Category Archives: Scientific Questions

Metagenomics allows us to address questions in ecology at the DNA level. Among other questions, we investigate microbial taxonomy and function in different environments by asking “which microbes are there?” and “what are the microbes doing?”.

Metagenomic Analysis of Oxygen Minimum Zone Viral Communities

Annual percentage oxygen saturation at 200m depth

Part of an international collaboration: ETSP OMZ.
OMZs are coastal marine areas that contain a hypoxic layer of <20 µM of dissolved oxygen. In the ETSP OMZ, microbes (small Eukaryotes, Bacteria, Archaea, and Viruses) metabolize nitrogen, carbon, and sulfur in the absence of oxygen. Sampling over three consecutive years, we have found that the ratio of virus-like particles to microbes fluctuates wildly in the anoxic layers and, unusually, reaches a 1:1 at some depths. Analysis of the prophage and viral communities from these unique marine habitats are in progress. These two viral metagenomes exhibit distinct community structures, indicating successful induction of OMZ prophages. Further analysis includes fine-grained investigation of the OMZ viral and prophage metabolism compared to the microbes.

 

Copper Tolerance of Kelp-Associated Bacteria

Kelp forests are one of the most widespread and productive of all ecosystems. They provide habitat and nutrition to diverse communities of microorganisms, invertebrates, and mammals. Many kelp forests are dominated byMacrocystis pyrifera, a species of large brown algae that produce negatively charged polysaccharides on their cell surfaces. The polysaccharides allow Macrocystis to accumulate heavy metals such as copper, normally an essential element involved in cellular pathways. Brown algae in environments with higher levels of heavy metals, such as those near human activity, accumulate toxic levels of copper by producing larger amounts of polysaccharides. Toxic amounts of copper can then bioaccumulate up the food chain. Continue reading Copper Tolerance of Kelp-Associated Bacteria

Microbial Ecology of the Alaskan Tundra

Collaboration with Dr. David Lipson, Department of Ecology, SDSU

In arctic peat soils, iron reduction is an important pathway for respiration in anaerobic environments. We are interested in the factors that contribute to CO2 and CH4 fluxes from the arctic soil ecosystem, especially the microbial communities. We are investigating metagenomes acquired from different depths of our research site on the Arctic Coastal plain near Barrow, Alaska. The soil  bacterial metagenomes were acquired from depths of 0 – 10m, 10-20m, 20-30m and 30-40m from the research site. Once the soil DNA was extracted, sequenced and assembled, they were uploaded onto the MG – RAST server (Metagenome – Rapid Annotation using Subsystems Technology) and annotated. I am currently comparing these metagenomes to look for similarities and more importantly, the differences and track the major metabolic pathways and functions at each depth in the Arctic tundra.