and quantifying complex ecological processes associated with changing aquatic and terrestrial ecosystems.
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Inferring regional access network topologies: methods and applications
Using a toolbox of Internet cartography methods, and new ways of applying them, we have undertaken a comprehensive active measurement-driven study of the topology of U.S. regional access ISPs. We used state-of-the-art approaches in various combinations to accommodate the geographic scope, scale, and architectural richness of U.S. regional access ISPs. In addition to vantage points from research platforms, we used public WiFi hotspots and public transit of mobile devices to acquire the visibility needed to thoroughly map access networks across regions. We observed many different approaches to aggregation and redundancy, across links, nodes, buildings, and at different levels of the hierarchy. One result is substantial disparity in latency from some Edge COs to their backbone COs, with implications for end users of cloud services. Our methods and results can inform future analysis of critical infrastructure, including resilience to disasters, persistence of the digital divide, and challenges for the future of 5G and edge computing.
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- NSF-PAR ID:
- 10351118
- Date Published:
- Journal Name:
- Proceedings of the 21st ACM Internet Measurement Conference (IMC '21)
- Page Range / eLocation ID:
- 720 to 738
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1145/3487552.3487812
