Christopher S Miller
Affiliation: University of California
- EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing dataChristopher S Miller
Department of Earth and Planetary Science, University of California, Berkeley, 307 McCone Hall 4767, Berkeley, CA 94720, USA
Genome Biol 12:R44. 2011..An implementation of the method is freely available at https://github.com/csmiller/EMIRGE...
- Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial communityKim M Handley
Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 4767, USA
ISME J 7:800-16. 2013..Results give an insight into ecosystem behavior following addition of simple organic carbon to the subsurface, and demonstrate a range of biological processes and community interactions were stimulated...
- Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting pointsKim M Handley
Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
Environ Microbiol 17:622-36. 2015..Results imply that neither the founding community nor neutral processes influenced succession following perturbation...
- Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sedimentsChristopher S Miller
Department of Earth and Planetary Science, University of California, Berkeley, California, United States of America
PLoS ONE 8:e56018. 2013..The method allows for sensitive, accurate profiling of the "long tail" of low abundance organisms that exist in many microbial communities, and can resolve population dynamics in response to environmental change...
- Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communitiesNicholas B Justice
University of California Berkeley, Berkeley, California, USA
Appl Environ Microbiol 78:8321-30. 2012..These findings indicate dominance of acidophilic archaea in degrading biofilms and suggest that they play roles in anaerobic nutrient cycling at low pH...
- Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystemKaren Andrade
Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
ISME J 9:2697-711. 2015..Results show the operation of a strong community-level diel cycle, probably driven by interconnected temperature, light abundance, dissolved oxygen concentration and nutrient flux effects. ..
- Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phylaKelly C Wrighton
Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA
Science 337:1661-5. 2012..For six organisms, the UGA stop codon is translated as tryptophan. All bacteria studied here may play previously unrecognized roles in hydrogen production, sulfur cycling, and fermentation of refractory sedimentary carbon...