Deepest Living Animals

Congratulations to Dr. Gaetan Borgonie and team for capturing some amazing video footage of animal life (and some beautiful biofilms) underground! Their recently published study extends previous work by Borgonie et al. that identified a nematode, Halicephalobus mephisto, in a 1.3 km deep gold mine in South Africa. Check out some pictures of the deepest living animal life in either the paper or these articles by BBC and the Washington Post.


Learn Metagenomics

Last spring I taught an introductory course to metagenomics at Princeton University. I wanted to share that the lecture notes and lab exercises are now available online here. Check it out if you’re looking to learn more about metagenomics!

Where the Wild Microbes Grow

Check out the new eBook Where the Wild Microbes Grow — now available, free on iBooks and pdf!  The book is fun way for young, future scientists and subterranauts to learn about “inter-terrestrials” and various ecosystems.  I learned about the book through my work with the Center for Dark Energy Biosphere Investigations and maybe you’ll even recognize some of the scientists on the last page!

The Week of Mars: Is the red planet habitable?

The question of whether or not life could/can survive on Mars was brought to the forefront of popular media this month with NASA’s announcement of water currently flowing on Mars, Matt Damon “science-ing the sh!t out” of the red planet in the Hollywood release of The Martian, and Google’s adorable doodle of Mars drinking a large gulp of water.  Together, these events have led to an increased interest in the habitability of Mars and, Continue reading

Plants in Space!

Today, Robert Ferl gave a seminar on space biology at the Princeton Environmental Geology and Geochemistry Seminar and it was so cool that I wanted to post about it here!  Robert is an expert on how plants respond to changes in gravity and has led experiments to study how Arabidopsis responds to parabolic flight campaigns (aka a vomit comet) and life on the International Space Station.  Now, it is pretty clear that zero g is probably one of the coolest “field sites” you could work at but what really got me excited was the amount of knowledge we can gain from such a small plant and the sophisticated methods that were being used.

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Searching for the 4th domain

This past weekend I participated in the first sampling for Phase II of the Microbial Dark Matter (MDM) project.  For this project we are searching for deep branching microbes with no cultured representatives that may reveal new phyla or domains of life using single cell genomics.  Prior to this study, Phase I of the MDM project identified genomes of microorganisms belonging to, what scientists proposed to be, two new super phyla and generated over 200 previously-unidentified genomes to help improve the taxonomic assignment of metagenomic reads.

With Phase II of this project, we want to continue the exploration of enigmatic members of the tree of life Continue reading

GUSTA ME: Statistics Helper

I am happy to report that, in a world of packages, a package that has been built to educate the user is finally here!  The GUide to STatistical Analysis in Microbial Ecology (GUSTA ME) is an online venue developed  by German researchers to explore different types of data analysis techniques and decide which method is appropriate for your problem at hand.  On top of that, they provide code to help you perform PCA, CCA, NMDS, ANOSIM, etc. on your data and an open forum for discussion.  Check it out!


The past few months I have been working with a microbial ecology toolkit called mothur.  So far, it is the most flexible tool I have found to calculate distance matrices from 16S alignments and, subsequently, cluster these sequences into OTUs.  Many people have asked me about how to use mothur so this post will serve as a tutorial.

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ISME Day 4

Today was the last day of ISME and a great conclusion to the conference.  Today’s theme seemed to surround microbial methods and my favorite talks were split between 2 subterranauts, Karen Lloyd and Roland Hatzenpichler.  Karen spoke in the archaea themed session about exploring single cell genomes and exploring novel enzyme function in the uncultured MCG archaea group and  Roland presented in the single cell session about a new technique to visualize newly synthesized proteins in situ.

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ISME Day 3

Today was a busy day but, at the end of the day, the one talk that stands out in my mind is Ruth Ley’s talk on the human microbiome.  Personally, I find this topic to be extremely interesting and Ruth’s presentation did not disappoint.  The talk began with an introduction to a phenomenon in human history: the introduction of agriculture.  Now, we can all imagine that during the shift from hunting and gathering to farming the human microbiome changed to adjust to the new diet.  Perhaps one of the most important changes was the introduction of starch heavy foods that were not the basis of hunter-gather diets.  One gene in particular, AMY1, codes for  Continue reading