DADA2 Pipeline for 16S datasets in R

By Kelly Shannon

###This pipeline is adapted from the benjjneb dada2 pipeline found on GitHub: and based on Callahan et al., 2016. DADA2: High Resolution Sample Inference from Illumina Amplicon Data. Nature Methods. As well as from one created by MK English in Dr. Ryan Mueller’s lab at OSU. ##The pipeline will be performed with 14 total paired-end sequence fastq files (7 individual samples) as an example flowthrough. These are V4 hypervariable region amplicon sequences performed by the Oregon State University CGRB on an Illumina MiSeq NGS sequencer.

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North Creek Ecosystem Rehabilitation

Dave Van Domelen and Rick, along with Tusi (the pup) filtering water for eDNA of anadromous fish. Photo by David Rothwell.

By Sarah Olsen

Fish runs in the Pacific Northwest play an important role in the region’s history, economy, and ecosystems. Anadromous salmon leave their saltwater homes to “run up” freshwater rivers on their way to spawn. Last summer, a new culvert was built over coastal Oregon’s North Creek, allowing anadromous salmon and other fish to swim upriver for the first time in 62 years. The culvert has opened miles of new habitat for aquatic organisms, including the threatened Oregon Coast Coho Salmon. This research project involves monitoring a much smaller aquatic organism tagging along with the fish: microbes. 

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Rust to the Rescue

Facing North on the Copper River Delta, AK. Photo by Rick Colwell.

History of Glaciation Events

Earth has an ancient and romantic relationship with the greenhouse effect and glacier/ice sheet formation.  When in the atmosphere, carbon dioxide (CO2) acts as a warm blanket around the Earth due to its ability to absorb energy from sun rays.  The retention of this heat, in turn, warms the whole planet, known as the greenhouse effect, and these alterations in atmospheric CO2 affect global climate and glacier formation.

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Wintertime Watersheds

Andrew Thurber retrieves an OsmoSampler from East River, CO during the wintertime. Photo by Laura Lapham.

Humans and the Hydrosphere

The Hydrosphere is the system of global water exchange between the atmosphere (vapor, clouds, and precipitation), biosphere (rivers, lakes, oceans), and geosphere (icebergs, glaciers, hot springs, groundwater).  Ecosystems all around the world rely on the hydrosphere in unique ways to access water for survival, from morning dew in arid deserts, to daily rainstorms in the tropics. Humans are not exempt from this cycle, and we have shared and accessed waters for thousands of years for drinking, farming, and industry.  Despite our reliance on the hydrosphere, we lack fundamental knowledge on the specific inner-workings inherent to hydrologic systems. Our modern world is experiencing disturbances in this precious resource through pollution, contamination, and droughts. Watersheds are areas of land where streams and rivers drain into lakes and ocean, and these ecological systems are particularly vulnerable to changes such as wildfires, erosion, and drought.  Our response to these changes in our water availability rely on our knowledge of how watersheds function, and how they are responding to climate change.

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